@article{bapatPatternsObjectPlay2025,
	title = {Patterns of object play behaviour and its functional implications in free-flying common ravens},
	volume = {15},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-024-83856-9},
	doi = {10.1038/s41598-024-83856-9},
	abstract = {Abstract
            Object play has been proposed to provide individuals with information about their environment, facilitating foraging skills and tool use. In species where object play co-occurs with locomotor or social play, it may have additional functional implications, such as facilitating the evaluation of peers or forming social bonds. For instance, ravens judge others’ competitiveness via play caching and engage in social play by exchanging objects. However, most raven studies were conducted on a restricted number of individuals and under controlled captive settings. To validate these findings and to gauge the functional scope of object play under field conditions, we investigated the patterns and characteristics of object play in individually marked free-flying ravens in the Austrian Alps. Using two large data sets, we show a decrease in object play with age and a preference for playing longer with novel objects, supporting findings from captivity. We also find adults occasionally playing with objects and no difference in the duration of social or non-social object play bouts across age classes. Taken together, our findings are in line with the assumption that raven object play likely has more than one function and serves to gain information about the individual’s physical and social environment.},
	language = {en},
	number = {1},
	urldate = {2025-12-03},
	journal = {Scientific Reports},
	author = {Bapat, Awani and Kempf, Anna E. and Friry, Salomé and Boucherie, Palmyre H. and Bugnyar, Thomas},
	month = jan,
	year = {2025},
	note = {Citations: 0 (Crossref) [2025-12-04]
Citations: 0 (SemanticScholar) [2025-12-04]},
	pages = {137},
}

Abstract Object play has been proposed to provide individuals with information about their environment, facilitating foraging skills and tool use. In species where object play co-occurs with locomotor or social play, it may have additional functional implications, such as facilitating the evaluation of peers or forming social bonds. For instance, ravens judge others’ competitiveness via play caching and engage in social play by exchanging objects. However, most raven studies were conducted on a restricted number of individuals and under controlled captive settings. To validate these findings and to gauge the functional scope of object play under field conditions, we investigated the patterns and characteristics of object play in individually marked free-flying ravens in the Austrian Alps. Using two large data sets, we show a decrease in object play with age and a preference for playing longer with novel objects, supporting findings from captivity. We also find adults occasionally playing with objects and no difference in the duration of social or non-social object play bouts across age classes. Taken together, our findings are in line with the assumption that raven object play likely has more than one function and serves to gain information about the individual’s physical and social environment.

@article{everettCoordinationPersistenceAggressive2025,
	title = {Coordination and persistence of aggressive visual communication in {Siamese} fighting fish},
	volume = {44},
	copyright = {All rights reserved},
	issn = {2211-1247},
	url = {https://www.cell.com/cell-reports/abstract/S2211-1247(24)01559-6},
	doi = {10.1016/j.celrep.2024.115208},
	language = {English},
	number = {1},
	urldate = {2025-01-21},
	journal = {Cell Reports},
	publisher = {Elsevier},
	author = {Everett, Claire P. and Norovich, Amy L. and Burke, Jessica E. and Whiteway, Matthew R. and Villamayor, Paula R. and Shih, Pei-Yin and Zhu, Yuyang and Paninski, Liam and Bendesky, Andres},
	month = jan,
	year = {2025},
	keywords = {Betta splendens, CP: Neuroscience, aggression, amygdala, animal communication, behavioral neuroscience, emotional states, neuroethology, social behavior, turn taking, visual neuroscience},
}

@article{hewettFinescaleSpatialVariation2025,
	title = {Fine-scale spatial variation in fitness, inbreeding, and inbreeding depression in a wild ungulate},
	copyright = {https://creativecommons.org/licenses/by/4.0/},
	issn = {2056-3744},
	url = {https://academic.oup.com/evlett/advance-article/doi/10.1093/evlett/qrae073/7945423},
	doi = {10.1093/evlett/qrae073},
	abstract = {Abstract
            Environmental stress can exacerbate inbreeding depression by amplifying differences between inbred and outbred individuals. In wild populations, where the environment is often unpredictable and stress can be highly detrimental, the interplay between inbreeding depression and environmental variation is potentially important. Here, we investigate variation in inbreeding level, fitness and strength of inbreeding depression across a fine-scale geographic area ({\textasciitilde}12 km2) in an individually monitored population of red deer (Cervus elaphus). We show that northern regions of the study area have lower birth weights, lower juvenile survival rates, and higher inbreeding coefficients. Such fine-scale differences in inbreeding coefficients could be caused by the mating system of red deer combined with female density variation. We then tested for an inbreeding depression-by-environment interaction (ID × E) in birth weight and juvenile survival, by fitting an interaction term between the inbreeding coefficient and geographic location. We find that inbreeding depression in juvenile survival is stronger in the harsher northern regions, indicating the presence of ID × E. We also highlight that the ability to infer ID × E is affected by the variation in inbreeding within each geographic region. Therefore, for future studies on ID × E in wild populations, we recommend first assessing whether inbreeding and traits vary spatially or temporally. Overall, this is one of only a handful of studies to find evidence for ID × E in a wild population—despite its prevalence in experimental systems—likely due to intense data demands or insufficient variation in environmental stress or inbreeding coefficients.},
	language = {en},
	urldate = {2025-03-22},
	journal = {Evolution Letters},
	author = {Hewett, Anna M and Johnston, Susan E and Albery, Gregory F and Morris, Alison and Morris, Sean J and Pemberton, Josephine M},
	month = jan,
	year = {2025},
	pages = {qrae073},
}

Abstract Environmental stress can exacerbate inbreeding depression by amplifying differences between inbred and outbred individuals. In wild populations, where the environment is often unpredictable and stress can be highly detrimental, the interplay between inbreeding depression and environmental variation is potentially important. Here, we investigate variation in inbreeding level, fitness and strength of inbreeding depression across a fine-scale geographic area (~12 km2) in an individually monitored population of red deer (Cervus elaphus). We show that northern regions of the study area have lower birth weights, lower juvenile survival rates, and higher inbreeding coefficients. Such fine-scale differences in inbreeding coefficients could be caused by the mating system of red deer combined with female density variation. We then tested for an inbreeding depression-by-environment interaction (ID × E) in birth weight and juvenile survival, by fitting an interaction term between the inbreeding coefficient and geographic location. We find that inbreeding depression in juvenile survival is stronger in the harsher northern regions, indicating the presence of ID × E. We also highlight that the ability to infer ID × E is affected by the variation in inbreeding within each geographic region. Therefore, for future studies on ID × E in wild populations, we recommend first assessing whether inbreeding and traits vary spatially or temporally. Overall, this is one of only a handful of studies to find evidence for ID × E in a wild population—despite its prevalence in experimental systems—likely due to intense data demands or insufficient variation in environmental stress or inbreeding coefficients.

@article{gonzalez-castellanoEstimationInbreedingDepression2025,
	title = {Estimation of {Inbreeding} {Depression} {From} {Overdominant} {Loci} {Using} {Molecular} {Markers}},
	volume = {18},
	issn = {1752-4571, 1752-4571},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/eva.70085},
	doi = {10.1111/eva.70085},
	abstract = {ABSTRACT
            
              Inbreeding depression is a highly relevant universal phenomenon in population and conservation genetics since it leads to a decline in the fitness of individuals. This phenomenon is due to the homozygous expression of alleles whose effects are hidden in heterozygotes (inbreeding load). The rate of inbreeding depression for quantitative traits can be quantified if the coefficient of inbreeding (
              F
              ) of individuals is known. This coefficient can be estimated from pedigrees or from the information of molecular markers, such as SNPs, using measures of homozygosity of individual markers or runs of homozygosity (ROH) across the genome. Several studies have investigated the accuracy of different
              F
              measures to estimate inbreeding depression, but always assuming that this is only due to recessive or partially recessive deleterious mutations. It is possible, though, that part of the inbreeding depression is due to variants with overdominant gene action (heterozygote advantage). In this study, we carried out computer simulations to assess the impact of overdominance on the estimation of inbreeding depression based on different measures of
              F
              . The results indicate that the estimators based on ROH provide the most robust estimates of inbreeding depression when this is due to overdominant loci. The estimators that use measures of homozygosity from individual markers may provide estimates with substantial biases, depending on whether or not low‐frequency alleles are discarded in the analyses; but among these SNP‐by‐SNP measures, those based on the correlation between uniting gametes are generally the most reliable.},
	language = {en},
	number = {3},
	urldate = {2025-03-22},
	journal = {Evolutionary Applications},
	author = {González‐Castellano, Inés and Ordás, Pilar and Caballero, Armando},
	month = mar,
	year = {2025},
	pages = {e70085},
}

ABSTRACT Inbreeding depression is a highly relevant universal phenomenon in population and conservation genetics since it leads to a decline in the fitness of individuals. This phenomenon is due to the homozygous expression of alleles whose effects are hidden in heterozygotes (inbreeding load). The rate of inbreeding depression for quantitative traits can be quantified if the coefficient of inbreeding ( F ) of individuals is known. This coefficient can be estimated from pedigrees or from the information of molecular markers, such as SNPs, using measures of homozygosity of individual markers or runs of homozygosity (ROH) across the genome. Several studies have investigated the accuracy of different F measures to estimate inbreeding depression, but always assuming that this is only due to recessive or partially recessive deleterious mutations. It is possible, though, that part of the inbreeding depression is due to variants with overdominant gene action (heterozygote advantage). In this study, we carried out computer simulations to assess the impact of overdominance on the estimation of inbreeding depression based on different measures of F . The results indicate that the estimators based on ROH provide the most robust estimates of inbreeding depression when this is due to overdominant loci. The estimators that use measures of homozygosity from individual markers may provide estimates with substantial biases, depending on whether or not low‐frequency alleles are discarded in the analyses; but among these SNP‐by‐SNP measures, those based on the correlation between uniting gametes are generally the most reliable.

@article{sarkarYoungPakistanisAre2024,
	chapter = {Feature},
	title = {Young {Pakistanis} are moving away from cousin marriage owing to the risk of genetic disorders},
	volume = {387},
	copyright = {Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions},
	issn = {1756-1833},
	url = {https://www.bmj.com/content/387/bmj.q2181},
	doi = {10.1136/bmj.q2181},
	abstract = {{\textless}p{\textgreater}The tradition of marrying close family members is rapidly declining in Pakistan, with rising awareness of genetic disorders. \textbf{Sonia Sarkar} reports{\textless}/p{\textgreater}},
	language = {en},
	urldate = {2025-03-31},
	journal = {BMJ},
	publisher = {British Medical Journal Publishing Group},
	author = {Sarkar, Sonia},
	month = nov,
	year = {2024},
	pages = {q2181},
}

\textlessp\textgreaterThe tradition of marrying close family members is rapidly declining in Pakistan, with rising awareness of genetic disorders. \textbfSonia Sarkar reports\textless/p\textgreater

@article{lavanchyDetectingInbreedingDepression2024,
	title = {Detecting inbreeding depression in structured populations},
	volume = {121},
	issn = {0027-8424, 1091-6490},
	url = {https://pnas.org/doi/10.1073/pnas.2315780121},
	doi = {10.1073/pnas.2315780121},
	abstract = {Measuring inbreeding and its consequences on fitness is central for many areas in biology including human genetics and the conservation of endangered species. However, there is no consensus on the best method, neither for quantification of inbreeding itself nor for the model to estimate its effect on specific traits. We simulated traits based on simulated genomes from a large pedigree and empirical whole-genome sequences of human data from populations with various sizes and structures (from the 1,000 Genomes project). We compare the ability of various inbreeding coefficients (
              
                
                  F
                
              
              ) to quantify the strength of inbreeding depression: allele-sharing, two versions of the correlation of uniting gametes which differ in the weight they attribute to each locus and two identical-by-descent segments-based estimators. We also compare two models: the standard linear model and a linear mixed model (LMM) including a genetic relatedness matrix (GRM) as random effect to account for the nonindependence of observations. We find LMMs give better results in scenarios with population or family structure. Within the LMM, we compare three different GRMs and show that in homogeneous populations, there is little difference among the different
              
                
                  F
                
              
              and GRM for inbreeding depression quantification. However, as soon as a strong population or family structure is present, the strength of inbreeding depression can be most efficiently estimated only if i) the phenotypes are regressed on
              
                
                  F
                
              
              based on a weighted version of the correlation of uniting gametes, giving more weight to common alleles and ii) with the GRM obtained from an allele-sharing relatedness estimator.},
	language = {en},
	number = {19},
	urldate = {2025-03-30},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Lavanchy, Eléonore and Weir, Bruce S. and Goudet, Jérôme},
	month = may,
	year = {2024},
	pages = {e2315780121},
}

Measuring inbreeding and its consequences on fitness is central for many areas in biology including human genetics and the conservation of endangered species. However, there is no consensus on the best method, neither for quantification of inbreeding itself nor for the model to estimate its effect on specific traits. We simulated traits based on simulated genomes from a large pedigree and empirical whole-genome sequences of human data from populations with various sizes and structures (from the 1,000 Genomes project). We compare the ability of various inbreeding coefficients ( F ) to quantify the strength of inbreeding depression: allele-sharing, two versions of the correlation of uniting gametes which differ in the weight they attribute to each locus and two identical-by-descent segments-based estimators. We also compare two models: the standard linear model and a linear mixed model (LMM) including a genetic relatedness matrix (GRM) as random effect to account for the nonindependence of observations. We find LMMs give better results in scenarios with population or family structure. Within the LMM, we compare three different GRMs and show that in homogeneous populations, there is little difference among the different F and GRM for inbreeding depression quantification. However, as soon as a strong population or family structure is present, the strength of inbreeding depression can be most efficiently estimated only if i) the phenotypes are regressed on F based on a weighted version of the correlation of uniting gametes, giving more weight to common alleles and ii) with the GRM obtained from an allele-sharing relatedness estimator.

@article{hasselgrenStronglyDeleteriousMutations2024,
	title = {Strongly deleterious mutations influence reproductive output and longevity in an endangered population},
	volume = {15},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-024-52741-4},
	doi = {10.1038/s41467-024-52741-4},
	abstract = {Abstract
            
              Inbreeding depression has been documented in various fitness traits in a wide range of species and taxa, however, the mutational basis is not yet well understood. We investigate how putatively deleterious variation influences fitness and is shaped by individual ancestry by re-sequencing complete genomes of 37 individuals in a natural arctic fox (
              Vulpes lagopus
              ) population subjected to both inbreeding depression and genetic rescue. We find that individuals with high proportion of homozygous loss of function genotypes (LoFs), which are predicted to exert a strong effect on fitness, generally have lower lifetime reproductive success and live shorter lives compared with individuals with lower proportion of LoFs. We also find that juvenile survival is negatively associated with the proportion of homozygous missense genotypes and positively associated with genome wide heterozygosity. Our results demonstrate that homozygosity of strongly and moderately deleterious mutations can be an important cause of trait specific inbreeding depression in wild populations, and mark an important step towards making more informed decisions using applied conservation genetics.},
	language = {en},
	number = {1},
	urldate = {2025-03-30},
	journal = {Nature Communications},
	author = {Hasselgren, Malin and Dussex, Nicolas and Von Seth, Johanna and Angerbjörn, Anders and Dalén, Love and Norén, Karin},
	month = sep,
	year = {2024},
	pages = {8378},
}

Abstract Inbreeding depression has been documented in various fitness traits in a wide range of species and taxa, however, the mutational basis is not yet well understood. We investigate how putatively deleterious variation influences fitness and is shaped by individual ancestry by re-sequencing complete genomes of 37 individuals in a natural arctic fox ( Vulpes lagopus ) population subjected to both inbreeding depression and genetic rescue. We find that individuals with high proportion of homozygous loss of function genotypes (LoFs), which are predicted to exert a strong effect on fitness, generally have lower lifetime reproductive success and live shorter lives compared with individuals with lower proportion of LoFs. We also find that juvenile survival is negatively associated with the proportion of homozygous missense genotypes and positively associated with genome wide heterozygosity. Our results demonstrate that homozygosity of strongly and moderately deleterious mutations can be an important cause of trait specific inbreeding depression in wild populations, and mark an important step towards making more informed decisions using applied conservation genetics.

@article{besnardMassiveDetectionCryptic2024,
	title = {Massive detection of cryptic recessive genetic defects in dairy cattle mining millions of life histories},
	volume = {25},
	issn = {1474-760X},
	url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03384-7},
	doi = {10.1186/s13059-024-03384-7},
	language = {en},
	number = {1},
	urldate = {2025-03-26},
	journal = {Genome Biology},
	author = {Besnard, Florian and Guintard, Ana and Grohs, Cécile and Guzylack-Piriou, Laurence and Cano, Margarita and Escouflaire, Clémentine and Hozé, Chris and Leclerc, Hélène and Buronfosse, Thierry and Dutheil, Lucie and Jourdain, Jeanlin and Barbat, Anne and Fritz, Sébastien and Deloche, Marie-Christine and Remot, Aude and Gaussères, Blandine and Clément, Adèle and Bouchier, Marion and Contat, Elise and Relun, Anne and Plassard, Vincent and Rivière, Julie and Péchoux, Christine and Vilotte, Marthe and Eche, Camille and Kuchly, Claire and Charles, Mathieu and Boulling, Arnaud and Viard, Guillaume and Minéry, Stéphanie and Barbey, Sarah and Birbes, Clément and Danchin-Burge, Coralie and Launay, Frédéric and Mattalia, Sophie and Allais-Bonnet, Aurélie and Ravary, Bérangère and Millemann, Yves and Guatteo, Raphaël and Klopp, Christophe and Gaspin, Christine and Iampietro, Carole and Donnadieu, Cécile and Milan, Denis and Arcangioli, Marie-Anne and Boussaha, Mekki and Foucras, Gilles and Boichard, Didier and Capitan, Aurélien},
	month = sep,
	year = {2024},
	pages = {248},
}

@article{niepothEvolutionNovelAdrenal2024,
	title = {Evolution of a novel adrenal cell type that promotes parental care},
	volume = {629},
	copyright = {All rights reserved},
	issn = {1476-4687},
	doi = {10.1038/s41586-024-07423-y},
	abstract = {Cell types with specialized functions fundamentally regulate animal behaviour, and yet the genetic mechanisms that underlie the emergence of novel cell types and their consequences for behaviour are not well understood1. Here we show that the monogamous oldfield mouse (Peromyscus polionotus) has recently evolved a novel cell type in the adrenal gland that expresses the enzyme AKR1C18, which converts progesterone into 20α-hydroxyprogesterone. We then demonstrate that 20α-hydroxyprogesterone is more abundant in oldfield mice, where it induces monogamous-typical parental behaviours, than in the closely related promiscuous deer mice (Peromyscus maniculatus). Using quantitative trait locus mapping in a cross between these species, we ultimately find interspecific genetic variation that drives expression of the nuclear protein GADD45A and the glycoprotein tenascin N, which contribute to the emergence and function of this cell type in oldfield mice. Our results provide an example by which the recent evolution of a new cell type in a gland outside the brain contributes to the evolution of social behaviour.},
	language = {eng},
	number = {8014},
	journal = {Nature},
	author = {Niepoth, Natalie and Merritt, Jennifer R. and Uminski, Michelle and Lei, Emily and Esquibies, Victoria S. and Bando, Ina B. and Hernandez, Kimberly and Gebhardt, Christoph and Wacker, Sarah A. and Lutzu, Stefano and Poudel, Asmita and Soma, Kiran K. and Rudolph, Stephanie and Bendesky, Andres},
	month = may,
	year = {2024},
	note = {2 citations (Crossref) [2024-06-30]},
	keywords = {Adrenal Glands, Animals, Biological Evolution, Female, Genetic Variation, Male, Paternal Behavior, Peromyscus, Progesterone, Quantitative Trait Loci, Social Behavior},
	pages = {1082--1090},
}

Cell types with specialized functions fundamentally regulate animal behaviour, and yet the genetic mechanisms that underlie the emergence of novel cell types and their consequences for behaviour are not well understood1. Here we show that the monogamous oldfield mouse (Peromyscus polionotus) has recently evolved a novel cell type in the adrenal gland that expresses the enzyme AKR1C18, which converts progesterone into 20α-hydroxyprogesterone. We then demonstrate that 20α-hydroxyprogesterone is more abundant in oldfield mice, where it induces monogamous-typical parental behaviours, than in the closely related promiscuous deer mice (Peromyscus maniculatus). Using quantitative trait locus mapping in a cross between these species, we ultimately find interspecific genetic variation that drives expression of the nuclear protein GADD45A and the glycoprotein tenascin N, which contribute to the emergence and function of this cell type in oldfield mice. Our results provide an example by which the recent evolution of a new cell type in a gland outside the brain contributes to the evolution of social behaviour.

@article{stoffelPurifyingBalancingSelection2024,
	title = {Purifying and balancing selection on embryonic semi-lethal haplotypes in a wild mammal},
	volume = {8},
	copyright = {https://creativecommons.org/licenses/by/4.0/},
	issn = {2056-3744},
	url = {https://academic.oup.com/evlett/article/8/2/222/7327097},
	doi = {10.1093/evlett/qrad053},
	abstract = {Abstract
            Embryonic lethal mutations are arguably the earliest and most severe manifestation of inbreeding depression, but their impact on wild populations is not well understood. Here, we combined genomic, fitness, and life-history data from 5,925 wild Soay sheep sampled over nearly three decades to explore the impact of embryonic lethal mutations and their evolutionary dynamics. We searched for haplotypes that in their homozygous state are unusually rare in the offspring of known carrier parents and found three putatively semi-lethal haplotypes with 27\%–46\% fewer homozygous offspring than expected. Two of these haplotypes are decreasing in frequency, and gene-dropping simulations through the pedigree suggest that this is partially due to purifying selection. In contrast, the frequency of the third semi-lethal haplotype remains relatively stable over time. We show that the haplotype could be maintained by balancing selection because it is also associated with increased postnatal survival and body weight and because its cumulative frequency change is lower than in most drift-only simulations. Our study highlights embryonic mutations as a largely neglected contributor to inbreeding depression and provides a rare example of how harmful genetic variation can be maintained through balancing selection in a wild mammal population.},
	language = {en},
	number = {2},
	urldate = {2025-03-24},
	journal = {Evolution Letters},
	author = {Stoffel, Martin A and Johnston, Susan E and Pilkington, Jill G and Pemberton, Josephine M},
	month = mar,
	year = {2024},
	pages = {222--230},
}

Abstract Embryonic lethal mutations are arguably the earliest and most severe manifestation of inbreeding depression, but their impact on wild populations is not well understood. Here, we combined genomic, fitness, and life-history data from 5,925 wild Soay sheep sampled over nearly three decades to explore the impact of embryonic lethal mutations and their evolutionary dynamics. We searched for haplotypes that in their homozygous state are unusually rare in the offspring of known carrier parents and found three putatively semi-lethal haplotypes with 27%–46% fewer homozygous offspring than expected. Two of these haplotypes are decreasing in frequency, and gene-dropping simulations through the pedigree suggest that this is partially due to purifying selection. In contrast, the frequency of the third semi-lethal haplotype remains relatively stable over time. We show that the haplotype could be maintained by balancing selection because it is also associated with increased postnatal survival and body weight and because its cumulative frequency change is lower than in most drift-only simulations. Our study highlights embryonic mutations as a largely neglected contributor to inbreeding depression and provides a rare example of how harmful genetic variation can be maintained through balancing selection in a wild mammal population.

@article{pattersonEffectsParentalCare2024,
	title = {Effects of parental care on the magnitude of inbreeding depression: {A} meta-analysis in fishes},
	volume = {203},
	issn = {0003-0147, 1537-5323},
	shorttitle = {Effects of {Parental} {Care} on the {Magnitude} of {Inbreeding} {Depression}},
	url = {https://www.journals.uchicago.edu/doi/10.1086/728001},
	doi = {10.1086/728001},
	language = {en},
	number = {2},
	urldate = {2025-03-24},
	journal = {The American Naturalist},
	author = {Patterson, Charlotte and Pilakouta, Natalie},
	month = feb,
	year = {2024},
	pages = {E50--E62},
}

@book{worldwidefundfornatureWWFLivingPlanet2024,
	address = {Berlin},
	edition = {1. unveränderte engl.-sprachige Gesamtausgabe 2024},
	title = {{WWF} {Living} {Planet} {Report} 2024 {A} system in peril},
	isbn = {978-2-88085-319-8},
	language = {eng},
	publisher = {WWF Deutschland},
	collaborator = {World Wide Fund for Nature, WWF International},
	year = {2024},
	note = {OCLC: 1483221189},
}

@article{smallMortalityMorbidityEducational2024,
	title = {Mortality, morbidity and educational outcomes in children of consanguineous parents in the {Born} in {Bradford} cohort},
	volume = {9},
	issn = {2398-502X},
	url = {https://wellcomeopenresearch.org/articles/9-319/v2},
	doi = {10.12688/wellcomeopenres.22547.2},
	abstract = {Background Children of consanguineous parents have a higher risk of infant and childhood mortality, morbidity and intellectual and developmental disability. Methods Using a UK based longitudinal cohort study we quantify differences according to the consanguinity status of children from birth to 10 in mortality, health care usage, two health and three educational outcomes. The cohort comprises 13727 children; 35.7\% White British, 43.7\% Pakistani heritage, and 20.8\% are from other ethnic groups. Results Compared to children whose parents were not related children whose parents were first cousins were more likely to die by age 10 (odds ratio 2.81, 95\% CI 1.82-4.35) to have higher rates of primary care appointments (incident rate ratio 1.39, 95\% CI 1.34-1.45) and more prescriptions (incident rate ratio 1.61, 95\% CI 1.50-1.73). Rates of hospital accident and emergency attendance (incident rate ratio 1.21,95\% CI 1.12-1.30) and hospital outpatients’ appointments (incident rate ratio 2.21,95\% CI 1.90-2.56) are higher. Children of first cousins have higher rates of speech/ language development difficulties (odds ratio 1.63, 95\% CI 1.36-1.96) and learning difficulties (odds ratio 1.89, 95\% CI 1.28-2.81). When they begin school they are less likely to reach phonics standards (odds ratio 0.73, 95\% CI 0.63-0.84) and less likely to show a good level of development (odds ratio 0.61, 95\% CI 0.54-0.68). At age 10 there are higher numbers with special educational needs from first cousin unions compared to all children whose parents are not blood relations (odds ratio 1.38, 95\% CI 1.20-1.58). Effect sizes for consanguinity status are similar in univariable and multivariable models where a range of control variables are added. Conclusions There is higher childhood mortality and greater use of health care as well as higher rates of learning difficulties, speech and language development challenges and substantive differences in education outcomes in children whose parents are first cousins.},
	language = {en},
	urldate = {2025-03-19},
	journal = {Wellcome Open Research},
	author = {Small, Neil and Kelly, Brian and Malawsky, Daniel S. and Lodh, Rajib and Oddie, Sam and Wright, John},
	month = sep,
	year = {2024},
	pages = {319},
}

Background Children of consanguineous parents have a higher risk of infant and childhood mortality, morbidity and intellectual and developmental disability. Methods Using a UK based longitudinal cohort study we quantify differences according to the consanguinity status of children from birth to 10 in mortality, health care usage, two health and three educational outcomes. The cohort comprises 13727 children; 35.7% White British, 43.7% Pakistani heritage, and 20.8% are from other ethnic groups. Results Compared to children whose parents were not related children whose parents were first cousins were more likely to die by age 10 (odds ratio 2.81, 95% CI 1.82-4.35) to have higher rates of primary care appointments (incident rate ratio 1.39, 95% CI 1.34-1.45) and more prescriptions (incident rate ratio 1.61, 95% CI 1.50-1.73). Rates of hospital accident and emergency attendance (incident rate ratio 1.21,95% CI 1.12-1.30) and hospital outpatients’ appointments (incident rate ratio 2.21,95% CI 1.90-2.56) are higher. Children of first cousins have higher rates of speech/ language development difficulties (odds ratio 1.63, 95% CI 1.36-1.96) and learning difficulties (odds ratio 1.89, 95% CI 1.28-2.81). When they begin school they are less likely to reach phonics standards (odds ratio 0.73, 95% CI 0.63-0.84) and less likely to show a good level of development (odds ratio 0.61, 95% CI 0.54-0.68). At age 10 there are higher numbers with special educational needs from first cousin unions compared to all children whose parents are not blood relations (odds ratio 1.38, 95% CI 1.20-1.58). Effect sizes for consanguinity status are similar in univariable and multivariable models where a range of control variables are added. Conclusions There is higher childhood mortality and greater use of health care as well as higher rates of learning difficulties, speech and language development challenges and substantive differences in education outcomes in children whose parents are first cousins.

@article{lavanchyTooBigPurge2024,
	title = {Too big to purge: persistence of deleterious {Mutations} in {Island} populations of the {European} {Barn} {Owl} ({Tyto} alba)},
	volume = {133},
	copyright = {2024 The Author(s)},
	issn = {1365-2540},
	shorttitle = {Too big to purge},
	url = {https://www.nature.com/articles/s41437-024-00728-8},
	doi = {10.1038/s41437-024-00728-8},
	abstract = {A key aspect of assessing the risk of extinction/extirpation for a particular wild species or population is the status of inbreeding, but the origin of inbreeding and the current mutational load are also two crucial factors to consider when determining survival probability of a population. In this study, we used samples from 502 barn owls from continental and island populations across Europe, with the aim of quantifying and comparing the level of inbreeding between populations with differing demographic histories. In addition to comparing inbreeding status, we determined whether inbreeding is due to non-random mating or high co-ancestry within the population. We show that islands have higher levels of inbreeding than continental populations, and that this is mainly due to small effective population sizes rather than recent consanguineous mating. We assess the probability that a region is autozygous along the genome and show that this probability decreased as the number of genes present in that region increased. Finally, we looked for evidence of reduced selection efficiency and purging in island populations. Among island populations, we found an increase in numbers of both neutral and deleterious minor alleles, possibly as a result of drift and decreased selection efficiency but we found no evidence of purging.},
	language = {en},
	number = {6},
	urldate = {2025-03-19},
	journal = {Heredity},
	author = {Lavanchy, Eléonore and Cumer, Tristan and Topaloudis, Alexandros and Ducrest, Anne-Lyse and Simon, Céline and Roulin, Alexandre and Goudet, Jérôme},
	month = dec,
	year = {2024},
	keywords = {Consanguinity, Genomics, Inbreeding, Population genetics},
	pages = {437--449},
}

A key aspect of assessing the risk of extinction/extirpation for a particular wild species or population is the status of inbreeding, but the origin of inbreeding and the current mutational load are also two crucial factors to consider when determining survival probability of a population. In this study, we used samples from 502 barn owls from continental and island populations across Europe, with the aim of quantifying and comparing the level of inbreeding between populations with differing demographic histories. In addition to comparing inbreeding status, we determined whether inbreeding is due to non-random mating or high co-ancestry within the population. We show that islands have higher levels of inbreeding than continental populations, and that this is mainly due to small effective population sizes rather than recent consanguineous mating. We assess the probability that a region is autozygous along the genome and show that this probability decreased as the number of genes present in that region increased. Finally, we looked for evidence of reduced selection efficiency and purging in island populations. Among island populations, we found an increase in numbers of both neutral and deleterious minor alleles, possibly as a result of drift and decreased selection efficiency but we found no evidence of purging.

@article{kardosWhatCanGenome2024,
	title = {What {Can} {Genome} {Sequence} {Data} {Reveal} {About} {Population} {Viability}?},
	issn = {0962-1083, 1365-294X},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/mec.17608},
	doi = {10.1111/mec.17608},
	abstract = {ABSTRACT 
            Biologists have long sought to understand the impacts of deleterious genetic variation on fitness and population viability. However, our understanding of these effects in the wild is incomplete, in part due to the rarity of sufficient genetic and demographic data needed to measure their impact. The genomics revolution is promising a potential solution by predicting the effects of deleterious genetic variants (genetic load) bioinformatically from genome sequences alone bypassing the need for costly demographic data. After a historical perspective on the theoretical and empirical basis of our understanding of the dynamics and fitness effects of deleterious genetic variation, we evaluate the potential for these new genomic measures of genetic load to predict population viability. We argue that current genomic analyses alone cannot reliably predict the effects of deleterious genetic variation on population growth, because these depend on demographic, ecological and genetic parameters that need more than just genome sequence data to be measured. Thus, while purely genomic analyses of genetic load promise to improve our understanding of the composition of the genetic load, they are currently of little use for evaluating population viability. Demographic data and ecological context remain crucial to our understanding of the consequences of deleterious genetic variation for population fitness. However, when combined with such demographic and ecological data, genomic information can offer important insights into genetic variation and inbreeding that are crucial for conservation decision making.},
	language = {en},
	urldate = {2025-03-19},
	journal = {Molecular Ecology},
	author = {Kardos, Marty and Keller, Lukas F. and Funk, W. Chris},
	month = dec,
	year = {2024},
	pages = {e17608},
}

ABSTRACT Biologists have long sought to understand the impacts of deleterious genetic variation on fitness and population viability. However, our understanding of these effects in the wild is incomplete, in part due to the rarity of sufficient genetic and demographic data needed to measure their impact. The genomics revolution is promising a potential solution by predicting the effects of deleterious genetic variants (genetic load) bioinformatically from genome sequences alone bypassing the need for costly demographic data. After a historical perspective on the theoretical and empirical basis of our understanding of the dynamics and fitness effects of deleterious genetic variation, we evaluate the potential for these new genomic measures of genetic load to predict population viability. We argue that current genomic analyses alone cannot reliably predict the effects of deleterious genetic variation on population growth, because these depend on demographic, ecological and genetic parameters that need more than just genome sequence data to be measured. Thus, while purely genomic analyses of genetic load promise to improve our understanding of the composition of the genetic load, they are currently of little use for evaluating population viability. Demographic data and ecological context remain crucial to our understanding of the consequences of deleterious genetic variation for population fitness. However, when combined with such demographic and ecological data, genomic information can offer important insights into genetic variation and inbreeding that are crucial for conservation decision making.

@article{iacopiniNotYourPrivate2024,
	title = {Not your private tête-à-tête: leveraging the power of higher-order networks to study animal communication},
	volume = {379},
	issn = {0962-8436, 1471-2970},
	shorttitle = {Not your private tête-à-tête},
	url = {https://royalsocietypublishing.org/doi/10.1098/rstb.2023.0190},
	doi = {10.1098/rstb.2023.0190},
	abstract = {Animal communication is frequently studied with conventional network representations that link pairs of individuals who interact, for example, through vocalization. However, acoustic signals often have multiple simultaneous receivers, or receivers integrate information from multiple signallers, meaning these interactions are not dyadic. Additionally, non-dyadic social structures often shape an individual’s behavioural response to vocal communication. Recently, major advances have been made in the study of these non-dyadic, higher-order networks (e.g. hypergraphs and simplicial complexes). Here, we show how these approaches can provide new insights into vocal communication through three case studies that illustrate how higher-order network models can: (i) alter predictions made about the outcome of vocally coordinated group departures; (ii) generate different patterns of song synchronization from models that only include dyadic interactions; and (iii) inform models of cultural evolution of vocal communication. Together, our examples highlight the potential power of higher-order networks to study animal vocal communication. We then build on our case studies to identify key challenges in applying higher-order network approaches in this context and outline important research questions that these techniques could help answer. This article is part of the theme issue ‘The power of sound: unravelling how acoustic communication shapes group dynamics’.},
	language = {en},
	number = {1905},
	urldate = {2025-02-07},
	journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
	author = {Iacopini, Iacopo and Foote, Jennifer R. and Fefferman, Nina H. and Derryberry, Elizabeth P. and Silk, Matthew J.},
	month = jul,
	year = {2024},
	pages = {20230190},
}

Animal communication is frequently studied with conventional network representations that link pairs of individuals who interact, for example, through vocalization. However, acoustic signals often have multiple simultaneous receivers, or receivers integrate information from multiple signallers, meaning these interactions are not dyadic. Additionally, non-dyadic social structures often shape an individual’s behavioural response to vocal communication. Recently, major advances have been made in the study of these non-dyadic, higher-order networks (e.g. hypergraphs and simplicial complexes). Here, we show how these approaches can provide new insights into vocal communication through three case studies that illustrate how higher-order network models can: (i) alter predictions made about the outcome of vocally coordinated group departures; (ii) generate different patterns of song synchronization from models that only include dyadic interactions; and (iii) inform models of cultural evolution of vocal communication. Together, our examples highlight the potential power of higher-order networks to study animal vocal communication. We then build on our case studies to identify key challenges in applying higher-order network approaches in this context and outline important research questions that these techniques could help answer. This article is part of the theme issue ‘The power of sound: unravelling how acoustic communication shapes group dynamics’.

@article{duttaSamplingRandomGraphs2024,
	title = {Sampling {Random} {Graphs} with {Specified} {Degree} {Sequences}},
	issn = {1061-8600, 1537-2715},
	url = {https://www.tandfonline.com/doi/full/10.1080/10618600.2024.2418817},
	doi = {10.1080/10618600.2024.2418817},
	abstract = {The configuration model is a standard tool for uniformly generating random graphs with a specified degree sequence, and is often used as a null model to evaluate how much of an observed network’s structure can be explained by its degree structure alone. A Markov chain Monte Carlo (MCMC) algorithm, based on a degreepreserving double-edge swap, provides an asymptotic solution to sample from the configuration model. However, accurately and efficiently detecting when this Markov chain is sufficiently close to its stationary distribution remains an unsolved problem. Here, we provide a solution to sample from the configuration model using this standard MCMC algorithm. We develop an algorithm, based on the assortativity of the sampled graphs, for estimating the gap between effectively independent MCMC states, and a computationally efficient gap-estimation heuristic derived from analyzing a corpus of 509 empirical networks. We provide a convergence detection method based on the Dickey-Fuller Generalized Least Squares test, which we show is more accurate and efficient than three alternative Markov chain convergence tests. Supplementary materials for the proposed methods can be found here.},
	language = {en},
	urldate = {2025-02-14},
	journal = {Journal of Computational and Graphical Statistics},
	author = {Dutta, Upasana and Fosdick, Bailey K. and Clauset, Aaron},
	month = dec,
	year = {2024},
	pages = {1--14},
}

The configuration model is a standard tool for uniformly generating random graphs with a specified degree sequence, and is often used as a null model to evaluate how much of an observed network’s structure can be explained by its degree structure alone. A Markov chain Monte Carlo (MCMC) algorithm, based on a degreepreserving double-edge swap, provides an asymptotic solution to sample from the configuration model. However, accurately and efficiently detecting when this Markov chain is sufficiently close to its stationary distribution remains an unsolved problem. Here, we provide a solution to sample from the configuration model using this standard MCMC algorithm. We develop an algorithm, based on the assortativity of the sampled graphs, for estimating the gap between effectively independent MCMC states, and a computationally efficient gap-estimation heuristic derived from analyzing a corpus of 509 empirical networks. We provide a convergence detection method based on the Dickey-Fuller Generalized Least Squares test, which we show is more accurate and efficient than three alternative Markov chain convergence tests. Supplementary materials for the proposed methods can be found here.

@article{salbanyaStructureMattersAssessing2024,
	title = {Structure matters: {Assessing} the statistical significance of network topologies},
	volume = {19},
	issn = {1932-6203},
	shorttitle = {Structure matters},
	url = {https://dx.plos.org/10.1371/journal.pone.0309005},
	doi = {10.1371/journal.pone.0309005},
	abstract = {Network analysis has found widespread utility in many research areas. However, assessing the statistical significance of observed relationships within networks remains a complex challenge. Traditional node permutation tests are often insufficient in capturing the effect of changing network topology by creating reliable null distributions. We propose two randomization alternatives to address this gap: random rewiring and controlled rewiring. These methods incorporate changes in the network topology through edge swaps. However, controlled rewiring allows for more nuanced alterations of the original network than random rewiring. In this sense, this paper introduces a novel evaluation tool, the Expanded Quadratic Assignment Procedure (EQAP), designed to calculate a specific p-value and interpret statistical tests with enhanced precision. The combination of EQAP and controlled rewiring provides a robust network comparison and statistical analysis framework. The methodology is exemplified through two real-world examples: the analysis of an organizational network structure, illustrated by the Enron-Email dataset, and a social network case, represented by the UK Faculty friendship network. The utility of these statistical tests is underscored by their capacity to safeguard researchers against Type I errors when exploring network metrics dependent on intricate topologies.},
	language = {en},
	number = {10},
	urldate = {2025-02-19},
	journal = {PLOS ONE},
	author = {Salbanya, Bernat and Carrasco-Farré, Carlos and Nin, Jordi},
	editor = {Bouffanais, Roland},
	month = oct,
	year = {2024},
	pages = {e0309005},
}

Network analysis has found widespread utility in many research areas. However, assessing the statistical significance of observed relationships within networks remains a complex challenge. Traditional node permutation tests are often insufficient in capturing the effect of changing network topology by creating reliable null distributions. We propose two randomization alternatives to address this gap: random rewiring and controlled rewiring. These methods incorporate changes in the network topology through edge swaps. However, controlled rewiring allows for more nuanced alterations of the original network than random rewiring. In this sense, this paper introduces a novel evaluation tool, the Expanded Quadratic Assignment Procedure (EQAP), designed to calculate a specific p-value and interpret statistical tests with enhanced precision. The combination of EQAP and controlled rewiring provides a robust network comparison and statistical analysis framework. The methodology is exemplified through two real-world examples: the analysis of an organizational network structure, illustrated by the Enron-Email dataset, and a social network case, represented by the UK Faculty friendship network. The utility of these statistical tests is underscored by their capacity to safeguard researchers against Type I errors when exploring network metrics dependent on intricate topologies.

@article{ghoreishifarGenomewideAssessmentMapping2023,
	title = {Genome-wide assessment and mapping of inbreeding depression identifies candidate genes associated with semen traits in {Holstein} bulls},
	volume = {24},
	issn = {1471-2164},
	url = {https://doi.org/10.1186/s12864-023-09298-1},
	doi = {10.1186/s12864-023-09298-1},
	abstract = {The reduction in phenotypic performance of a population due to mating between close relatives is called inbreeding depression. The genetic background of inbreeding depression for semen traits is poorly understood. Thus, the objectives were to estimate the effect of inbreeding and to identify genomic regions underlying inbreeding depression of semen traits including ejaculate volume (EV), sperm concentration (SC), and sperm motility (SM). The dataset comprised {\textasciitilde} 330 K semen records from {\textasciitilde} 1.5 K Holstein bulls genotyped with 50 K single nucleotide polymorphism (SNP) BeadChip. Genomic inbreeding coefficients were estimated using runs of homozygosity (i.e., FROH {\textgreater} 1 Mb) and excess of SNP homozygosity (FSNP). The effect of inbreeding was estimated by regressing phenotypes of semen traits on inbreeding coefficients. Associated variants with inbreeding depression were also detected by regressing phenotypes on ROH state of the variants.},
	number = {1},
	urldate = {2025-03-31},
	journal = {BMC Genomics},
	author = {Ghoreishifar, Mohammad and Vahedi, Seyed Milad and Salek Ardestani, Siavash and Khansefid, Majid and Pryce, Jennie E.},
	month = may,
	year = {2023},
	keywords = {Dairy cattle, Inbreeding depression, Male fertility, Runs of homozygosity (ROH), Sperm quality},
	pages = {230},
}

The reduction in phenotypic performance of a population due to mating between close relatives is called inbreeding depression. The genetic background of inbreeding depression for semen traits is poorly understood. Thus, the objectives were to estimate the effect of inbreeding and to identify genomic regions underlying inbreeding depression of semen traits including ejaculate volume (EV), sperm concentration (SC), and sperm motility (SM). The dataset comprised ~ 330 K semen records from ~ 1.5 K Holstein bulls genotyped with 50 K single nucleotide polymorphism (SNP) BeadChip. Genomic inbreeding coefficients were estimated using runs of homozygosity (i.e., FROH \textgreater 1 Mb) and excess of SNP homozygosity (FSNP). The effect of inbreeding was estimated by regressing phenotypes of semen traits on inbreeding coefficients. Associated variants with inbreeding depression were also detected by regressing phenotypes on ROH state of the variants.

@article{dorseyTasteFamiliarExplaining2023,
	title = {A taste for the familiar: explaining the inbreeding paradox},
	volume = {38},
	issn = {01695347},
	shorttitle = {A taste for the familiar},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0169534722002270},
	doi = {10.1016/j.tree.2022.09.007},
	language = {en},
	number = {2},
	urldate = {2025-03-30},
	journal = {Trends in Ecology \& Evolution},
	author = {Dorsey, Owen C. and Rosenthal, Gil G.},
	month = feb,
	year = {2023},
	pages = {132--142},
}

@incollection{richardsonBehavioralEcologyPerspective2023,
	title = {A behavioral ecology perspective on inbreeding and inbreeding depression},
	volume = {55},
	copyright = {https://www.elsevier.com/tdm/userlicense/1.0/},
	isbn = {978-0-443-19354-5},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S006534542200016X},
	doi = {10.1016/bs.asb.2022.11.002},
	language = {en},
	urldate = {2025-03-30},
	booktitle = {Advances in the {Study} of {Behavior}},
	publisher = {Elsevier},
	author = {Richardson, Jon and Smiseth, Per T.},
	year = {2023},
	pages = {37--54},
}

@article{oddssonDeficitHomozygosity1522023,
	title = {Deficit of homozygosity among 1.52 million individuals and genetic causes of recessive lethality},
	volume = {14},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-023-38951-2},
	doi = {10.1038/s41467-023-38951-2},
	abstract = {Abstract
            Genotypes causing pregnancy loss and perinatal mortality are depleted among living individuals and are therefore difficult to find. To explore genetic causes of recessive lethality, we searched for sequence variants with deficit of homozygosity among 1.52 million individuals from six European populations. In this study, we identified 25 genes harboring protein-altering sequence variants with a strong deficit of homozygosity (10\% or less of predicted homozygotes). Sequence variants in 12 of the genes cause Mendelian disease under a recessive mode of inheritance, two under a dominant mode, but variants in the remaining 11 have not been reported to cause disease. Sequence variants with a strong deficit of homozygosity are over-represented among genes essential for growth of human cell lines and genes orthologous to mouse genes known to affect viability. The function of these genes gives insight into the genetics of intrauterine lethality. We also identified 1077 genes with homozygous predicted loss-of-function genotypes not previously described, bringing the total set of genes completely knocked out in humans to 4785.},
	language = {en},
	number = {1},
	urldate = {2025-03-26},
	journal = {Nature Communications},
	author = {Oddsson, Asmundur and Sulem, Patrick and Sveinbjornsson, Gardar and Arnadottir, Gudny A. and Steinthorsdottir, Valgerdur and Halldorsson, Gisli H. and Atlason, Bjarni A. and Oskarsson, Gudjon R. and Helgason, Hannes and Nielsen, Henriette Svarre and Westergaard, David and Karjalainen, Juha M. and Katrinardottir, Hildigunnur and Fridriksdottir, Run and Jensson, Brynjar O. and Tragante, Vinicius and Ferkingstad, Egil and Jonsson, Hakon and Gudjonsson, Sigurjon A. and Beyter, Doruk and Moore, Kristjan H. S. and Thordardottir, Helga B. and Kristmundsdottir, Snaedis and Stefansson, Olafur A. and Rantapää-Dahlqvist, Solbritt and Sonderby, Ida Elken and Didriksen, Maria and Stridh, Pernilla and Haavik, Jan and Tryggvadottir, Laufey and Frei, Oleksandr and Walters, G. Bragi and Kockum, Ingrid and Hjalgrim, Henrik and Olafsdottir, Thorunn A. and Selbaek, Geir and Nyegaard, Mette and Erikstrup, Christian and Brodersen, Thorsten and Saevarsdottir, Saedis and Olsson, Tomas and Nielsen, Kaspar Rene and Haraldsson, Asgeir and Bruun, Mie Topholm and Hansen, Thomas Folkmann and {DBDS Genomic Consortium} and Brunak, Søren and Nielsen, Kasper Rene and Brun, Mie Topholm and Stefánsson, Hreinn and Þorsteinsdóttir, Unnur and Steingrimsdottir, Thora and Jacobsen, Rikke Louise and Lie, Rolv T. and Djurovic, Srdjan and Alfredsson, Lars and Lopez De Lapuente Portilla, Aitzkoa and Brunak, Soren and Melsted, Pall and Halldorsson, Bjarni V. and Saemundsdottir, Jona and Magnusson, Olafur Th. and Padyukov, Leonid and Banasik, Karina and Rafnar, Thorunn and Askling, Johan and Klareskog, Lars and Pedersen, Ole Birger and Masson, Gisli and Havdahl, Alexandra and Nilsson, Bjorn and Andreassen, Ole A. and Daly, Mark and Ostrowski, Sisse Rye and Jonsdottir, Ingileif and Stefansson, Hreinn and Holm, Hilma and Helgason, Agnar and Thorsteinsdottir, Unnur and Stefansson, Kari and Gudbjartsson, Daniel F.},
	month = jun,
	year = {2023},
	pages = {3453},
}

Abstract Genotypes causing pregnancy loss and perinatal mortality are depleted among living individuals and are therefore difficult to find. To explore genetic causes of recessive lethality, we searched for sequence variants with deficit of homozygosity among 1.52 million individuals from six European populations. In this study, we identified 25 genes harboring protein-altering sequence variants with a strong deficit of homozygosity (10% or less of predicted homozygotes). Sequence variants in 12 of the genes cause Mendelian disease under a recessive mode of inheritance, two under a dominant mode, but variants in the remaining 11 have not been reported to cause disease. Sequence variants with a strong deficit of homozygosity are over-represented among genes essential for growth of human cell lines and genes orthologous to mouse genes known to affect viability. The function of these genes gives insight into the genetics of intrauterine lethality. We also identified 1077 genes with homozygous predicted loss-of-function genotypes not previously described, bringing the total set of genes completely knocked out in humans to 4785.

@article{palmiottiGeneticManipulationBetta2023,
	title = {Genetic manipulation of betta fish},
	volume = {5},
	copyright = {All rights reserved},
	issn = {2673-3439},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10401044/},
	doi = {10.3389/fgeed.2023.1167093},
	abstract = {Betta splendens, also known as Siamese fighting fish or “betta,” is a freshwater fish species renowned for its astonishing morphological diversity and extreme aggressive behavior. Despite recent advances in our understanding of the genetics and neurobiology of betta, the lack of tools to manipulate their genome has hindered progress at functional and mechanistic levels. In this study, we outline the use of three genetic manipulation technologies, which we have optimized for use in betta: CRISPR/Cas9-mediated knockout, CRISPR/Cas9-mediated knockin, and Tol2-mediated transgenesis. We knocked out three genes: alkal2l, bco1l, and mitfa, and analyzed their effects on viability and pigmentation. Furthermore, we knocked in a fluorescent protein into the mitfa locus, a proof-of-principle experiment of this powerful technology in betta. Finally, we used Tol2-mediated transgenesis to create fish with ubiquitous expression of GFP, and then developed a bicistronic plasmid with heart-specific expression of a red fluorescent protein to serve as a visible marker of successful transgenesis. Our work highlights the potential for the genetic manipulation of betta, providing valuable resources for the effective use of genetic tools in this animal model.},
	urldate = {2024-06-05},
	journal = {Frontiers in Genome Editing},
	author = {Palmiotti, Alec and Lichak, Madison R. and Shih, Pei-Yin and Kwon, Young Mi and Bendesky, Andres},
	month = jul,
	year = {2023},
	note = {0 citations (Crossref) [2024-06-05]},
	pages = {1167093},
}

Betta splendens, also known as Siamese fighting fish or “betta,” is a freshwater fish species renowned for its astonishing morphological diversity and extreme aggressive behavior. Despite recent advances in our understanding of the genetics and neurobiology of betta, the lack of tools to manipulate their genome has hindered progress at functional and mechanistic levels. In this study, we outline the use of three genetic manipulation technologies, which we have optimized for use in betta: CRISPR/Cas9-mediated knockout, CRISPR/Cas9-mediated knockin, and Tol2-mediated transgenesis. We knocked out three genes: alkal2l, bco1l, and mitfa, and analyzed their effects on viability and pigmentation. Furthermore, we knocked in a fluorescent protein into the mitfa locus, a proof-of-principle experiment of this powerful technology in betta. Finally, we used Tol2-mediated transgenesis to create fish with ubiquitous expression of GFP, and then developed a bicistronic plasmid with heart-specific expression of a red fluorescent protein to serve as a visible marker of successful transgenesis. Our work highlights the potential for the genetic manipulation of betta, providing valuable resources for the effective use of genetic tools in this animal model.

@article{bickWhatAreHigherOrder2023,
	title = {What {Are} {Higher}-{Order} {Networks}?},
	volume = {65},
	issn = {0036-1445, 1095-7200},
	url = {https://epubs.siam.org/doi/10.1137/21M1414024},
	doi = {10.1137/21M1414024},
	abstract = {Network-based modeling of complex systems and data using the language of graphs has become an essential topic across a range of different disciplines. Arguably, this graph-based perspective derives its success from the relative simplicity of graphs: A graph consists of nothing more than a set of vertices and a set of edges, describing relationships between pairs of such vertices. This simple combinatorial structure makes graphs interpretable and flexible modeling tools. The simplicity of graphs as system models, however, has been scrutinized in the literature recently. Specifically, it has been argued from a variety of different angles that there is a need for higher-order networks, which go beyond the paradigm of modeling pairwise relationships, as encapsulated by graphs. In this survey article we take stock of these recent developments. Our goals are to clarify (i) what higherorder networks are, (ii) why these are interesting objects of study, and (iii) how they can be used in applications.},
	language = {en},
	number = {3},
	urldate = {2025-02-12},
	journal = {SIAM Review},
	author = {Bick, Christian and Gross, Elizabeth and Harrington, Heather A. and Schaub, Michael T.},
	month = aug,
	year = {2023},
	pages = {686--731},
}

Network-based modeling of complex systems and data using the language of graphs has become an essential topic across a range of different disciplines. Arguably, this graph-based perspective derives its success from the relative simplicity of graphs: A graph consists of nothing more than a set of vertices and a set of edges, describing relationships between pairs of such vertices. This simple combinatorial structure makes graphs interpretable and flexible modeling tools. The simplicity of graphs as system models, however, has been scrutinized in the literature recently. Specifically, it has been argued from a variety of different angles that there is a need for higher-order networks, which go beyond the paradigm of modeling pairwise relationships, as encapsulated by graphs. In this survey article we take stock of these recent developments. Our goals are to clarify (i) what higherorder networks are, (ii) why these are interesting objects of study, and (iii) how they can be used in applications.

@article{ruggeriCommunityDetectionLarge2023,
	title = {Community detection in large hypergraphs},
	volume = {9},
	number = {28},
	journal = {Science Advances},
	publisher = {American Association for the Advancement of Science},
	author = {Ruggeri, Nicolò and Contisciani, Martina and Battiston, Federico and De Bacco, Caterina},
	year = {2023},
	pages = {eadg9159},
}

@article{vasilyevaDistancesHigherorderNetworks2023,
	title = {Distances in higher-order networks and the metric structure of hypergraphs},
	volume = {25},
	number = {6},
	journal = {Entropy},
	publisher = {MDPI},
	author = {Vasilyeva, Ekaterina and Romance, Miguel and Samoylenko, Ivan and Kovalenko, Kirill and Musatov, Daniil and Raigorodskii, Andrey Mihailovich and Boccaletti, Stefano},
	year = {2023},
	pages = {923},
}

@article{hauserComparingGenomebasedEstimates2022,
	title = {Comparing genome‐based estimates of relatedness for use in pedigree‐based conservation management},
	volume = {22},
	issn = {1755-098X, 1755-0998},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13630},
	doi = {10.1111/1755-0998.13630},
	abstract = {Abstract
            
              Researchers have long debated which estimator of relatedness best captures the degree of relationship between two individuals. In the genomics era, this debate continues, with relatedness estimates being sensitive to the methods used to generate markers, marker quality, and levels of diversity in sampled individuals. Here, we compare six commonly used genome‐based relatedness estimators (kinship genetic distance [KGD], Wang maximum likelihood [TrioML], Queller and Goodnight [
              R
              xy
              ], Kinship INference for Genome‐wide association studies [KING‐robust), and pairwise relatedness [
              R
              AB
              ], allele‐sharing coancestry [AS]) across five species bred in captivity–including three birds and two mammals–with varying degrees of reliable pedigree data, using reduced‐representation and whole genome resequencing data. Genome‐based relatedness estimates varied widely across estimators, sequencing methods, and species, yet the most consistent results for known first order relationships were found using
              R
              xy
              ,
              R
              AB
              , and AS. However, AS was found to be less consistently correlated with known pedigree relatedness than either
              R
              xy
              or
              R
              AB
              . Our combined results indicate there is not a single genome‐based estimator that is ideal across different species and data types. To determine the most appropriate genome‐based relatedness estimator for each new data set, we recommend assessing the relative: (1) correlation of candidate estimators with known relationships in the pedigree and (2) precision of candidate estimators with known first‐order relationships. These recommendations are broadly applicable to conservation breeding programmes, particularly where genome‐based estimates of relatedness can complement and complete poorly pedigreed populations. Given a growing interest in the application of wild pedigrees, our results are also applicable to in situ wildlife management.},
	language = {en},
	number = {7},
	urldate = {2025-03-31},
	journal = {Molecular Ecology Resources},
	author = {Hauser, Samantha S. and Galla, Stephanie J. and Putnam, Andrea S. and Steeves, Tammy E. and Latch, Emily K.},
	month = oct,
	year = {2022},
	pages = {2546--2558},
}

Abstract Researchers have long debated which estimator of relatedness best captures the degree of relationship between two individuals. In the genomics era, this debate continues, with relatedness estimates being sensitive to the methods used to generate markers, marker quality, and levels of diversity in sampled individuals. Here, we compare six commonly used genome‐based relatedness estimators (kinship genetic distance [KGD], Wang maximum likelihood [TrioML], Queller and Goodnight [ R xy ], Kinship INference for Genome‐wide association studies [KING‐robust), and pairwise relatedness [ R AB ], allele‐sharing coancestry [AS]) across five species bred in captivity–including three birds and two mammals–with varying degrees of reliable pedigree data, using reduced‐representation and whole genome resequencing data. Genome‐based relatedness estimates varied widely across estimators, sequencing methods, and species, yet the most consistent results for known first order relationships were found using R xy , R AB , and AS. However, AS was found to be less consistently correlated with known pedigree relatedness than either R xy or R AB . Our combined results indicate there is not a single genome‐based estimator that is ideal across different species and data types. To determine the most appropriate genome‐based relatedness estimator for each new data set, we recommend assessing the relative: (1) correlation of candidate estimators with known relationships in the pedigree and (2) precision of candidate estimators with known first‐order relationships. These recommendations are broadly applicable to conservation breeding programmes, particularly where genome‐based estimates of relatedness can complement and complete poorly pedigreed populations. Given a growing interest in the application of wild pedigrees, our results are also applicable to in situ wildlife management.

@article{hauserComparingGenomebasedEstimates2022a,
	title = {Comparing genome‐based estimates of relatedness for use in pedigree‐based conservation management},
	volume = {22},
	issn = {1755-098X, 1755-0998},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13630},
	doi = {10.1111/1755-0998.13630},
	abstract = {Abstract
            
              Researchers have long debated which estimator of relatedness best captures the degree of relationship between two individuals. In the genomics era, this debate continues, with relatedness estimates being sensitive to the methods used to generate markers, marker quality, and levels of diversity in sampled individuals. Here, we compare six commonly used genome‐based relatedness estimators (kinship genetic distance [KGD], Wang maximum likelihood [TrioML], Queller and Goodnight [
              R
              xy
              ], Kinship INference for Genome‐wide association studies [KING‐robust), and pairwise relatedness [
              R
              AB
              ], allele‐sharing coancestry [AS]) across five species bred in captivity–including three birds and two mammals–with varying degrees of reliable pedigree data, using reduced‐representation and whole genome resequencing data. Genome‐based relatedness estimates varied widely across estimators, sequencing methods, and species, yet the most consistent results for known first order relationships were found using
              R
              xy
              ,
              R
              AB
              , and AS. However, AS was found to be less consistently correlated with known pedigree relatedness than either
              R
              xy
              or
              R
              AB
              . Our combined results indicate there is not a single genome‐based estimator that is ideal across different species and data types. To determine the most appropriate genome‐based relatedness estimator for each new data set, we recommend assessing the relative: (1) correlation of candidate estimators with known relationships in the pedigree and (2) precision of candidate estimators with known first‐order relationships. These recommendations are broadly applicable to conservation breeding programmes, particularly where genome‐based estimates of relatedness can complement and complete poorly pedigreed populations. Given a growing interest in the application of wild pedigrees, our results are also applicable to in situ wildlife management.},
	language = {en},
	number = {7},
	urldate = {2025-03-31},
	journal = {Molecular Ecology Resources},
	author = {Hauser, Samantha S. and Galla, Stephanie J. and Putnam, Andrea S. and Steeves, Tammy E. and Latch, Emily K.},
	month = oct,
	year = {2022},
	pages = {2546--2558},
}

Abstract Researchers have long debated which estimator of relatedness best captures the degree of relationship between two individuals. In the genomics era, this debate continues, with relatedness estimates being sensitive to the methods used to generate markers, marker quality, and levels of diversity in sampled individuals. Here, we compare six commonly used genome‐based relatedness estimators (kinship genetic distance [KGD], Wang maximum likelihood [TrioML], Queller and Goodnight [ R xy ], Kinship INference for Genome‐wide association studies [KING‐robust), and pairwise relatedness [ R AB ], allele‐sharing coancestry [AS]) across five species bred in captivity–including three birds and two mammals–with varying degrees of reliable pedigree data, using reduced‐representation and whole genome resequencing data. Genome‐based relatedness estimates varied widely across estimators, sequencing methods, and species, yet the most consistent results for known first order relationships were found using R xy , R AB , and AS. However, AS was found to be less consistently correlated with known pedigree relatedness than either R xy or R AB . Our combined results indicate there is not a single genome‐based estimator that is ideal across different species and data types. To determine the most appropriate genome‐based relatedness estimator for each new data set, we recommend assessing the relative: (1) correlation of candidate estimators with known relationships in the pedigree and (2) precision of candidate estimators with known first‐order relationships. These recommendations are broadly applicable to conservation breeding programmes, particularly where genome‐based estimates of relatedness can complement and complete poorly pedigreed populations. Given a growing interest in the application of wild pedigrees, our results are also applicable to in situ wildlife management.

@article{morganPopulationStructureInbreeding2022,
	title = {Population structure and inbreeding in wild house mice ({Mus} musculus) at different geographic scales},
	volume = {129},
	issn = {0018-067X, 1365-2540},
	url = {https://www.nature.com/articles/s41437-022-00551-z},
	doi = {10.1038/s41437-022-00551-z},
	language = {en},
	number = {3},
	urldate = {2025-03-30},
	journal = {Heredity},
	author = {Morgan, Andrew P. and Hughes, Jonathan J. and Didion, John P. and Jolley, Wesley J. and Campbell, Karl J. and Threadgill, David W. and Bonhomme, Francois and Searle, Jeremy B. and De Villena, Fernando Pardo-Manuel},
	month = sep,
	year = {2022},
	pages = {183--194},
}

@article{rungeParentoffspringInferenceInbred2022,
	title = {Parent-offspring inference in inbred populations},
	volume = {22},
	doi = {https://doi.org/10.1111/1755-0998.13680},
	number = {8},
	journal = {Molecular Ecology Resources},
	publisher = {Wiley Online Library},
	author = {Runge, Jan-Niklas and König, Barbara and Lindholm, Anna K and Bendesky, Andres},
	year = {2022},
	pages = {2981--2993},
}

@article{kwonGenomicConsequencesDomestication2022,
	title = {Genomic consequences of domestication of the {Siamese} fighting fish},
	volume = {8},
	copyright = {All rights reserved},
	url = {https://www.science.org/doi/10.1126/sciadv.abm4950},
	doi = {10.1126/sciadv.abm4950},
	number = {10},
	urldate = {2022-07-14},
	journal = {Science Advances},
	publisher = {American Association for the Advancement of Science},
	author = {Kwon, Young Mi and Vranken, Nathan and Hoge, Carla and Lichak, Madison R. and Norovich, Amy L. and Francis, Kerel X. and Camacho-Garcia, Julia and Bista, Iliana and Wood, Jonathan and McCarthy, Shane and Chow, William and Tan, Heok Hui and Howe, Kerstin and Bandara, Sepalika and von Lintig, Johannes and Rüber, Lukas and Durbin, Richard and Svardal, Hannes and Bendesky, Andres},
	month = mar,
	year = {2022},
	note = {8 citations (Crossref) [2023-02-11]},
	pages = {eabm4950},
}

@article{ferrariCooperationNecessityCondition2022,
	title = {Cooperation by necessity: condition- and density-dependent reproductive tactics of female house mice},
	volume = {5},
	issn = {2399-3642},
	shorttitle = {Cooperation by necessity},
	url = {https://www.nature.com/articles/s42003-022-03267-2},
	doi = {10.1038/s42003-022-03267-2},
	abstract = {Abstract
            
              Optimal reproductive strategies evolve from the interplay between an individual’s intrinsic state and extrinsic environment, both factors that are rarely fixed over its lifetime. Conditional breeding tactics might be one evolutionary trajectory allowing individuals to maximize fitness. We apply multi-state capture-mark-recapture analysis to a detailed 8-year data set of free-ranging house mice in a growing population to discern causes and fitness consequences of two alternative reproductive tactics in females, communal and solitary breeding. This allows us to integrate natural variation in life-history traits when analysing the expression of two alternative reproductive tactics in females. We find that communal breeding reduces average population fitness, but nevertheless increases over our 8-year study period. The tactic proves to be expressed conditionally dependent on both population density and female body mass – allowing females to breed under subpar conditions,
              i.e
              . at high density or when of low body mass. Our results contradict previous laboratory studies and emphasize the importance of studying cooperation under natural conditions, including natural variation in state-dependent survival and breeding probabilities.},
	language = {en},
	number = {1},
	urldate = {2025-03-19},
	journal = {Communications Biology},
	author = {Ferrari, Manuela and Lindholm, Anna K. and Ozgul, Arpat and Oli, Madan K. and König, Barbara},
	month = apr,
	year = {2022},
	pages = {348},
}

Abstract Optimal reproductive strategies evolve from the interplay between an individual’s intrinsic state and extrinsic environment, both factors that are rarely fixed over its lifetime. Conditional breeding tactics might be one evolutionary trajectory allowing individuals to maximize fitness. We apply multi-state capture-mark-recapture analysis to a detailed 8-year data set of free-ranging house mice in a growing population to discern causes and fitness consequences of two alternative reproductive tactics in females, communal and solitary breeding. This allows us to integrate natural variation in life-history traits when analysing the expression of two alternative reproductive tactics in females. We find that communal breeding reduces average population fitness, but nevertheless increases over our 8-year study period. The tactic proves to be expressed conditionally dependent on both population density and female body mass – allowing females to breed under subpar conditions, i.e . at high density or when of low body mass. Our results contradict previous laboratory studies and emphasize the importance of studying cooperation under natural conditions, including natural variation in state-dependent survival and breeding probabilities.

@article{vega-trejoSexspecificInbreedingDepression2022,
	title = {Sex‐specific inbreeding depression: {A} meta‐analysis},
	volume = {25},
	issn = {1461-023X, 1461-0248},
	shorttitle = {Sex‐specific inbreeding depression},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/ele.13961},
	doi = {10.1111/ele.13961},
	abstract = {Abstract
            Inbreeding depression, the reduced fitness of the offspring of related individuals, can affect males and females differently. Although a comprehensive theoretical framework describing the causes of sex‐specific inbreeding depression is lacking, empirical evidence suggests that often one sex tends to be more vulnerable than the other. However, the generality, direction, and degree of sex‐specific difference in inbreeding depression remains enigmatic as studies on this topic have reported conflicting results. Here, we conduct a meta‐analysis to test for sex‐specific differences in the magnitude of inbreeding depression. We synthetised 321 effect sizes of experimental studies across 47 species and found a small difference in inbreeding depression between the sexes: females suffered slightly higher inbreeding depression than males. Furthermore, a higher inbreeding coefficient was correlated with higher inbreeding depression. However, there was a large amount of heterogeneity that remained unexplained, even when considering different factors that could affect inbreeding between the sexes, such as sexual size dimorphism, heterogamety, the type of trait measured and whether animals were tested in a stressful environment. As such, we highlight the need to further explore inbreeding depression across different species to determine the occurrence and causes of sex differences to increase our understanding of the evolutionary consequences of sex‐specific inbreeding depression.},
	language = {en},
	number = {4},
	urldate = {2025-03-19},
	journal = {Ecology Letters},
	author = {Vega‐Trejo, Regina and De Boer, Raïssa A. and Fitzpatrick, John L. and Kotrschal, Alexander},
	editor = {Sánchez‐Tójar, Alfredo},
	month = apr,
	year = {2022},
	pages = {1009--1026},
}

Abstract Inbreeding depression, the reduced fitness of the offspring of related individuals, can affect males and females differently. Although a comprehensive theoretical framework describing the causes of sex‐specific inbreeding depression is lacking, empirical evidence suggests that often one sex tends to be more vulnerable than the other. However, the generality, direction, and degree of sex‐specific difference in inbreeding depression remains enigmatic as studies on this topic have reported conflicting results. Here, we conduct a meta‐analysis to test for sex‐specific differences in the magnitude of inbreeding depression. We synthetised 321 effect sizes of experimental studies across 47 species and found a small difference in inbreeding depression between the sexes: females suffered slightly higher inbreeding depression than males. Furthermore, a higher inbreeding coefficient was correlated with higher inbreeding depression. However, there was a large amount of heterogeneity that remained unexplained, even when considering different factors that could affect inbreeding between the sexes, such as sexual size dimorphism, heterogamety, the type of trait measured and whether animals were tested in a stressful environment. As such, we highlight the need to further explore inbreeding depression across different species to determine the occurrence and causes of sex differences to increase our understanding of the evolutionary consequences of sex‐specific inbreeding depression.

@article{bovetFlowStabilityDynamic2022,
	title = {Flow stability for dynamic community detection},
	volume = {8},
	copyright = {Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License (CC-BY-NC-SA)},
	issn = {2375-2548},
	url = {https://www.science.org/doi/10.1126/sciadv.abj3063},
	doi = {10.1126/sciadv.abj3063},
	abstract = {Many systems exhibit complex temporal dynamics due to the presence of different processes taking place simultaneously. An important task in these systems is to extract a simplified view of their time-dependent network of interactions. Community detection in temporal networks usually relies on aggregation over time windows or consider sequences of different stationary epochs. For dynamics-based methods, attempts to generalize static-network methodologies also face the fundamental difficulty that a stationary state of the dynamics does not always exist. Here, we derive a method based on a dynamical process evolving on the temporal network. Our method allows dynamics that do not reach a steady state and uncovers two sets of communities for a given time interval that accounts for the ordering of edges in forward and backward time. We show that our method provides a natural way to disentangle the different dynamical scales present in a system with synthetic and real-world examples. , The flow stability method extracts simplified descriptions of complex time-resolved datasets at different dynamical scales.},
	language = {en},
	number = {19},
	urldate = {2022-05-12},
	journal = {Science Advances},
	author = {Bovet, Alexandre and Delvenne, Jean-Charles and Lambiotte, Renaud},
	month = may,
	year = {2022},
	pages = {eabj3063},
}

Many systems exhibit complex temporal dynamics due to the presence of different processes taking place simultaneously. An important task in these systems is to extract a simplified view of their time-dependent network of interactions. Community detection in temporal networks usually relies on aggregation over time windows or consider sequences of different stationary epochs. For dynamics-based methods, attempts to generalize static-network methodologies also face the fundamental difficulty that a stationary state of the dynamics does not always exist. Here, we derive a method based on a dynamical process evolving on the temporal network. Our method allows dynamics that do not reach a steady state and uncovers two sets of communities for a given time interval that accounts for the ordering of edges in forward and backward time. We show that our method provides a natural way to disentangle the different dynamical scales present in a system with synthetic and real-world examples. , The flow stability method extracts simplified descriptions of complex time-resolved datasets at different dynamical scales.

@article{majhiDynamicsHigherorderNetworks2022,
	title = {Dynamics on higher-order networks: a review},
	volume = {19},
	issn = {1742-5662},
	shorttitle = {Dynamics on higher-order networks},
	url = {https://royalsocietypublishing.org/doi/10.1098/rsif.2022.0043},
	doi = {10.1098/rsif.2022.0043},
	abstract = {Network science has evolved into an indispensable platform for studying complex systems. But recent research has identified limits of classical networks, where links connect pairs of nodes, to comprehensively describe group interactions. Higher-order networks, where a link can connect more than two nodes, have therefore emerged as a new frontier in network science. Since group interactions are common in social, biological and technological systems, higher-order networks have recently led to important new discoveries across many fields of research. Here, we review these works, focusing in particular on the novel aspects of the dynamics that emerges on higher-order networks. We cover a variety of dynamical processes that have thus far been studied, including different synchronization phenomena, contagion processes, the evolution of cooperation and consensus formation. We also outline open challenges and promising directions for future research.},
	language = {en},
	number = {188},
	urldate = {2025-02-23},
	journal = {Journal of The Royal Society Interface},
	author = {Majhi, Soumen and Perc, Matjaž and Ghosh, Dibakar},
	month = mar,
	year = {2022},
	pages = {20220043},
}

Network science has evolved into an indispensable platform for studying complex systems. But recent research has identified limits of classical networks, where links connect pairs of nodes, to comprehensively describe group interactions. Higher-order networks, where a link can connect more than two nodes, have therefore emerged as a new frontier in network science. Since group interactions are common in social, biological and technological systems, higher-order networks have recently led to important new discoveries across many fields of research. Here, we review these works, focusing in particular on the novel aspects of the dynamics that emerges on higher-order networks. We cover a variety of dynamical processes that have thus far been studied, including different synchronization phenomena, contagion processes, the evolution of cooperation and consensus formation. We also outline open challenges and promising directions for future research.

@incollection{erikssonFlowbasedCommunityDetection2022,
	title = {Flow-based community detection in hypergraphs},
	booktitle = {Higher-{Order} {Systems}},
	publisher = {Springer},
	author = {Eriksson, Anton and Carletti, Timoteo and Lambiotte, Renaud and Rojas, Alexis and Rosvall, Martin},
	year = {2022},
	pages = {141--161},
}

@article{kovalenkoVectorCentralityHypergraphs2022,
	title = {Vector centrality in hypergraphs},
	volume = {162},
	journal = {Chaos, Solitons \& Fractals},
	publisher = {Elsevier},
	author = {Kovalenko, Kirill and Romance, Miguel and Vasilyeva, Ekaterina and Aleja, David and Criado, Regino and Musatov, Daniil and Raigorodskii, Andrei M and Flores, Julio and Samoylenko, Ivan and Alfaro-Bittner, Karin and {others}},
	year = {2022},
	pages = {112397},
}

@article{gerberPopulationDensityTemperature2021,
	title = {Population density and temperature influence the return on maternal investment in wild house mice},
	volume = {8},
	issn = {2296-701X},
	url = {https://www.frontiersin.org/articles/10.3389/fevo.2020.602359/full},
	doi = {10.3389/fevo.2020.602359},
	abstract = {In mammals, reproduction is influenced by sexual competition, temperature and food availability and these factors might be crucial already during early life. Favorable early life environment and high maternal investment are expected to improve survival and reproduction. For example, in mammals, maternal investment via lactation predicts offspring growth. As body mass is often associated with fitness consequences, females have the potential to influence offspring fitness through their level of investment, which might interact with effects of population density and temperature. Here, we investigate the relationship between house mouse (
              Mus musculus domesticus
              ) pup body mass at day 13 (used as approximation for weaning mass) and individual reproductive parameters, as well as longevity, under natural variation in population density and temperature (as approximation for season). Further, we assessed the extent to which mothers influence the body mass of their offspring until weaning. To do so, we analyzed life data of 384 house mice from a free-living wild commensal population that was not food limited. The mother’s contribution accounted for 49\% of the variance in pup body mass. Further, we found a complex effect of population density, temperature and maternal investment on life-history traits related to fitness: shorter longevity with increasing pup body mass at day 13, delayed first reproduction of heavier pups when raised at warmer temperatures, and increased lifetime reproductive success for heavier pups at high densities. Our study shows that the effects of maternal investment are not independent of the effects of the environment. It thus highlights the importance of considering ecological conditions in combination with maternal effects to unravel the complexity of pup body mass on fitness measures.},
	urldate = {2025-03-30},
	journal = {Frontiers in Ecology and Evolution},
	author = {Gerber, Nina and Auclair, Yannick and König, Barbara and Lindholm, Anna K.},
	month = feb,
	year = {2021},
	pages = {602359},
}

In mammals, reproduction is influenced by sexual competition, temperature and food availability and these factors might be crucial already during early life. Favorable early life environment and high maternal investment are expected to improve survival and reproduction. For example, in mammals, maternal investment via lactation predicts offspring growth. As body mass is often associated with fitness consequences, females have the potential to influence offspring fitness through their level of investment, which might interact with effects of population density and temperature. Here, we investigate the relationship between house mouse ( Mus musculus domesticus ) pup body mass at day 13 (used as approximation for weaning mass) and individual reproductive parameters, as well as longevity, under natural variation in population density and temperature (as approximation for season). Further, we assessed the extent to which mothers influence the body mass of their offspring until weaning. To do so, we analyzed life data of 384 house mice from a free-living wild commensal population that was not food limited. The mother’s contribution accounted for 49% of the variance in pup body mass. Further, we found a complex effect of population density, temperature and maternal investment on life-history traits related to fitness: shorter longevity with increasing pup body mass at day 13, delayed first reproduction of heavier pups when raised at warmer temperatures, and increased lifetime reproductive success for heavier pups at high densities. Our study shows that the effects of maternal investment are not independent of the effects of the environment. It thus highlights the importance of considering ecological conditions in combination with maternal effects to unravel the complexity of pup body mass on fitness measures.

@article{deboerMetaanalyticEvidenceThat2021a,
	title = {Meta-analytic evidence that animals rarely avoid inbreeding},
	volume = {5},
	issn = {2397-334X},
	url = {https://www.nature.com/articles/s41559-021-01453-9},
	doi = {10.1038/s41559-021-01453-9},
	language = {en},
	number = {7},
	urldate = {2025-03-30},
	journal = {Nature Ecology \& Evolution},
	author = {De Boer, Raïssa A. and Vega-Trejo, Regina and Kotrschal, Alexander and Fitzpatrick, John L.},
	month = may,
	year = {2021},
	pages = {949--964},
}

@article{pikeWhyDontAll2021,
	title = {Why don't all animals avoid inbreeding?},
	volume = {288},
	issn = {0962-8452, 1471-2954},
	url = {https://royalsocietypublishing.org/doi/10.1098/rspb.2021.1045},
	doi = {10.1098/rspb.2021.1045},
	abstract = {Individuals are expected to avoid mating with relatives as inbreeding can reduce offspring fitness, a phenomenon known as inbreeding depression. This has led to the widespread assumption that selection will favour individuals that avoid mating with relatives. However, the strength of inbreeding avoidance is variable across species and there are numerous cases where related mates are not avoided. Here we test if the frequency that related males and females encounter each other explains variation in inbreeding avoidance using phylogenetic meta-analysis of 41 different species from six classes across the animal kingdom. In species reported to mate randomly with respect to relatedness, individuals were either unlikely to encounter relatives, or inbreeding had negligible effects on offspring fitness. Mechanisms for avoiding inbreeding, including active mate choice, post-copulatory processes and sex-biased dispersal, were only found in species with inbreeding depression. These results help explain why some species seem to care more about inbreeding than others: inbreeding avoidance through mate choice only evolves when there is both a risk of inbreeding depression and related sexual partners frequently encounter each other.},
	language = {en},
	number = {1956},
	urldate = {2025-03-30},
	journal = {Proceedings of the Royal Society B: Biological Sciences},
	author = {Pike, Victoria L. and Cornwallis, Charlie K. and Griffin, Ashleigh S.},
	month = aug,
	year = {2021},
	pages = {20211045},
}

Individuals are expected to avoid mating with relatives as inbreeding can reduce offspring fitness, a phenomenon known as inbreeding depression. This has led to the widespread assumption that selection will favour individuals that avoid mating with relatives. However, the strength of inbreeding avoidance is variable across species and there are numerous cases where related mates are not avoided. Here we test if the frequency that related males and females encounter each other explains variation in inbreeding avoidance using phylogenetic meta-analysis of 41 different species from six classes across the animal kingdom. In species reported to mate randomly with respect to relatedness, individuals were either unlikely to encounter relatives, or inbreeding had negligible effects on offspring fitness. Mechanisms for avoiding inbreeding, including active mate choice, post-copulatory processes and sex-biased dispersal, were only found in species with inbreeding depression. These results help explain why some species seem to care more about inbreeding than others: inbreeding avoidance through mate choice only evolves when there is both a risk of inbreeding depression and related sexual partners frequently encounter each other.

@article{khanGenomicEvidenceInbreeding2021,
	title = {Genomic evidence for inbreeding depression and purging of deleterious genetic variation in {Indian} tigers},
	volume = {118},
	issn = {0027-8424, 1091-6490},
	url = {https://pnas.org/doi/full/10.1073/pnas.2023018118},
	doi = {10.1073/pnas.2023018118},
	abstract = {Significance
            Habitat fragmentation is sequestering species into small and isolated populations, with high chances of extinction. Are small and isolated populations at risk for extinction from inbreeding depression? Or does inbreeding and purging of deleterious alleles reduce such threat? Using whole genomes from several wild Indian tiger populations, we provide evidence supporting purging of highly deleterious variants in a small–isolated population. However, our analyses also indicate that the remaining highly deleterious alleles are at high frequencies, suggesting continued inbreeding depression despite some successful purging. We discuss the implications of our results for conservation, including possible genomics-informed genetic rescue strategies.
          , 
            
              Increasing habitat fragmentation leads to wild populations becoming small, isolated, and threatened by inbreeding depression. However, small populations may be able to purge recessive deleterious alleles as they become expressed in homozygotes, thus reducing inbreeding depression and increasing population viability. We used whole-genome sequences from 57 tigers to estimate individual inbreeding and mutation load in a small–isolated and two large–connected populations in India. As expected, the small–isolated population had substantially higher average genomic inbreeding (
              F
              ROH
              = 0.57) than the large–connected (
              F
              ROH
              = 0.35 and
              F
              ROH
              = 0.46) populations. The small–isolated population had the lowest loss-of-function mutation load, likely due to purging of highly deleterious recessive mutations. The large populations had lower missense mutation loads than the small–isolated population, but were not identical, possibly due to different demographic histories. While the number of the loss-of-function alleles in the small–isolated population was lower, these alleles were at higher frequencies and homozygosity than in the large populations. Together, our data and analyses provide evidence of 1) high mutation load, 2) purging, and 3) the highest predicted inbreeding depression, despite purging, in the small–isolated population. Frequency distributions of damaging and neutral alleles uncover genomic evidence that purifying selection has removed part of the mutation load across Indian tiger populations. These results provide genomic evidence for purifying selection in both small and large populations, but also suggest that the remaining deleterious alleles may have inbreeding-associated fitness costs. We suggest that genetic rescue from sources selected based on genome-wide differentiation could offset any possible impacts of inbreeding depression.},
	language = {en},
	number = {49},
	urldate = {2025-03-30},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Khan, Anubhab and Patel, Kaushalkumar and Shukla, Harsh and Viswanathan, Ashwin and Van Der Valk, Tom and Borthakur, Udayan and Nigam, Parag and Zachariah, Arun and Jhala, Yadavendradev V. and Kardos, Marty and Ramakrishnan, Uma},
	month = dec,
	year = {2021},
	pages = {e2023018118},
}

Significance Habitat fragmentation is sequestering species into small and isolated populations, with high chances of extinction. Are small and isolated populations at risk for extinction from inbreeding depression? Or does inbreeding and purging of deleterious alleles reduce such threat? Using whole genomes from several wild Indian tiger populations, we provide evidence supporting purging of highly deleterious variants in a small–isolated population. However, our analyses also indicate that the remaining highly deleterious alleles are at high frequencies, suggesting continued inbreeding depression despite some successful purging. We discuss the implications of our results for conservation, including possible genomics-informed genetic rescue strategies. , Increasing habitat fragmentation leads to wild populations becoming small, isolated, and threatened by inbreeding depression. However, small populations may be able to purge recessive deleterious alleles as they become expressed in homozygotes, thus reducing inbreeding depression and increasing population viability. We used whole-genome sequences from 57 tigers to estimate individual inbreeding and mutation load in a small–isolated and two large–connected populations in India. As expected, the small–isolated population had substantially higher average genomic inbreeding ( F ROH = 0.57) than the large–connected ( F ROH = 0.35 and F ROH = 0.46) populations. The small–isolated population had the lowest loss-of-function mutation load, likely due to purging of highly deleterious recessive mutations. The large populations had lower missense mutation loads than the small–isolated population, but were not identical, possibly due to different demographic histories. While the number of the loss-of-function alleles in the small–isolated population was lower, these alleles were at higher frequencies and homozygosity than in the large populations. Together, our data and analyses provide evidence of 1) high mutation load, 2) purging, and 3) the highest predicted inbreeding depression, despite purging, in the small–isolated population. Frequency distributions of damaging and neutral alleles uncover genomic evidence that purifying selection has removed part of the mutation load across Indian tiger populations. These results provide genomic evidence for purifying selection in both small and large populations, but also suggest that the remaining deleterious alleles may have inbreeding-associated fitness costs. We suggest that genetic rescue from sources selected based on genome-wide differentiation could offset any possible impacts of inbreeding depression.

@article{kheraCooperativelyBreedingBanded2021,
	title = {Cooperatively breeding banded mongooses do not avoid inbreeding through familiarity-based kin recognition},
	volume = {75},
	issn = {0340-5443, 1432-0762},
	url = {https://link.springer.com/10.1007/s00265-021-03076-3},
	doi = {10.1007/s00265-021-03076-3},
	abstract = {Abstract
              
                In species that live in family groups, such as cooperative breeders, inbreeding is usually avoided through the recognition of familiar kin. For example, individuals may avoid mating with conspecifics encountered regularly in infancy, as these likely include parents, siblings, and closely related alloparents. Other mechanisms have also been reported, albeit rarely; for example, individuals may compare their own phenotype to that of others, with close matches representing likely relatives (“phenotype matching”). However, determinants of the primary inbreeding avoidance mechanisms used by a given species remain poorly understood. We use 24 years of life history and genetic data to investigate inbreeding avoidance in wild cooperatively breeding banded mongooses (
                Mungos mungo
                ). We find that inbreeding avoidance occurs within social groups but is far from maximised (mean pedigree relatedness between 351 breeding pairs = 0.144). Unusually for a group-living vertebrate, we find no evidence that females avoid breeding with males with which they are familiar in early life. This is probably explained by communal breeding; females give birth in tight synchrony and pups are cared for communally, thus reducing the reliability of familiarity-based proxies of relatedness. We also found little evidence that inbreeding is avoided by preferentially breeding with males of specific age classes. Instead, females may exploit as-yet unknown proxies of relatedness, for example, through phenotype matching, or may employ postcopulatory inbreeding avoidance mechanisms. Investigation of species with unusual breeding systems helps to identify constraints against inbreeding avoidance and contributes to our understanding of the distribution of inbreeding across species.
              
            
            
              Significance statement
              Choosing the right mate is never easy, but it may be particularly difficult for banded mongooses. In most social animals, individuals avoid mating with those that were familiar to them as infants, as these are likely to be relatives. However, we show that this rule does not work in banded mongooses. Here, the offspring of several mothers are raised in large communal litters by their social group, and parents seem unable to identify or direct care towards their own pups. This may make it difficult to recognise relatives based on their level of familiarity and is likely to explain why banded mongooses frequently inbreed. Nevertheless, inbreeding is lower than expected if mates are chosen at random, suggesting that alternative pre- or post-copulatory inbreeding avoidance mechanisms are used.},
	language = {en},
	number = {9},
	urldate = {2025-03-24},
	journal = {Behavioral Ecology and Sociobiology},
	author = {Khera, Monil and Arbuckle, Kevin and Hoffman, Joseph I. and Sanderson, Jennifer L. and Cant, Michael A. and Nichols, Hazel J.},
	month = sep,
	year = {2021},
	pages = {135},
}

Abstract In species that live in family groups, such as cooperative breeders, inbreeding is usually avoided through the recognition of familiar kin. For example, individuals may avoid mating with conspecifics encountered regularly in infancy, as these likely include parents, siblings, and closely related alloparents. Other mechanisms have also been reported, albeit rarely; for example, individuals may compare their own phenotype to that of others, with close matches representing likely relatives (“phenotype matching”). However, determinants of the primary inbreeding avoidance mechanisms used by a given species remain poorly understood. We use 24 years of life history and genetic data to investigate inbreeding avoidance in wild cooperatively breeding banded mongooses ( Mungos mungo ). We find that inbreeding avoidance occurs within social groups but is far from maximised (mean pedigree relatedness between 351 breeding pairs = 0.144). Unusually for a group-living vertebrate, we find no evidence that females avoid breeding with males with which they are familiar in early life. This is probably explained by communal breeding; females give birth in tight synchrony and pups are cared for communally, thus reducing the reliability of familiarity-based proxies of relatedness. We also found little evidence that inbreeding is avoided by preferentially breeding with males of specific age classes. Instead, females may exploit as-yet unknown proxies of relatedness, for example, through phenotype matching, or may employ postcopulatory inbreeding avoidance mechanisms. Investigation of species with unusual breeding systems helps to identify constraints against inbreeding avoidance and contributes to our understanding of the distribution of inbreeding across species. Significance statement Choosing the right mate is never easy, but it may be particularly difficult for banded mongooses. In most social animals, individuals avoid mating with those that were familiar to them as infants, as these are likely to be relatives. However, we show that this rule does not work in banded mongooses. Here, the offspring of several mothers are raised in large communal litters by their social group, and parents seem unable to identify or direct care towards their own pups. This may make it difficult to recognise relatives based on their level of familiarity and is likely to explain why banded mongooses frequently inbreed. Nevertheless, inbreeding is lower than expected if mates are chosen at random, suggesting that alternative pre- or post-copulatory inbreeding avoidance mechanisms are used.

@article{stoffelGeneticArchitectureLifetime2021,
	title = {Genetic architecture and lifetime dynamics of inbreeding depression in a wild mammal},
	volume = {12},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-021-23222-9},
	doi = {10.1038/s41467-021-23222-9},
	abstract = {Abstract
            
              Inbreeding depression is ubiquitous, but we still know little about its genetic architecture and precise effects in wild populations. Here, we combine long-term life-history data with 417 K imputed SNP genotypes for 5952 wild Soay sheep to explore inbreeding depression on a key fitness component, annual survival. Inbreeding manifests in long runs of homozygosity (ROH), which make up nearly half of the genome in the most inbred individuals. The ROH landscape varies widely across the genome, with islands where up to 87\% and deserts where only 4\% of individuals have ROH. The fitness consequences of inbreeding are severe; a 10\% increase in individual inbreeding
              F
              ROH
              is associated with a 60\% reduction in the odds of survival in lambs, though inbreeding depression decreases with age. Finally, a genome-wide association scan on ROH shows that many loci with small effects and five loci with larger effects contribute to inbreeding depression in survival.},
	language = {en},
	number = {1},
	urldate = {2025-03-19},
	journal = {Nature Communications},
	author = {Stoffel, M. A. and Johnston, S. E. and Pilkington, J. G. and Pemberton, J. M.},
	month = may,
	year = {2021},
	pages = {2972},
}

Abstract Inbreeding depression is ubiquitous, but we still know little about its genetic architecture and precise effects in wild populations. Here, we combine long-term life-history data with 417 K imputed SNP genotypes for 5952 wild Soay sheep to explore inbreeding depression on a key fitness component, annual survival. Inbreeding manifests in long runs of homozygosity (ROH), which make up nearly half of the genome in the most inbred individuals. The ROH landscape varies widely across the genome, with islands where up to 87% and deserts where only 4% of individuals have ROH. The fitness consequences of inbreeding are severe; a 10% increase in individual inbreeding F ROH is associated with a 60% reduction in the odds of survival in lambs, though inbreeding depression decreases with age. Finally, a genome-wide association scan on ROH shows that many loci with small effects and five loci with larger effects contribute to inbreeding depression in survival.

@article{doekesHowDepressingInbreeding2021,
	title = {How depressing {Is} inbreeding? {A} meta-analysis of 30 {Years} of research on the effects of inbreeding in livestock},
	volume = {12},
	copyright = {https://creativecommons.org/licenses/by/4.0/},
	issn = {2073-4425},
	shorttitle = {How {Depressing} {Is} {Inbreeding}?},
	url = {https://www.mdpi.com/2073-4425/12/6/926},
	doi = {10.3390/genes12060926},
	abstract = {Inbreeding depression has been widely documented for livestock and other animal and plant populations. Inbreeding is generally expected to have a stronger unfavorable effect on fitness traits than on other traits. Traditionally, the degree of inbreeding depression in livestock has been estimated as the slope of the linear regression of phenotypic values on pedigree-based inbreeding coefficients. With the increasing availability of SNP-data, pedigree inbreeding can now be replaced by SNP-based measures. We performed a meta-analysis of 154 studies, published from 1990 to 2020 on seven livestock species, and compared the degree of inbreeding depression (1) across different trait groups, and (2) across different pedigree-based and SNP-based measures of inbreeding. Across all studies and traits, a 1\% increase in pedigree inbreeding was associated with a median decrease in phenotypic value of 0.13\% of a trait’s mean, or 0.59\% of a trait’s standard deviation. Inbreeding had an unfavorable effect on all sorts of traits and there was no evidence for a stronger effect on primary fitness traits (e.g., reproduction/survival traits) than on other traits (e.g., production traits or morphological traits). p-values of inbreeding depression estimates were smaller for SNP-based inbreeding measures than for pedigree inbreeding, suggesting more power for SNP-based measures. There were no consistent differences in p-values for percentage of homozygous SNPs, inbreeding based on runs of homozygosity (ROH) or inbreeding based on a genomic relationship matrix. The number of studies that directly compares these different measures, however, is limited and comparisons are furthermore complicated by differences in scale and arbitrary definitions of particularly ROH-based inbreeding. To facilitate comparisons across studies in future, we provide the dataset with inbreeding depression estimates of 154 studies and stress the importance of always reporting detailed information (on traits, inbreeding coefficients, and models used) along with inbreeding depression estimates.},
	language = {en},
	number = {6},
	urldate = {2025-03-19},
	journal = {Genes},
	author = {Doekes, Harmen P. and Bijma, Piter and Windig, Jack J.},
	month = jun,
	year = {2021},
	pages = {926},
}

Inbreeding depression has been widely documented for livestock and other animal and plant populations. Inbreeding is generally expected to have a stronger unfavorable effect on fitness traits than on other traits. Traditionally, the degree of inbreeding depression in livestock has been estimated as the slope of the linear regression of phenotypic values on pedigree-based inbreeding coefficients. With the increasing availability of SNP-data, pedigree inbreeding can now be replaced by SNP-based measures. We performed a meta-analysis of 154 studies, published from 1990 to 2020 on seven livestock species, and compared the degree of inbreeding depression (1) across different trait groups, and (2) across different pedigree-based and SNP-based measures of inbreeding. Across all studies and traits, a 1% increase in pedigree inbreeding was associated with a median decrease in phenotypic value of 0.13% of a trait’s mean, or 0.59% of a trait’s standard deviation. Inbreeding had an unfavorable effect on all sorts of traits and there was no evidence for a stronger effect on primary fitness traits (e.g., reproduction/survival traits) than on other traits (e.g., production traits or morphological traits). p-values of inbreeding depression estimates were smaller for SNP-based inbreeding measures than for pedigree inbreeding, suggesting more power for SNP-based measures. There were no consistent differences in p-values for percentage of homozygous SNPs, inbreeding based on runs of homozygosity (ROH) or inbreeding based on a genomic relationship matrix. The number of studies that directly compares these different measures, however, is limited and comparisons are furthermore complicated by differences in scale and arbitrary definitions of particularly ROH-based inbreeding. To facilitate comparisons across studies in future, we provide the dataset with inbreeding depression estimates of 154 studies and stress the importance of always reporting detailed information (on traits, inbreeding coefficients, and models used) along with inbreeding depression estimates.

@article{deboerMetaanalyticEvidenceThat2021,
	title = {Meta-analytic evidence that animals rarely avoid inbreeding},
	volume = {5},
	issn = {2397-334X},
	url = {https://www.nature.com/articles/s41559-021-01453-9},
	doi = {10.1038/s41559-021-01453-9},
	language = {en},
	number = {7},
	urldate = {2025-03-19},
	journal = {Nature Ecology \& Evolution},
	author = {De Boer, Raïssa A. and Vega-Trejo, Regina and Kotrschal, Alexander and Fitzpatrick, John L.},
	month = may,
	year = {2021},
	pages = {949--964},
}

@article{evansFamilyDynamicsReveal2021,
	title = {Family dynamics reveal that female house mice preferentially breed in their maternal community},
	doi = {10.1093/beheco/arab128},
	language = {en},
	journal = {Behavioral Ecology},
	author = {Evans, Julian C and Lindholm, Anna K and König, Barbara},
	year = {2021},
	pages = {11},
}

@article{evansLongtermOverlapSocial2021,
	title = {Long-term overlap of social and genetic structure in free-ranging house mice reveals dynamic seasonal and group size effects},
	volume = {67},
	issn = {2396-9814},
	url = {https://academic.oup.com/cz/article/67/1/59/5859526},
	doi = {10.1093/cz/zoaa030},
	abstract = {Associating with relatives in social groups can bring benefits such as reduced risk of aggression and increased likelihood of cooperation. Competition among relatives over limited resources, on the other hand, can induce individuals to alter their patterns of association. Population density might further affect the costs and benefits of associating with relatives by altering resource competition or by changing the structure of social groups; preventing easy association with relatives. Consequently, the overlap between genetic and social structure is expected to decrease with increasing population size, as well as during times of increased breeding activity. Here, we use multi-layer network techniques to quantify the similarity between long-term, high resolution genetic, and behavioral data from a large population of free-ranging house mice (Mus musculus domesticus), studied over 10 years. We infer how the benefit of associating with genetically similar individuals might fluctuate in relation to breeding behavior and environmental conditions. We found a clear seasonal effect, with decreased overlap between social and genetic structure during summer months, characterized by high temperatures and high breeding activity. Though the effect of overall population size was relatively weak, we found a clear decrease in the overlap between genetic similarity and social associations within larger groups. As well as longer-term within-group changes, these results reveal population-wide short-term shifts in how individuals associate with relatives. Our study suggests that resource competition modifies the trade-off between the costs and benefits of interacting with relatives.},
	language = {en},
	number = {1},
	urldate = {2022-09-06},
	journal = {Current Zoology},
	author = {Evans, Julian C and Lindholm, Anna K and König, Barbara},
	editor = {Fisher, David},
	month = feb,
	year = {2021},
	pages = {59--69},
}

Associating with relatives in social groups can bring benefits such as reduced risk of aggression and increased likelihood of cooperation. Competition among relatives over limited resources, on the other hand, can induce individuals to alter their patterns of association. Population density might further affect the costs and benefits of associating with relatives by altering resource competition or by changing the structure of social groups; preventing easy association with relatives. Consequently, the overlap between genetic and social structure is expected to decrease with increasing population size, as well as during times of increased breeding activity. Here, we use multi-layer network techniques to quantify the similarity between long-term, high resolution genetic, and behavioral data from a large population of free-ranging house mice (Mus musculus domesticus), studied over 10 years. We infer how the benefit of associating with genetically similar individuals might fluctuate in relation to breeding behavior and environmental conditions. We found a clear seasonal effect, with decreased overlap between social and genetic structure during summer months, characterized by high temperatures and high breeding activity. Though the effect of overall population size was relatively weak, we found a clear decrease in the overlap between genetic similarity and social associations within larger groups. As well as longer-term within-group changes, these results reveal population-wide short-term shifts in how individuals associate with relatives. Our study suggests that resource competition modifies the trade-off between the costs and benefits of interacting with relatives.

@incollection{bovetCentralitiesComplexNetworks2021,
	address = {Berlin, Heidelberg},
	title = {Centralities in {Complex} {Networks}},
	copyright = {All rights reserved},
	isbn = {978-3-642-27737-5},
	url = {https://doi.org/10.1007/978-3-642-27737-5_765-1},
	doi = {10.1007/978-3-642-27737-5_765-1},
	abstract = {In network science complex systems are represented as a mathematical graphs consisting of a set of nodes representing the components and a set of edges representing their interactions. The framework of networks has led to significant advances in the understanding of the structure, formation and function of complex systems. Social and biological processes such as the dynamics of epidemics, the diffusion of information in social media, the interactions between species in ecosystems or the communication between neurons in our brains are all actively studied using dynamical models on complex networks. In all of these systems, the patterns of connections at the individual level play a fundamental role on the global dynamics and finding the most important nodes allows one to better understand and predict their behaviors. An important research effort in network science has therefore been dedicated to the development of methods allowing to find the most important nodes in networks. In this short entry, we describe network centrality measures based on the notions of network traversal they rely on. This entry aims at being an introduction to this extremely vast topic, with many contributions from several fields, and is by no means an exhaustive review of all the literature about network centralities.},
	booktitle = {Encyclopedia of {Complexity} and {Systems} {Science}},
	publisher = {Springer Berlin Heidelberg},
	author = {Bovet, Alexandre and Makse, Hernán A.},
	editor = {Meyers, Robert A},
	year = {2021},
	pages = {1--11},
}

In network science complex systems are represented as a mathematical graphs consisting of a set of nodes representing the components and a set of edges representing their interactions. The framework of networks has led to significant advances in the understanding of the structure, formation and function of complex systems. Social and biological processes such as the dynamics of epidemics, the diffusion of information in social media, the interactions between species in ecosystems or the communication between neurons in our brains are all actively studied using dynamical models on complex networks. In all of these systems, the patterns of connections at the individual level play a fundamental role on the global dynamics and finding the most important nodes allows one to better understand and predict their behaviors. An important research effort in network science has therefore been dedicated to the development of methods allowing to find the most important nodes in networks. In this short entry, we describe network centrality measures based on the notions of network traversal they rely on. This entry aims at being an introduction to this extremely vast topic, with many contributions from several fields, and is by no means an exhaustive review of all the literature about network centralities.

@article{tudiscoNodeEdgeNonlinear2021,
	title = {Node and edge nonlinear eigenvector centrality for hypergraphs},
	volume = {4},
	issn = {2399-3650},
	url = {https://www.nature.com/articles/s42005-021-00704-2},
	doi = {10.1038/s42005-021-00704-2},
	abstract = {Abstract Network scientists have shown that there is great value in studying pairwise interactions between components in a system. From a linear algebra point of view, this involves defining and evaluating functions of the associated adjacency matrix. Recent work indicates that there are further benefits from accounting directly for higher order interactions, notably through a hypergraph representation where an edge may involve multiple nodes. Building on these ideas, we motivate, define and analyze a class of spectral centrality measures for identifying important nodes and hyperedges in hypergraphs, generalizing existing network science concepts. By exploiting the latest developments in nonlinear Perron−Frobenius theory, we show how the resulting constrained nonlinear eigenvalue problems have unique solutions that can be computed efficiently via a nonlinear power method iteration. We illustrate the measures on realistic data sets.},
	language = {en},
	number = {1},
	urldate = {2022-07-27},
	journal = {Communications Physics},
	author = {Tudisco, Francesco and Higham, Desmond J.},
	month = dec,
	year = {2021},
	pages = {201},
}

Abstract Network scientists have shown that there is great value in studying pairwise interactions between components in a system. From a linear algebra point of view, this involves defining and evaluating functions of the associated adjacency matrix. Recent work indicates that there are further benefits from accounting directly for higher order interactions, notably through a hypergraph representation where an edge may involve multiple nodes. Building on these ideas, we motivate, define and analyze a class of spectral centrality measures for identifying important nodes and hyperedges in hypergraphs, generalizing existing network science concepts. By exploiting the latest developments in nonlinear Perron−Frobenius theory, we show how the resulting constrained nonlinear eigenvalue problems have unique solutions that can be computed efficiently via a nonlinear power method iteration. We illustrate the measures on realistic data sets.

@article{battistonPhysicsHigherorderInteractions2021,
	title = {The physics of higher-order interactions in complex systems},
	volume = {17},
	issn = {1745-2473, 1745-2481},
	url = {https://www.nature.com/articles/s41567-021-01371-4},
	doi = {10.1038/s41567-021-01371-4},
	language = {en},
	number = {10},
	urldate = {2025-02-23},
	journal = {Nature Physics},
	author = {Battiston, Federico and Amico, Enrico and Barrat, Alain and Bianconi, Ginestra and Ferraz De Arruda, Guilherme and Franceschiello, Benedetta and Iacopini, Iacopo and Kéfi, Sonia and Latora, Vito and Moreno, Yamir and Murray, Micah M. and Peixoto, Tiago P. and Vaccarino, Francesco and Petri, Giovanni},
	month = oct,
	year = {2021},
	pages = {1093--1098},
}

@article{grossenPurgingHighlyDeleterious2020,
	title = {Purging of highly deleterious mutations through severe bottlenecks in {Alpine} ibex},
	volume = {11},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-020-14803-1},
	doi = {10.1038/s41467-020-14803-1},
	abstract = {Abstract
            Human activity has caused dramatic population declines in many wild species. The resulting bottlenecks have a profound impact on the genetic makeup of a species with unknown consequences for health. A key genetic factor for species survival is the evolution of deleterious mutation load, but how bottleneck strength and mutation load interact lacks empirical evidence. We analyze 60 complete genomes of six ibex species and the domestic goat. We show that historic bottlenecks rather than the current conservation status predict levels of genome-wide variation. By analyzing the exceptionally well-characterized population bottlenecks of the once nearly extinct Alpine ibex, we find genomic evidence of concurrent purging of highly deleterious mutations but accumulation of mildly deleterious mutations. This suggests that recolonization bottlenecks induced both relaxed selection and purging, thus reshaping the landscape of deleterious mutation load. Our findings highlight that even populations of {\textasciitilde}1000 individuals can accumulate mildly deleterious mutations. Conservation efforts should focus on preventing population declines below such levels to ensure long-term survival of species.},
	language = {en},
	number = {1},
	urldate = {2025-03-30},
	journal = {Nature Communications},
	author = {Grossen, Christine and Guillaume, Frédéric and Keller, Lukas F. and Croll, Daniel},
	month = feb,
	year = {2020},
	pages = {1001},
}

Abstract Human activity has caused dramatic population declines in many wild species. The resulting bottlenecks have a profound impact on the genetic makeup of a species with unknown consequences for health. A key genetic factor for species survival is the evolution of deleterious mutation load, but how bottleneck strength and mutation load interact lacks empirical evidence. We analyze 60 complete genomes of six ibex species and the domestic goat. We show that historic bottlenecks rather than the current conservation status predict levels of genome-wide variation. By analyzing the exceptionally well-characterized population bottlenecks of the once nearly extinct Alpine ibex, we find genomic evidence of concurrent purging of highly deleterious mutations but accumulation of mildly deleterious mutations. This suggests that recolonization bottlenecks induced both relaxed selection and purging, thus reshaping the landscape of deleterious mutation load. Our findings highlight that even populations of ~1000 individuals can accumulate mildly deleterious mutations. Conservation efforts should focus on preventing population declines below such levels to ensure long-term survival of species.

@article{wellsInbreedingDepressesAltruism2020a,
	title = {Inbreeding depresses altruism in a cooperative society},
	volume = {23},
	issn = {1461-023X, 1461-0248},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/ele.13578},
	doi = {10.1111/ele.13578},
	abstract = {In some animal species, individuals regularly breed with relatives, including siblings and parents. Given the high fitness costs of inbreeding, evolutionary biologists have found it challenging to understand the persistence of these inbred societies in nature. One appealing but untested explanation is that early life care may create a benign environment that offsets inbreeding depression, allowing inbred societies to evolve. We test this possibility using 21 years of data from a wild cooperatively breeding mammal, the banded mongoose, a species where almost one in ten young result from close inbreeding. We show that care provided by parents and alloparents mitigates inbreeding depression for early survival. However, as adults, inbred individuals provide less care, reducing the amount of help available to the next generation. Our results suggest that inbred cooperative societies are rare in nature partly because the protective care that enables elevated levels of inbreeding can be reduced by inbreeding depression.},
	language = {en},
	number = {10},
	urldate = {2025-03-26},
	journal = {Ecology Letters},
	author = {Wells, David A. and Cant, Michael A. and Hoffman, Joseph I. and Nichols, Hazel J.},
	editor = {Van Baalen, Minus},
	month = oct,
	year = {2020},
	pages = {1460--1467},
}

In some animal species, individuals regularly breed with relatives, including siblings and parents. Given the high fitness costs of inbreeding, evolutionary biologists have found it challenging to understand the persistence of these inbred societies in nature. One appealing but untested explanation is that early life care may create a benign environment that offsets inbreeding depression, allowing inbred societies to evolve. We test this possibility using 21 years of data from a wild cooperatively breeding mammal, the banded mongoose, a species where almost one in ten young result from close inbreeding. We show that care provided by parents and alloparents mitigates inbreeding depression for early survival. However, as adults, inbred individuals provide less care, reducing the amount of help available to the next generation. Our results suggest that inbred cooperative societies are rare in nature partly because the protective care that enables elevated levels of inbreeding can be reduced by inbreeding depression.

@article{wellsInbreedingDepressesAltruism2020,
	title = {Inbreeding depresses altruism in a cooperative society},
	volume = {23},
	issn = {1461-023X, 1461-0248},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/ele.13578},
	doi = {10.1111/ele.13578},
	abstract = {Abstract
            In some animal species, individuals regularly breed with relatives, including siblings and parents. Given the high fitness costs of inbreeding, evolutionary biologists have found it challenging to understand the persistence of these inbred societies in nature. One appealing but untested explanation is that early life care may create a benign environment that offsets inbreeding depression, allowing inbred societies to evolve. We test this possibility using 21 years of data from a wild cooperatively breeding mammal, the banded mongoose, a species where almost one in ten young result from close inbreeding. We show that care provided by parents and alloparents mitigates inbreeding depression for early survival. However, as adults, inbred individuals provide less care, reducing the amount of help available to the next generation. Our results suggest that inbred cooperative societies are rare in nature partly because the protective care that enables elevated levels of inbreeding can be reduced by inbreeding depression.},
	language = {en},
	number = {10},
	urldate = {2025-03-24},
	journal = {Ecology Letters},
	author = {Wells, David A. and Cant, Michael A. and Hoffman, Joseph I. and Nichols, Hazel J.},
	editor = {Van Baalen, Minus},
	month = oct,
	year = {2020},
	pages = {1460--1467},
}

Abstract In some animal species, individuals regularly breed with relatives, including siblings and parents. Given the high fitness costs of inbreeding, evolutionary biologists have found it challenging to understand the persistence of these inbred societies in nature. One appealing but untested explanation is that early life care may create a benign environment that offsets inbreeding depression, allowing inbred societies to evolve. We test this possibility using 21 years of data from a wild cooperatively breeding mammal, the banded mongoose, a species where almost one in ten young result from close inbreeding. We show that care provided by parents and alloparents mitigates inbreeding depression for early survival. However, as adults, inbred individuals provide less care, reducing the amount of help available to the next generation. Our results suggest that inbred cooperative societies are rare in nature partly because the protective care that enables elevated levels of inbreeding can be reduced by inbreeding depression.

@article{manserPolyandryBlocksGene2020,
	title = {Polyandry blocks gene drive in a wild house mouse population},
	volume = {11},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-020-18967-8},
	doi = {10.1038/s41467-020-18967-8},
	abstract = {Abstract
            
              Gene drives are genetic elements that manipulate Mendelian inheritance ratios in their favour. Understanding the forces that explain drive frequency in natural populations is a long-standing focus of evolutionary research. Recently, the possibility to create artificial drive constructs to modify pest populations has exacerbated our need to understand how drive spreads in natural populations. Here, we study the impact of polyandry on a well-known gene drive, called
              t
              haplotype, in an intensively monitored population of wild house mice. First, we show that house mice are highly polyandrous: 47\% of 682 litters were sired by more than one male. Second, we find that drive-carrying males are particularly compromised in sperm competition, resulting in reduced reproductive success. As a result, drive frequency decreased during the 4.5 year observation period. Overall, we provide the first direct evidence that the spread of a gene drive is hampered by reproductive behaviour in a natural population.},
	language = {en},
	number = {1},
	urldate = {2025-03-22},
	journal = {Nature Communications},
	author = {Manser, Andri and König, Barbara and Lindholm, Anna K.},
	month = nov,
	year = {2020},
	pages = {5590},
}

Abstract Gene drives are genetic elements that manipulate Mendelian inheritance ratios in their favour. Understanding the forces that explain drive frequency in natural populations is a long-standing focus of evolutionary research. Recently, the possibility to create artificial drive constructs to modify pest populations has exacerbated our need to understand how drive spreads in natural populations. Here, we study the impact of polyandry on a well-known gene drive, called t haplotype, in an intensively monitored population of wild house mice. First, we show that house mice are highly polyandrous: 47% of 682 litters were sired by more than one male. Second, we find that drive-carrying males are particularly compromised in sperm competition, resulting in reduced reproductive success. As a result, drive frequency decreased during the 4.5 year observation period. Overall, we provide the first direct evidence that the spread of a gene drive is hampered by reproductive behaviour in a natural population.

@article{carlettiRandomWalksHypergraphs2020,
	title = {Random walks on hypergraphs},
	volume = {101},
	issn = {2470-0045, 2470-0053},
	url = {https://link.aps.org/doi/10.1103/PhysRevE.101.022308},
	doi = {10.1103/PhysRevE.101.022308},
	language = {en},
	number = {2},
	urldate = {2025-02-07},
	journal = {Physical Review E},
	author = {Carletti, Timoteo and Battiston, Federico and Cencetti, Giulia and Fanelli, Duccio},
	month = feb,
	year = {2020},
	pages = {022308},
}

@article{battistonNetworksPairwiseInteractions2020,
	title = {Networks beyond pairwise interactions: {Structure} and dynamics},
	volume = {874},
	issn = {03701573},
	shorttitle = {Networks beyond pairwise interactions},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0370157320302489},
	doi = {10.1016/j.physrep.2020.05.004},
	abstract = {The complexity of many biological, social and technological systems stems from the richness of the interactions among their units. Over the past decades, a variety of complex systems has been successfully described as networks whose interacting pairs of nodes are connected by links. Yet, from human communications to chemical reactions and ecological systems, interactions can often occur in groups of three or more nodes and cannot be described simply in terms of dyads. Until recently little attention has been devoted to the higher-order architecture of real complex systems. However, a mounting body of evidence is showing that taking the higher-order structure of these systems into account can enhance our modeling capacities and help us understand and predict their dynamical behavior. Here we present a complete overview of the emerging field of networks beyond pairwise interactions. We discuss how to represent higherorder interactions and introduce the different frameworks used to describe higher-order systems, highlighting the links between the existing concepts and representations. We review the measures designed to characterize the structure of these systems and the models proposed to generate synthetic structures, such as random and growing bipartite graphs, hypergraphs and simplicial complexes. We introduce the rapidly growing research on higher-order dynamical systems and dynamical topology, discussing the relations between higher-order interactions and collective behavior. We focus in particular on new emergent phenomena characterizing dynamical processes, such as diffusion, synchronization, spreading, social dynamics and games, when extended beyond pairwise interactions. We conclude with a summary of empirical applications, and an outlook on current modeling and conceptual frontiers.},
	language = {en},
	urldate = {2022-12-17},
	journal = {Physics Reports},
	author = {Battiston, Federico and Cencetti, Giulia and Iacopini, Iacopo and Latora, Vito and Lucas, Maxime and Patania, Alice and Young, Jean-Gabriel and Petri, Giovanni},
	month = aug,
	year = {2020},
	pages = {1--92},
}

The complexity of many biological, social and technological systems stems from the richness of the interactions among their units. Over the past decades, a variety of complex systems has been successfully described as networks whose interacting pairs of nodes are connected by links. Yet, from human communications to chemical reactions and ecological systems, interactions can often occur in groups of three or more nodes and cannot be described simply in terms of dyads. Until recently little attention has been devoted to the higher-order architecture of real complex systems. However, a mounting body of evidence is showing that taking the higher-order structure of these systems into account can enhance our modeling capacities and help us understand and predict their dynamical behavior. Here we present a complete overview of the emerging field of networks beyond pairwise interactions. We discuss how to represent higherorder interactions and introduce the different frameworks used to describe higher-order systems, highlighting the links between the existing concepts and representations. We review the measures designed to characterize the structure of these systems and the models proposed to generate synthetic structures, such as random and growing bipartite graphs, hypergraphs and simplicial complexes. We introduce the rapidly growing research on higher-order dynamical systems and dynamical topology, discussing the relations between higher-order interactions and collective behavior. We focus in particular on new emergent phenomena characterizing dynamical processes, such as diffusion, synchronization, spreading, social dynamics and games, when extended beyond pairwise interactions. We conclude with a summary of empirical applications, and an outlook on current modeling and conceptual frontiers.

@article{ferrariFitnessConsequencesFemale2019,
	title = {Fitness consequences of female alternative reproductive tactics in house mice ( \textit{{Mus} musculus domesticus} )},
	volume = {193},
	issn = {0003-0147, 1537-5323},
	url = {https://www.journals.uchicago.edu/doi/10.1086/700567},
	doi = {10.1086/700567},
	language = {en},
	number = {1},
	urldate = {2025-03-30},
	journal = {The American Naturalist},
	author = {Ferrari, Manuela and Lindholm, Anna K. and König, Barbara},
	month = jan,
	year = {2019},
	pages = {106--124},
}

@article{dawesGeneDiscoveryInformatics2019,
	title = {Gene discovery informatics toolkit defines candidate genes for unexplained infertility and prenatal or infantile mortality},
	volume = {4},
	issn = {2056-7944},
	url = {https://www.nature.com/articles/s41525-019-0081-z},
	doi = {10.1038/s41525-019-0081-z},
	abstract = {Abstract
            Despite a recent surge in novel gene discovery, genetic causes of prenatal-lethal phenotypes remain poorly defined. To advance gene discovery in prenatal-lethal disorders, we created an easy-to-mine database integrating known human phenotypes with inheritance pattern, scores of genetic constraint, and murine and cellular knockout phenotypes—then critically assessed defining features of known prenatal-lethal genes, among 3187 OMIM genes, and relative to 16,009 non-disease genes. While around one-third (39\%) of protein-coding genes are essential for murine development, we curate only 3\% (624) of human protein-coding genes linked currently to prenatal/infantile lethal disorders. 75\% prenatal-lethal genes are linked to developmental lethality in knockout mice, compared to 54\% for all OMIM genes and 34\% among non-disease genes. Genetic constraint correlates with inheritance pattern (autosomal recessive {\textless}{\textless}autosomal dominant {\textless}X-linked), and is greatest among prenatal-lethal genes. Importantly, {\textgreater}90\% of recessive genes show neither missense nor loss-of-function constraint, even for prenatal-lethal genes. Detailed ontology mapping for 624 prenatal-lethal genes shows marked enrichment among dominant genes for nuclear proteins with roles in RNA/DNA biology, with recessive genes enriched in cytoplasmic (mitochondrial) metabolic proteins. We conclude that genes without genetic constraint should not be excluded as potential novel disease genes, and especially for recessive conditions ({\textless}10\% constrained). Prenatal lethal genes are 5.9-fold more likely to be associated with a lethal murine phenotype than non-disease genes. Cell essential genes are largely a subset of mouse-lethal genes, notably under-represented among known OMIM genes, and strong candidates for gamete/embryo non-viability. We therefore curate 3435 ‘candidate developmental lethal’ human genes: essential for murine development or cellular viability, not yet linked to human disorders, presenting strong candidates for unexplained infertility and prenatal/infantile mortality.},
	language = {en},
	number = {1},
	urldate = {2025-03-30},
	journal = {npj Genomic Medicine},
	author = {Dawes, Ruebena and Lek, Monkol and Cooper, Sandra T.},
	month = apr,
	year = {2019},
	pages = {8},
}

Abstract Despite a recent surge in novel gene discovery, genetic causes of prenatal-lethal phenotypes remain poorly defined. To advance gene discovery in prenatal-lethal disorders, we created an easy-to-mine database integrating known human phenotypes with inheritance pattern, scores of genetic constraint, and murine and cellular knockout phenotypes—then critically assessed defining features of known prenatal-lethal genes, among 3187 OMIM genes, and relative to 16,009 non-disease genes. While around one-third (39%) of protein-coding genes are essential for murine development, we curate only 3% (624) of human protein-coding genes linked currently to prenatal/infantile lethal disorders. 75% prenatal-lethal genes are linked to developmental lethality in knockout mice, compared to 54% for all OMIM genes and 34% among non-disease genes. Genetic constraint correlates with inheritance pattern (autosomal recessive \textless\textlessautosomal dominant \textlessX-linked), and is greatest among prenatal-lethal genes. Importantly, \textgreater90% of recessive genes show neither missense nor loss-of-function constraint, even for prenatal-lethal genes. Detailed ontology mapping for 624 prenatal-lethal genes shows marked enrichment among dominant genes for nuclear proteins with roles in RNA/DNA biology, with recessive genes enriched in cytoplasmic (mitochondrial) metabolic proteins. We conclude that genes without genetic constraint should not be excluded as potential novel disease genes, and especially for recessive conditions (\textless10% constrained). Prenatal lethal genes are 5.9-fold more likely to be associated with a lethal murine phenotype than non-disease genes. Cell essential genes are largely a subset of mouse-lethal genes, notably under-represented among known OMIM genes, and strong candidates for gamete/embryo non-viability. We therefore curate 3435 ‘candidate developmental lethal’ human genes: essential for murine development or cellular viability, not yet linked to human disorders, presenting strong candidates for unexplained infertility and prenatal/infantile mortality.

@article{chenAlleleFrequencyDynamics2019,
	title = {Allele frequency dynamics in a pedigreed natural population},
	volume = {116},
	url = {https://www.pnas.org/doi/10.1073/pnas.1813852116},
	doi = {10.1073/pnas.1813852116},
	abstract = {A central goal of population genetics is to understand how genetic drift, natural selection, and gene flow shape allele frequencies through time. However, the actual processes underlying these changes—variation in individual survival, reproductive success, and movement—are often difficult to quantify. Fully understanding these processes requires the population pedigree, the set of relationships among all individuals in the population through time. Here, we use extensive pedigree and genomic information from a long-studied natural population of Florida Scrub-Jays (Aphelocoma coerulescens) to directly characterize the relative roles of different evolutionary processes in shaping patterns of genetic variation through time. We performed gene dropping simulations to estimate individual genetic contributions to the population and model drift on the known pedigree. We found that observed allele frequency changes are generally well predicted by accounting for the different genetic contributions of founders. Our results show that the genetic contribution of recent immigrants is substantial, with some large allele frequency shifts that otherwise may have been attributed to selection actually due to gene flow. We identified a few SNPs under directional short-term selection after appropriately accounting for gene flow. Using models that account for changes in population size, we partitioned the proportion of variance in allele frequency change through time. Observed allele frequency changes are primarily due to variation in survival and reproductive success, with gene flow making a smaller contribution. This study provides one of the most complete descriptions of short-term evolutionary change in allele frequencies in a natural population to date.},
	number = {6},
	urldate = {2025-03-26},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {Proceedings of the National Academy of Sciences},
	author = {Chen, Nancy and Juric, Ivan and Cosgrove, Elissa J. and Bowman, Reed and Fitzpatrick, John W. and Schoech, Stephan J. and Clark, Andrew G. and Coop, Graham},
	month = feb,
	year = {2019},
	pages = {2158--2164},
}

A central goal of population genetics is to understand how genetic drift, natural selection, and gene flow shape allele frequencies through time. However, the actual processes underlying these changes—variation in individual survival, reproductive success, and movement—are often difficult to quantify. Fully understanding these processes requires the population pedigree, the set of relationships among all individuals in the population through time. Here, we use extensive pedigree and genomic information from a long-studied natural population of Florida Scrub-Jays (Aphelocoma coerulescens) to directly characterize the relative roles of different evolutionary processes in shaping patterns of genetic variation through time. We performed gene dropping simulations to estimate individual genetic contributions to the population and model drift on the known pedigree. We found that observed allele frequency changes are generally well predicted by accounting for the different genetic contributions of founders. Our results show that the genetic contribution of recent immigrants is substantial, with some large allele frequency shifts that otherwise may have been attributed to selection actually due to gene flow. We identified a few SNPs under directional short-term selection after appropriately accounting for gene flow. Using models that account for changes in population size, we partitioned the proportion of variance in allele frequency change through time. Observed allele frequency changes are primarily due to variation in survival and reproductive success, with gene flow making a smaller contribution. This study provides one of the most complete descriptions of short-term evolutionary change in allele frequencies in a natural population to date.

@article{townsendApparentInbreedingPreference2019,
	title = {Apparent inbreeding preference despite inbreeding depression in the {American} crow},
	volume = {28},
	issn = {0962-1083, 1365-294X},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/mec.14866},
	doi = {10.1111/mec.14866},
	abstract = {Abstract
            
              Although matings between relatives can have negative effects on offspring fitness, apparent inbreeding preference has been reported in a growing number of systems, including those with documented inbreeding depression. Here, we examined evidence for inbreeding depression and inbreeding preference in two populations (Clinton, New York, and Davis, California,
              USA
              ) of the cooperatively breeding American crow (
              Corvus brachyrhynchos
              ). We then compared observed inbreeding strategies with theoretical expectations for optimal, adaptive levels of inbreeding, given the inclusive fitness benefits and population‐specific magnitude of inbreeding depression. We found that low heterozygosity at a panel of 33 microsatellite markers was associated with low survival probability (fledging success) and low white blood cell counts among offspring in both populations. Despite these costs, our data were more consistent with inbreeding preference than avoidance: The observed heterozygosity among 396 sampled crow offspring was significantly lower than expected if local adults were mating by random chance. This pattern was consistent across a range of spatial scales in both populations. Adaptive levels of inbreeding, given the magnitude of inbreeding depression, were predicted to be very low in the California population, whereas complete disassortative mating was predicted in the New York population. Sexual conflict might have contributed to the apparent absence of inbreeding avoidance in crows. These data add to an increasing number of examples of an “inbreeding paradox,” where inbreeding appears to be preferred despite inbreeding depression.},
	language = {en},
	number = {5},
	urldate = {2025-03-24},
	journal = {Molecular Ecology},
	author = {Townsend, Andrea K. and Taff, Conor C. and Jones, Melissa L. and Getman, Katherine H. and Wheeler, Sarah S. and Hinton, Mitch G. and Logsdon, Ryane M.},
	month = mar,
	year = {2019},
	pages = {1116--1126},
}

Abstract Although matings between relatives can have negative effects on offspring fitness, apparent inbreeding preference has been reported in a growing number of systems, including those with documented inbreeding depression. Here, we examined evidence for inbreeding depression and inbreeding preference in two populations (Clinton, New York, and Davis, California, USA ) of the cooperatively breeding American crow ( Corvus brachyrhynchos ). We then compared observed inbreeding strategies with theoretical expectations for optimal, adaptive levels of inbreeding, given the inclusive fitness benefits and population‐specific magnitude of inbreeding depression. We found that low heterozygosity at a panel of 33 microsatellite markers was associated with low survival probability (fledging success) and low white blood cell counts among offspring in both populations. Despite these costs, our data were more consistent with inbreeding preference than avoidance: The observed heterozygosity among 396 sampled crow offspring was significantly lower than expected if local adults were mating by random chance. This pattern was consistent across a range of spatial scales in both populations. Adaptive levels of inbreeding, given the magnitude of inbreeding depression, were predicted to be very low in the California population, whereas complete disassortative mating was predicted in the New York population. Sexual conflict might have contributed to the apparent absence of inbreeding avoidance in crows. These data add to an increasing number of examples of an “inbreeding paradox,” where inbreeding appears to be preferred despite inbreeding depression.

@article{nietlisbachNonequivalentLethalEquivalents2019,
	title = {Nonequivalent lethal equivalents: {Models} and inbreeding metrics for unbiased estimation of inbreeding load},
	volume = {12},
	issn = {1752-4571, 1752-4571},
	shorttitle = {Nonequivalent lethal equivalents},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/eva.12713},
	doi = {10.1111/eva.12713},
	abstract = {Abstract 
            Inbreeding depression, the deterioration in mean trait value in progeny of related parents, is a fundamental quantity in genetics, evolutionary biology, animal and plant breeding, and conservation biology. The magnitude of inbreeding depression can be quantified by the inbreeding load, typically measured in numbers of lethal equivalents, a population genetic quantity that allows for comparisons between environments, populations or species. However, there is as yet no quantitative assessment of which combinations of statistical models and metrics of inbreeding can yield such estimates. Here, we review statistical models that have been used to estimate inbreeding load and use population genetic simulations to investigate how unbiased estimates can be obtained using genomic and pedigree‐based metrics of inbreeding. We use simulated binary viability data (i.e., dead versus alive) as our example, but the concepts apply to any trait that exhibits inbreeding depression. We show that the increasingly popular generalized linear models with logit link do not provide comparable and unbiased population genetic measures of inbreeding load, independent of the metric of inbreeding used. Runs of homozygosity result in unbiased estimates of inbreeding load, whereas inbreeding measured from pedigrees results in slight overestimates. Due to widespread use of models that do not yield unbiased measures of the inbreeding load, some estimates in the literature cannot be compared meaningfully. We surveyed the literature for reliable estimates of the mean inbreeding load from wild vertebrate populations and found an average of 3.5 haploid lethal equivalents for survival to sexual maturity. To obtain comparable estimates, we encourage researchers to use generalized linear models with logarithmic links or maximum‐likelihood estimation of the exponential equation, and inbreeding coefficients calculated from runs of homozygosity, provided an assembled reference genome of sufficient quality and enough genetic marker data are available.},
	language = {en},
	number = {2},
	urldate = {2025-03-19},
	journal = {Evolutionary Applications},
	author = {Nietlisbach, Pirmin and Muff, Stefanie and Reid, Jane M. and Whitlock, Michael C. and Keller, Lukas F.},
	month = feb,
	year = {2019},
	pages = {266--279},
}

Abstract Inbreeding depression, the deterioration in mean trait value in progeny of related parents, is a fundamental quantity in genetics, evolutionary biology, animal and plant breeding, and conservation biology. The magnitude of inbreeding depression can be quantified by the inbreeding load, typically measured in numbers of lethal equivalents, a population genetic quantity that allows for comparisons between environments, populations or species. However, there is as yet no quantitative assessment of which combinations of statistical models and metrics of inbreeding can yield such estimates. Here, we review statistical models that have been used to estimate inbreeding load and use population genetic simulations to investigate how unbiased estimates can be obtained using genomic and pedigree‐based metrics of inbreeding. We use simulated binary viability data (i.e., dead versus alive) as our example, but the concepts apply to any trait that exhibits inbreeding depression. We show that the increasingly popular generalized linear models with logit link do not provide comparable and unbiased population genetic measures of inbreeding load, independent of the metric of inbreeding used. Runs of homozygosity result in unbiased estimates of inbreeding load, whereas inbreeding measured from pedigrees results in slight overestimates. Due to widespread use of models that do not yield unbiased measures of the inbreeding load, some estimates in the literature cannot be compared meaningfully. We surveyed the literature for reliable estimates of the mean inbreeding load from wild vertebrate populations and found an average of 3.5 haploid lethal equivalents for survival to sexual maturity. To obtain comparable estimates, we encourage researchers to use generalized linear models with logarithmic links or maximum‐likelihood estimation of the exponential equation, and inbreeding coefficients calculated from runs of homozygosity, provided an assembled reference genome of sufficient quality and enough genetic marker data are available.

@article{bensonThreeHypergraphEigenvector2019,
	title = {Three hypergraph eigenvector centralities},
	volume = {1},
	number = {2},
	journal = {SIAM Journal on Mathematics of Data Science},
	publisher = {SIAM},
	author = {Benson, Austin R},
	year = {2019},
	pages = {293--312},
}

@article{leeReviewStochasticBlock2019,
	title = {A review of stochastic block models and extensions for graph clustering},
	volume = {4},
	issn = {2364-8228},
	url = {https://appliednetsci.springeropen.com/articles/10.1007/s41109-019-0232-2},
	doi = {10.1007/s41109-019-0232-2},
	abstract = {There have been rapid developments in model-based clustering of graphs, also known as block modelling, over the last ten years or so. We review different approaches and extensions proposed for different aspects in this area, such as the type of the graph, the clustering approach, the inference approach, and whether the number of groups is selected or estimated. We also review models that combine block modelling with topic modelling and/or longitudinal modelling, regarding how these models deal with multiple types of data. How different approaches cope with various issues will be summarised and compared, to facilitate the demand of practitioners for a concise overview of the current status of these areas of literature.},
	language = {en},
	number = {1},
	urldate = {2024-02-22},
	journal = {Applied Network Science},
	author = {Lee, Clement and Wilkinson, Darren J.},
	month = dec,
	year = {2019},
	pages = {122},
}

There have been rapid developments in model-based clustering of graphs, also known as block modelling, over the last ten years or so. We review different approaches and extensions proposed for different aspects in this area, such as the type of the graph, the clustering approach, the inference approach, and whether the number of groups is selected or estimated. We also review models that combine block modelling with topic modelling and/or longitudinal modelling, regarding how these models deal with multiple types of data. How different approaches cope with various issues will be summarised and compared, to facilitate the demand of practitioners for a concise overview of the current status of these areas of literature.

@article{duthieEvolutionPrecopulatoryPostcopulatory2018,
	title = {Evolution of precopulatory and post-copulatory strategies of inbreeding avoidance and associated polyandry},
	volume = {31},
	copyright = {https://creativecommons.org/licenses/by/4.0/},
	issn = {1420-9101, 1010-061X},
	url = {https://academic.oup.com/jeb/article/31/1/31-45/7382071},
	doi = {10.1111/jeb.13189},
	abstract = {Abstract
            Inbreeding depression is widely hypothesized to drive adaptive evolution of precopulatory and post-copulatory mechanisms of inbreeding avoidance, which in turn are hypothesized to affect evolution of polyandry (i.e. female multiple mating). However, surprisingly little theory or modelling critically examines selection for precopulatory or post-copulatory inbreeding avoidance, or both strategies, given evolutionary constraints and direct costs, or examines how evolution of inbreeding avoidance strategies might feed back to affect evolution of polyandry. Selection for post-copulatory inbreeding avoidance, but not for precopulatory inbreeding avoidance, requires polyandry, whereas interactions between precopulatory and post-copulatory inbreeding avoidance might cause functional redundancy (i.e. ‘degeneracy’) potentially generating complex evolutionary dynamics among inbreeding strategies and polyandry. We used individual-based modelling to quantify evolution of interacting precopulatory and post-copulatory inbreeding avoidance and associated polyandry given strong inbreeding depression and different evolutionary constraints and direct costs. We found that evolution of post-copulatory inbreeding avoidance increased selection for initially rare polyandry and that evolution of a costly inbreeding avoidance strategy became negligible over time given a lower-cost alternative strategy. Further, fixed precopulatory inbreeding avoidance often completely precluded evolution of polyandry and hence post-copulatory inbreeding avoidance, but fixed post-copulatory inbreeding avoidance did not preclude evolution of precopulatory inbreeding avoidance. Evolution of inbreeding avoidance phenotypes and associated polyandry is therefore affected by evolutionary feedbacks and degeneracy. All else being equal, evolution of precopulatory inbreeding avoidance and resulting low polyandry is more likely when post-copulatory inbreeding avoidance is precluded or costly, and evolution of post-copulatory inbreeding avoidance greatly facilitates evolution of costly polyandry.},
	language = {en},
	number = {1},
	urldate = {2025-03-30},
	journal = {Journal of Evolutionary Biology},
	author = {Duthie, A. B. and Bocedi, G. and Germain, R. R. and Reid, J. M.},
	month = jan,
	year = {2018},
	pages = {31--45},
}

Abstract Inbreeding depression is widely hypothesized to drive adaptive evolution of precopulatory and post-copulatory mechanisms of inbreeding avoidance, which in turn are hypothesized to affect evolution of polyandry (i.e. female multiple mating). However, surprisingly little theory or modelling critically examines selection for precopulatory or post-copulatory inbreeding avoidance, or both strategies, given evolutionary constraints and direct costs, or examines how evolution of inbreeding avoidance strategies might feed back to affect evolution of polyandry. Selection for post-copulatory inbreeding avoidance, but not for precopulatory inbreeding avoidance, requires polyandry, whereas interactions between precopulatory and post-copulatory inbreeding avoidance might cause functional redundancy (i.e. ‘degeneracy’) potentially generating complex evolutionary dynamics among inbreeding strategies and polyandry. We used individual-based modelling to quantify evolution of interacting precopulatory and post-copulatory inbreeding avoidance and associated polyandry given strong inbreeding depression and different evolutionary constraints and direct costs. We found that evolution of post-copulatory inbreeding avoidance increased selection for initially rare polyandry and that evolution of a costly inbreeding avoidance strategy became negligible over time given a lower-cost alternative strategy. Further, fixed precopulatory inbreeding avoidance often completely precluded evolution of polyandry and hence post-copulatory inbreeding avoidance, but fixed post-copulatory inbreeding avoidance did not preclude evolution of precopulatory inbreeding avoidance. Evolution of inbreeding avoidance phenotypes and associated polyandry is therefore affected by evolutionary feedbacks and degeneracy. All else being equal, evolution of precopulatory inbreeding avoidance and resulting low polyandry is more likely when post-copulatory inbreeding avoidance is precluded or costly, and evolution of post-copulatory inbreeding avoidance greatly facilitates evolution of costly polyandry.

@article{rungeCarryingSelfishGenetic2018,
	title = {Carrying a selfish genetic element predicts increased migration propensity in free-living wild house mice},
	volume = {285},
	issn = {0962-8452, 1471-2954},
	url = {https://royalsocietypublishing.org/doi/10.1098/rspb.2018.1333},
	doi = {10.1098/rspb.2018.1333},
	abstract = {Life is built on cooperation between genes, which makes it vulnerable to parasitism. Selfish genetic elements that exploit this cooperation can achieve large fitness gains by increasing their transmission relative to the rest of the genome. This leads to counter-adaptations that generate unique selection pressures on the selfish genetic element. This arms race is similar to host–parasite coevolution, as some multi-host parasites alter the host’s behaviour to increase the chance of transmission to the next host. Here, we ask if, similarly to these parasites, a selfish genetic element in house mice, the
              t
              haplotype, also manipulates host behaviour, specifically the host’s migration propensity. Variants of the
              t
              that manipulate migration propensity could increase in fitness in a meta-population. We show that juvenile mice carrying the
              t
              haplotype were more likely to emigrate from and were more often found as migrants within a long-term free-living house mouse population. This result may have applied relevance as the
              t
              has been proposed as a basis for artificial gene drive systems for use in population control.},
	language = {en},
	number = {1888},
	urldate = {2025-03-23},
	journal = {Proceedings of the Royal Society B: Biological Sciences},
	author = {Runge, Jan-Niklas and Lindholm, Anna K.},
	month = oct,
	year = {2018},
	pages = {20181333},
}

Life is built on cooperation between genes, which makes it vulnerable to parasitism. Selfish genetic elements that exploit this cooperation can achieve large fitness gains by increasing their transmission relative to the rest of the genome. This leads to counter-adaptations that generate unique selection pressures on the selfish genetic element. This arms race is similar to host–parasite coevolution, as some multi-host parasites alter the host’s behaviour to increase the chance of transmission to the next host. Here, we ask if, similarly to these parasites, a selfish genetic element in house mice, the t haplotype, also manipulates host behaviour, specifically the host’s migration propensity. Variants of the t that manipulate migration propensity could increase in fitness in a meta-population. We show that juvenile mice carrying the t haplotype were more likely to emigrate from and were more often found as migrants within a long-term free-living house mouse population. This result may have applied relevance as the t has been proposed as a basis for artificial gene drive systems for use in population control.

@article{harrisonFemaleNursingPartner2018,
	title = {Female nursing partner choice in a population of wild house mice ({Mus} musculus domesticus)},
	volume = {15},
	issn = {1742-9994},
	url = {https://frontiersinzoology.biomedcentral.com/articles/10.1186/s12983-018-0251-3},
	doi = {10.1186/s12983-018-0251-3},
	language = {en},
	number = {1},
	urldate = {2025-03-23},
	journal = {Frontiers in Zoology},
	author = {Harrison, Nicola and Lindholm, Anna K. and Dobay, Akos and Halloran, Olivia and Manser, Andri and König, Barbara},
	month = dec,
	year = {2018},
	pages = {4},
}

@article{geigerLongitudinalStudyPhenotypic2018,
	title = {A longitudinal study of phenotypic changes in early domestication of house mice},
	volume = {5},
	issn = {2054-5703},
	url = {https://royalsocietypublishing.org/doi/10.1098/rsos.172099},
	doi = {10.1098/rsos.172099},
	abstract = {Similar phenotypic changes occur across many species as a result of domestication, e.g. in pigmentation and snout size. Experimental studies of domestication have concentrated on intense and directed selection regimes, while conditions that approximate the commensal and indirect interactions with humans have not been explored. We examine long-term data on a free-living population of wild house mice that have been indirectly selected for tameness by regular exposure to humans. In the course of a decade, this mouse population exhibited significantly increased occurrence of white patches of fur and decreased head length. These phenotypic changes fit to the predictions of the ‘domestication syndrome'.},
	language = {en},
	number = {3},
	urldate = {2025-03-19},
	journal = {Royal Society Open Science},
	author = {Geiger, Madeleine and Sánchez-Villagra, Marcelo R. and Lindholm, Anna K.},
	month = mar,
	year = {2018},
	pages = {172099},
}

Similar phenotypic changes occur across many species as a result of domestication, e.g. in pigmentation and snout size. Experimental studies of domestication have concentrated on intense and directed selection regimes, while conditions that approximate the commensal and indirect interactions with humans have not been explored. We examine long-term data on a free-living population of wild house mice that have been indirectly selected for tameness by regular exposure to humans. In the course of a decade, this mouse population exhibited significantly increased occurrence of white patches of fur and decreased head length. These phenotypic changes fit to the predictions of the ‘domestication syndrome'.

@article{fosdickConfiguringRandomGraph2018,
	title = {Configuring {Random} {Graph} {Models} with {Fixed} {Degree} {Sequences}},
	volume = {60},
	issn = {0036-1445, 1095-7200},
	url = {https://epubs.siam.org/doi/10.1137/16M1087175},
	doi = {10.1137/16M1087175},
	abstract = {Random graph null models have found widespread application in diverse research communities analyzing network datasets, including social, information, and economic networks, as well as food webs, protein-protein interactions, and neuronal networks. The most popular random graph null models, called configuration models, are defined as uniform distributions over a space of graphs with a fixed degree sequence. Commonly, properties of an empirical network are compared to properties of an ensemble of graphs from a configuration model in order to quantify whether empirical network properties are meaningful or whether they are instead a common consequence of the particular degree sequence. In this work we study the subtle but important decisions underlying the specification of a configuration model, and we investigate the role these choices play in graph sampling procedures and a suite of applications. We place particular emphasis on the importance of specifying the appropriate graph labeling—stub-labeled or vertex-labeled—under which to consider a null model, a choice that closely connects the study of random graphs to the study of random contingency tables. We show that the choice of graph labeling is inconsequential for studies of simple graphs, but can have a significant impact on analyses of multigraphs or graphs with self-loops. The importance of these choices is demonstrated through a series of three in-depth vignettes, analyzing three different network datasets under many different configuration models and observing substantial differences in study conclusions under different models. We argue that in each case, only one of the possible configuration models is appropriate. While our work focuses on undirected static networks, it aims to guide the study of directed networks, dynamic networks, and all other network contexts that are suitably studied through the lens of random graph null models.},
	language = {en},
	number = {2},
	urldate = {2022-08-11},
	journal = {SIAM Review},
	author = {Fosdick, Bailey K. and Larremore, Daniel B. and Nishimura, Joel and Ugander, Johan},
	month = jan,
	year = {2018},
	pages = {315--355},
}

Random graph null models have found widespread application in diverse research communities analyzing network datasets, including social, information, and economic networks, as well as food webs, protein-protein interactions, and neuronal networks. The most popular random graph null models, called configuration models, are defined as uniform distributions over a space of graphs with a fixed degree sequence. Commonly, properties of an empirical network are compared to properties of an ensemble of graphs from a configuration model in order to quantify whether empirical network properties are meaningful or whether they are instead a common consequence of the particular degree sequence. In this work we study the subtle but important decisions underlying the specification of a configuration model, and we investigate the role these choices play in graph sampling procedures and a suite of applications. We place particular emphasis on the importance of specifying the appropriate graph labeling—stub-labeled or vertex-labeled—under which to consider a null model, a choice that closely connects the study of random graphs to the study of random contingency tables. We show that the choice of graph labeling is inconsequential for studies of simple graphs, but can have a significant impact on analyses of multigraphs or graphs with self-loops. The importance of these choices is demonstrated through a series of three in-depth vignettes, analyzing three different network datasets under many different configuration models and observing substantial differences in study conclusions under different models. We argue that in each case, only one of the possible configuration models is appropriate. While our work focuses on undirected static networks, it aims to guide the study of directed networks, dynamic networks, and all other network contexts that are suitably studied through the lens of random graph null models.

@article{shorterMaleInfertilityResponsible2017,
	title = {Male infertility {Is} responsible for nearly half of the extinction observed in the {Mouse} {Collaborative} {Cross}},
	volume = {206},
	copyright = {https://academic.oup.com/journals/pages/open\_access/funder\_policies/chorus/standard\_publication\_model},
	issn = {1943-2631},
	url = {https://academic.oup.com/genetics/article/206/2/557/6064214},
	doi = {10.1534/genetics.116.199596},
	abstract = {Abstract
            The goal of the Collaborative Cross (CC) project was to generate and distribute over 1000 independent mouse recombinant inbred strains derived from eight inbred founders. With inbreeding nearly complete, we estimated the extinction rate among CC lines at a remarkable 95\%, which is substantially higher than in the derivation of other mouse recombinant inbred populations. Here, we report genome-wide allele frequencies in 347 extinct CC lines. Contrary to expectations, autosomes had equal allelic contributions from the eight founders, but chromosome X had significantly lower allelic contributions from the two inbred founders with underrepresented subspecific origins (PWK/PhJ and CAST/EiJ). By comparing extinct CC lines to living CC strains, we conclude that a complex genetic architecture is driving extinction, and selection pressures are different on the autosomes and chromosome X. Male infertility played a large role in extinction as 47\% of extinct lines had males that were infertile. Males from extinct lines had high variability in reproductive organ size, low sperm counts, low sperm motility, and a high rate of vacuolization of seminiferous tubules. We performed QTL mapping and identified nine genomic regions associated with male fertility and reproductive phenotypes. Many of the allelic effects in the QTL were driven by the two founders with underrepresented subspecific origins, including a QTL on chromosome X for infertility that was driven by the PWK/PhJ haplotype. We also performed the first example of cross validation using complementary CC resources to verify the effect of sperm curvilinear velocity from the PWK/PhJ haplotype on chromosome 2 in an independent population across multiple generations. While selection typically constrains the examination of reproductive traits toward the more fertile alleles, the CC extinct lines provided a unique opportunity to study the genetic architecture of fertility in a widely genetically variable population. We hypothesize that incompatibilities between alleles with different subspecific origins is a key driver of infertility. These results help clarify the factors that drove strain extinction in the CC, reveal the genetic regions associated with poor fertility in the CC, and serve as a resource to further study mammalian infertility.},
	language = {en},
	number = {2},
	urldate = {2025-03-27},
	journal = {Genetics},
	author = {Shorter, John R and Odet, Fanny and Aylor, David L and Pan, Wenqi and Kao, Chia-Yu and Fu, Chen-Ping and Morgan, Andrew P and Greenstein, Seth and Bell, Timothy A and Stevans, Alicia M and Feathers, Ryan W and Patel, Sunny and Cates, Sarah E and Shaw, Ginger D and Miller, Darla R and Chesler, Elissa J and McMillian, Leonard and O’Brien, Deborah A and Villena, Fernando Pardo-Manuel De},
	month = jun,
	year = {2017},
	pages = {557--572},
}

Abstract The goal of the Collaborative Cross (CC) project was to generate and distribute over 1000 independent mouse recombinant inbred strains derived from eight inbred founders. With inbreeding nearly complete, we estimated the extinction rate among CC lines at a remarkable 95%, which is substantially higher than in the derivation of other mouse recombinant inbred populations. Here, we report genome-wide allele frequencies in 347 extinct CC lines. Contrary to expectations, autosomes had equal allelic contributions from the eight founders, but chromosome X had significantly lower allelic contributions from the two inbred founders with underrepresented subspecific origins (PWK/PhJ and CAST/EiJ). By comparing extinct CC lines to living CC strains, we conclude that a complex genetic architecture is driving extinction, and selection pressures are different on the autosomes and chromosome X. Male infertility played a large role in extinction as 47% of extinct lines had males that were infertile. Males from extinct lines had high variability in reproductive organ size, low sperm counts, low sperm motility, and a high rate of vacuolization of seminiferous tubules. We performed QTL mapping and identified nine genomic regions associated with male fertility and reproductive phenotypes. Many of the allelic effects in the QTL were driven by the two founders with underrepresented subspecific origins, including a QTL on chromosome X for infertility that was driven by the PWK/PhJ haplotype. We also performed the first example of cross validation using complementary CC resources to verify the effect of sperm curvilinear velocity from the PWK/PhJ haplotype on chromosome 2 in an independent population across multiple generations. While selection typically constrains the examination of reproductive traits toward the more fertile alleles, the CC extinct lines provided a unique opportunity to study the genetic architecture of fertility in a widely genetically variable population. We hypothesize that incompatibilities between alleles with different subspecific origins is a key driver of infertility. These results help clarify the factors that drove strain extinction in the CC, reveal the genetic regions associated with poor fertility in the CC, and serve as a resource to further study mammalian infertility.

@article{pembertonInbreedingDepressionEnvironment2017,
	title = {Inbreeding depression by environment interactions in a free-living mammal population},
	volume = {118},
	issn = {0018-067X, 1365-2540},
	url = {https://www.nature.com/articles/hdy2016100},
	doi = {10.1038/hdy.2016.100},
	abstract = {Abstract
            
              Experimental studies often find that inbreeding depression is more severe in harsh environments, but the few studies of
              in situ
              wild populations available to date rarely find strong support for this effect. We investigated evidence for inbreeding depression by environment interactions in nine traits in the individually monitored Soay sheep population of St Kilda, using genomic inbreeding coefficients based on 37 037 single-nucleotide polymorphism loci, and population density as an axis of environmental variation. All traits showed variation with population density and all traits showed some evidence for depression because of either an individual’s own inbreeding or maternal inbreeding. However, only six traits showed evidence for an interaction in the expected direction, and only two interactions were statistically significant. We identify three possible reasons why wild population studies may generally fail to find strong support for interactions between inbreeding depression and environmental variation compared with experimental studies. First, for species with biparental inbreeding only, the amount of observed inbreeding in natural populations is generally low compared with that used in experimental studies. Second, it is possible that experimental studies sometimes actually impose higher levels of stress than organisms experience in the wild. Third, some purging of the deleterious recessive alleles that underpin interaction effects may occur in the wild.},
	language = {en},
	number = {1},
	urldate = {2025-03-26},
	journal = {Heredity},
	author = {Pemberton, J M and Ellis, P E and Pilkington, J G and Bérénos, C},
	month = jan,
	year = {2017},
	pages = {64--77},
}

Abstract Experimental studies often find that inbreeding depression is more severe in harsh environments, but the few studies of in situ wild populations available to date rarely find strong support for this effect. We investigated evidence for inbreeding depression by environment interactions in nine traits in the individually monitored Soay sheep population of St Kilda, using genomic inbreeding coefficients based on 37 037 single-nucleotide polymorphism loci, and population density as an axis of environmental variation. All traits showed variation with population density and all traits showed some evidence for depression because of either an individual’s own inbreeding or maternal inbreeding. However, only six traits showed evidence for an interaction in the expected direction, and only two interactions were statistically significant. We identify three possible reasons why wild population studies may generally fail to find strong support for interactions between inbreeding depression and environmental variation compared with experimental studies. First, for species with biparental inbreeding only, the amount of observed inbreeding in natural populations is generally low compared with that used in experimental studies. Second, it is possible that experimental studies sometimes actually impose higher levels of stress than organisms experience in the wild. Third, some purging of the deleterious recessive alleles that underpin interaction effects may occur in the wild.

@article{bendeskyGeneticBasisParental2017,
	title = {The genetic basis of parental care evolution in monogamous mice.},
	volume = {544},
	issn = {1476-4687},
	url = {http://www.nature.com/doifinder/10.1038/nature22074},
	doi = {10.1038/nature22074},
	abstract = {Parental care is essential for the survival of mammals, yet the mechanisms underlying its evolution remain largely unknown. Here we show that two sister species of mice, Peromyscus polionotus and Peromyscus maniculatus, have large and heritable differences in parental behaviour. Using quantitative genetics, we identify 12 genomic regions that affect parental care, 8 of which have sex-specific effects, suggesting that parental care can evolve independently in males and females. Furthermore, some regions affect parental care broadly, whereas others affect specific behaviours, such as nest building. Of the genes linked to differences in nest-building behaviour, vasopressin is differentially expressed in the hypothalamus of the two species, with increased levels associated with less nest building. Using pharmacology in Peromyscus and chemogenetics in Mus, we show that vasopressin inhibits nest building but not other parental behaviours. Together, our results indicate that variation in an ancient neuropeptide contributes to interspecific differences in parental care.},
	number = {7651},
	urldate = {2017-05-02},
	journal = {Nature},
	author = {Bendesky, Andres and Kwon, Young-Mi and Lassance, Jean-Marc and Lewarch, Caitlin L and Yao, Shenqin and Peterson, Brant K and He, Meng Xiao and Dulac, Catherine and Hoekstra, Hopi E},
	month = apr,
	year = {2017},
	note = {171 citations (Crossref) [2023-02-11]},
	pages = {434--439},
}

Parental care is essential for the survival of mammals, yet the mechanisms underlying its evolution remain largely unknown. Here we show that two sister species of mice, Peromyscus polionotus and Peromyscus maniculatus, have large and heritable differences in parental behaviour. Using quantitative genetics, we identify 12 genomic regions that affect parental care, 8 of which have sex-specific effects, suggesting that parental care can evolve independently in males and females. Furthermore, some regions affect parental care broadly, whereas others affect specific behaviours, such as nest building. Of the genes linked to differences in nest-building behaviour, vasopressin is differentially expressed in the hypothalamus of the two species, with increased levels associated with less nest building. Using pharmacology in Peromyscus and chemogenetics in Mus, we show that vasopressin inhibits nest building but not other parental behaviours. Together, our results indicate that variation in an ancient neuropeptide contributes to interspecific differences in parental care.

@article{corbett-detigHiddenMarkovModel2017,
	title = {A hidden {Markov} model approach for simultaneously estimating local ancestry and admixture time using next generation sequence data in samples of arbitrary ploidy.},
	volume = {13},
	issn = {1553-7404 (Electronic)},
	doi = {10.1371/journal.pgen.1006529},
	abstract = {Admixture-the mixing of genomes from divergent populations-is increasingly appreciated as a central process in evolution. To characterize and quantify patterns of admixture across the genome, a number of methods have been developed for local ancestry inference. However, existing approaches have a number of shortcomings. First, all local ancestry inference methods require some prior assumption about the expected ancestry tract lengths. Second, existing methods generally require genotypes, which is not feasible to obtain for many next-generation sequencing projects. Third, many methods assume samples are diploid, however a wide variety of sequencing applications will fail to meet this assumption. To address these issues, we introduce a novel hidden Markov model for estimating local ancestry that models the read pileup data, rather than genotypes, is generalized to arbitrary ploidy, and can estimate the time since admixture during local ancestry inference. We demonstrate that our method can simultaneously estimate the time since admixture and local ancestry with good accuracy, and that it performs well on samples of high ploidy-i.e. 100 or more chromosomes. As this method is very general, we expect it will be useful for local ancestry inference in a wider variety of populations than what previously has been possible. We then applied our method to pooled sequencing data derived from populations of Drosophila melanogaster on an ancestry cline on the east coast of North America. We find that regions of local recombination rates are negatively correlated with the proportion of African ancestry, suggesting that selection against foreign ancestry is the least efficient in low recombination regions. Finally we show that clinal outlier loci are enriched for genes associated with gene regulatory functions, consistent with a role of regulatory evolution in ecological adaptation of admixed D. melanogaster populations. Our results illustrate the potential of local ancestry inference for elucidating fundamental evolutionary processes.},
	language = {eng},
	number = {1},
	journal = {PLoS genetics},
	author = {Corbett-Detig, Russell and Nielsen, Rasmus},
	month = jan,
	year = {2017},
	note = {95 citations (Crossref) [2023-02-11]},
	keywords = {Animals, Drosophila melanogaster, Evolution, Genetic, Genome, Insect, Markov Chains, Models, Molecular, Pedigree, Ploidies, Selection, genetics},
	pages = {e1006529},
}

Admixture-the mixing of genomes from divergent populations-is increasingly appreciated as a central process in evolution. To characterize and quantify patterns of admixture across the genome, a number of methods have been developed for local ancestry inference. However, existing approaches have a number of shortcomings. First, all local ancestry inference methods require some prior assumption about the expected ancestry tract lengths. Second, existing methods generally require genotypes, which is not feasible to obtain for many next-generation sequencing projects. Third, many methods assume samples are diploid, however a wide variety of sequencing applications will fail to meet this assumption. To address these issues, we introduce a novel hidden Markov model for estimating local ancestry that models the read pileup data, rather than genotypes, is generalized to arbitrary ploidy, and can estimate the time since admixture during local ancestry inference. We demonstrate that our method can simultaneously estimate the time since admixture and local ancestry with good accuracy, and that it performs well on samples of high ploidy-i.e. 100 or more chromosomes. As this method is very general, we expect it will be useful for local ancestry inference in a wider variety of populations than what previously has been possible. We then applied our method to pooled sequencing data derived from populations of Drosophila melanogaster on an ancestry cline on the east coast of North America. We find that regions of local recombination rates are negatively correlated with the proportion of African ancestry, suggesting that selection against foreign ancestry is the least efficient in low recombination regions. Finally we show that clinal outlier loci are enriched for genes associated with gene regulatory functions, consistent with a role of regulatory evolution in ecological adaptation of admixed D. melanogaster populations. Our results illustrate the potential of local ancestry inference for elucidating fundamental evolutionary processes.

@article{farineGuideNullModels2017,
	title = {A guide to null models for animal social network analysis},
	volume = {8},
	copyright = {http://creativecommons.org/licenses/by/4.0/},
	issn = {2041-210X, 2041-210X},
	url = {https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.12772},
	doi = {10.1111/2041-210X.12772},
	abstract = {Summary Null models are an important component of the social network analysis toolbox. However, their use in hypothesis testing is still not widespread. Furthermore, several different approaches for constructing null models exist, each with their relative strengths and weaknesses, and often testing different hypotheses. In this study, I highlight why null models are important for robust hypothesis testing in studies of animal social networks. Using simulated data containing a known observation bias, I test how different statistical tests and null models perform if such a bias was unknown. I show that permutations of the raw observational (or ‘pre‐network’) data consistently account for underlying structure in the generated social network, and thus can reduce both type I and type II error rates. However, permutations of pre‐network data remain relatively uncommon in animal social network analysis because they are challenging to implement for certain data types, particularly those from focal follows and GPS tracking. I explain simple routines that can easily be implemented across different types of data, and supply R code that applies each type of null model to the same simulated dataset. The R code can easily be modified to test hypotheses with empirical data. Widespread use of pre‐network data permutation methods will benefit researchers by facilitating robust hypothesis testing.},
	language = {en},
	number = {10},
	urldate = {2025-01-10},
	journal = {Methods in Ecology and Evolution},
	author = {Farine, Damien R.},
	editor = {Freckleton, Robert and Rands, Sean},
	month = oct,
	year = {2017},
	pages = {1309--1320},
}

Summary Null models are an important component of the social network analysis toolbox. However, their use in hypothesis testing is still not widespread. Furthermore, several different approaches for constructing null models exist, each with their relative strengths and weaknesses, and often testing different hypotheses. In this study, I highlight why null models are important for robust hypothesis testing in studies of animal social networks. Using simulated data containing a known observation bias, I test how different statistical tests and null models perform if such a bias was unknown. I show that permutations of the raw observational (or ‘pre‐network’) data consistently account for underlying structure in the generated social network, and thus can reduce both type I and type II error rates. However, permutations of pre‐network data remain relatively uncommon in animal social network analysis because they are challenging to implement for certain data types, particularly those from focal follows and GPS tracking. I explain simple routines that can easily be implemented across different types of data, and supply R code that applies each type of null model to the same simulated dataset. The R code can easily be modified to test hypotheses with empirical data. Widespread use of pre‐network data permutation methods will benefit researchers by facilitating robust hypothesis testing.

@article{narasimhanBCFtoolsRoHHidden2016,
	title = {{BCFtools}/{RoH}: a hidden {Markov} model approach for detecting autozygosity from next-generation sequencing data},
	volume = {32},
	copyright = {http://creativecommons.org/licenses/by/4.0/},
	issn = {1367-4811, 1367-4803},
	shorttitle = {{BCFtools}/{RoH}},
	url = {https://academic.oup.com/bioinformatics/article/32/11/1749/1742869},
	doi = {10.1093/bioinformatics/btw044},
	abstract = {Abstract
            Summary: Runs of homozygosity (RoHs) are genomic stretches of a diploid genome that show identical alleles on both chromosomes. Longer RoHs are unlikely to have arisen by chance but are likely to denote autozygosity, whereby both copies of the genome descend from the same recent ancestor. Early tools to detect RoH used genotype array data, but substantially more information is available from sequencing data. Here, we present and evaluate BCFtools/RoH, an extension to the BCFtools software package, that detects regions of autozygosity in sequencing data, in particular exome data, using a hidden Markov model. By applying it to simulated data and real data from the 1000 Genomes Project we estimate its accuracy and show that it has higher sensitivity and specificity than existing methods under a range of sequencing error rates and levels of autozygosity.
            Availability and implementation: BCFtools/RoH and its associated binary/source files are freely available from https://github.com/samtools/BCFtools.
            Contact:  vn2@sanger.ac.uk or pd3@sanger.ac.uk
            Supplementary information:  Supplementary data are available at Bioinformatics online.},
	language = {en},
	number = {11},
	urldate = {2025-03-30},
	journal = {Bioinformatics},
	author = {Narasimhan, Vagheesh and Danecek, Petr and Scally, Aylwyn and Xue, Yali and Tyler-Smith, Chris and Durbin, Richard},
	month = jun,
	year = {2016},
	pages = {1749--1751},
}

Abstract Summary: Runs of homozygosity (RoHs) are genomic stretches of a diploid genome that show identical alleles on both chromosomes. Longer RoHs are unlikely to have arisen by chance but are likely to denote autozygosity, whereby both copies of the genome descend from the same recent ancestor. Early tools to detect RoH used genotype array data, but substantially more information is available from sequencing data. Here, we present and evaluate BCFtools/RoH, an extension to the BCFtools software package, that detects regions of autozygosity in sequencing data, in particular exome data, using a hidden Markov model. By applying it to simulated data and real data from the 1000 Genomes Project we estimate its accuracy and show that it has higher sensitivity and specificity than existing methods under a range of sequencing error rates and levels of autozygosity. Availability and implementation: BCFtools/RoH and its associated binary/source files are freely available from https://github.com/samtools/BCFtools. Contact:  vn2@sanger.ac.uk or pd3@sanger.ac.uk Supplementary information:  Supplementary data are available at Bioinformatics online.

@article{duthieEvolutionInbreedingAvoidance2016,
	title = {Evolution of inbreeding avoidance and inbreeding preference through mate choice among interacting relatives},
	volume = {188},
	issn = {0003-0147, 1537-5323},
	url = {https://www.journals.uchicago.edu/doi/10.1086/688919},
	doi = {10.1086/688919},
	language = {en},
	number = {6},
	urldate = {2025-03-30},
	journal = {The American Naturalist},
	author = {Duthie, A. Bradley and Reid, Jane M.},
	month = dec,
	year = {2016},
	pages = {651--667},
}

@article{colePhenotypicGeneticEffects2016,
	title = {Phenotypic and genetic effects of recessive haplotypes on yield, longevity, and fertility},
	volume = {99},
	copyright = {https://www.elsevier.com/tdm/userlicense/1.0/},
	issn = {00220302},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0022030216304209},
	doi = {10.3168/jds.2015-10777},
	language = {en},
	number = {9},
	urldate = {2025-03-30},
	journal = {Journal of Dairy Science},
	author = {Cole, J.B. and Null, D.J. and VanRaden, P.M.},
	month = sep,
	year = {2016},
	pages = {7274--7288},
}

@article{beckerPhenotypeassociatedInbreedingBiases2016,
	title = {Phenotype‐associated inbreeding biases estimates of inbreeding depression in a wild bird population},
	volume = {29},
	issn = {1010-061X, 1420-9101},
	url = {https://academic.oup.com/jeb/article/29/1/35-46/7381562},
	doi = {10.1111/jeb.12759},
	abstract = {Abstract
            
              Inbreeding depression is usually quantified by regressing individual phenotypic values on inbreeding coefficients, implicitly assuming there is no correlation between an individual's phenotype and the kinship coefficient to its mate. If such an association between parental phenotype and parental kinship exists, and if the trait of interest is heritable, estimates of inbreeding depression can be biased. Here we first derive the expected bias as a function of the covariance between mean parental breeding value and parental kinship. Subsequently, we use simulated data to confirm the existence of this bias, and show that it can be accounted for in a quantitative genetic animal model. Finally, we use long‐term individual‐based data for white‐throated dippers (
              Cinclus cinclus
              ), a bird species in which inbreeding is relatively common, to obtain an empirical estimate of this bias. We show that during part of the study period, parents of inbred birds had shorter wings than those of outbred birds, and as wing length is heritable, inbred individuals were smaller, independent of any inbreeding effects. This resulted in the overestimation of inbreeding effects. Similarly, during a period when parents of inbred birds had longer wings, we found that inbreeding effects were underestimated. We discuss how such associations may have arisen in this system, and why they are likely to occur in others, too. Overall, we demonstrate how less biased estimates of inbreeding depression can be obtained within a quantitative genetic framework, and suggest that inbreeding and additive genetic effects should be accounted for simultaneously whenever possible.},
	language = {en},
	number = {1},
	urldate = {2025-03-29},
	journal = {Journal of Evolutionary Biology},
	author = {Becker, P. J. J. and Hegelbach, J. and Keller, L. F. and Postma, E.},
	month = jan,
	year = {2016},
	pages = {35--46},
}

Abstract Inbreeding depression is usually quantified by regressing individual phenotypic values on inbreeding coefficients, implicitly assuming there is no correlation between an individual's phenotype and the kinship coefficient to its mate. If such an association between parental phenotype and parental kinship exists, and if the trait of interest is heritable, estimates of inbreeding depression can be biased. Here we first derive the expected bias as a function of the covariance between mean parental breeding value and parental kinship. Subsequently, we use simulated data to confirm the existence of this bias, and show that it can be accounted for in a quantitative genetic animal model. Finally, we use long‐term individual‐based data for white‐throated dippers ( Cinclus cinclus ), a bird species in which inbreeding is relatively common, to obtain an empirical estimate of this bias. We show that during part of the study period, parents of inbred birds had shorter wings than those of outbred birds, and as wing length is heritable, inbred individuals were smaller, independent of any inbreeding effects. This resulted in the overestimation of inbreeding effects. Similarly, during a period when parents of inbred birds had longer wings, we found that inbreeding effects were underestimated. We discuss how such associations may have arisen in this system, and why they are likely to occur in others, too. Overall, we demonstrate how less biased estimates of inbreeding depression can be obtained within a quantitative genetic framework, and suggest that inbreeding and additive genetic effects should be accounted for simultaneously whenever possible.

@article{traskEvidencePhenotypicExpression2016,
	title = {Evidence of the phenotypic expression of a lethal recessive allele under inbreeding in a wild population of conservation concern},
	volume = {85},
	copyright = {http://creativecommons.org/licenses/by/4.0/},
	issn = {0021-8790, 1365-2656},
	url = {https://besjournals.onlinelibrary.wiley.com/doi/10.1111/1365-2656.12503},
	doi = {10.1111/1365-2656.12503},
	abstract = {Summary
            
              
                
                  Deleterious recessive alleles that are masked in outbred populations are predicted to be expressed in small, inbred populations, reducing both individual fitness and population viability. However, there are few definitive examples of phenotypic expression of lethal recessive alleles under inbreeding conditions in wild populations. Studies that demonstrate the action of such alleles, and infer their distribution and dynamics, are required to understand their potential impact on population viability and inform management responses.
                
                
                  
                    The Scottish population of red‐billed choughs (
                    
                      P
                      yrrhocorax pyrrhocorax
                    
                    ), which currently totals {\textless}60 breeding pairs and is of major conservation concern, has recently been affected by lethal blindness in nestlings. We used family data to show that the pattern of occurrence of blindness within and across affected families that produced blind nestlings was exactly 0·25, matching that expected given a single‐locus autosomal lethal recessive allele. Furthermore, the observed distribution of blind nestlings within affected families did not differ from that expected given
                    M
                    endelian inheritance of such an allele.
                  
                
                
                  Relatedness estimates showed that individuals from affected families were not more closely related to each other than they were to individuals from unaffected families that did not produce blind nestlings. Blind individuals tended to be less heterozygous than non‐blind individuals, as expected if blindness was caused by the expression of a recessive allele under inbreeding. However, there was no difference in the variance in heterozygosity estimates, suggesting that some blind individuals were relatively outbred. These results suggest carriers of the blindness allele may be widely distributed across contemporary families rather than restricted to a single family lineage, implying that the allele has persisted across multiple generations.
                
                
                  Blindness occurred at low frequency (affecting 1·6\% of observed nestlings since 1981). However, affected families had larger initial brood sizes than unaffected families. Such high fecundity of carriers of a lethal recessive allele might reflect overdominance, potentially reducing purging and increasing allele persistence probability.
                
                
                  We thereby demonstrate the phenotypic expression of a lethal recessive allele in a wild population of conservation concern, and provide a general framework for inferring allele distribution and persistence and informing management responses.},
	language = {en},
	number = {4},
	urldate = {2025-03-26},
	journal = {Journal of Animal Ecology},
	author = {Trask, Amanda E. and Bignal, Eric M. and McCracken, Davy I. and Monaghan, Pat and Piertney, Stuart B. and Reid, Jane M.},
	editor = {Eizaguirre, Christophe},
	month = jul,
	year = {2016},
	pages = {879--891},
}

Summary Deleterious recessive alleles that are masked in outbred populations are predicted to be expressed in small, inbred populations, reducing both individual fitness and population viability. However, there are few definitive examples of phenotypic expression of lethal recessive alleles under inbreeding conditions in wild populations. Studies that demonstrate the action of such alleles, and infer their distribution and dynamics, are required to understand their potential impact on population viability and inform management responses. The Scottish population of red‐billed choughs ( P yrrhocorax pyrrhocorax ), which currently totals \textless60 breeding pairs and is of major conservation concern, has recently been affected by lethal blindness in nestlings. We used family data to show that the pattern of occurrence of blindness within and across affected families that produced blind nestlings was exactly 0·25, matching that expected given a single‐locus autosomal lethal recessive allele. Furthermore, the observed distribution of blind nestlings within affected families did not differ from that expected given M endelian inheritance of such an allele. Relatedness estimates showed that individuals from affected families were not more closely related to each other than they were to individuals from unaffected families that did not produce blind nestlings. Blind individuals tended to be less heterozygous than non‐blind individuals, as expected if blindness was caused by the expression of a recessive allele under inbreeding. However, there was no difference in the variance in heterozygosity estimates, suggesting that some blind individuals were relatively outbred. These results suggest carriers of the blindness allele may be widely distributed across contemporary families rather than restricted to a single family lineage, implying that the allele has persisted across multiple generations. Blindness occurred at low frequency (affecting 1·6% of observed nestlings since 1981). However, affected families had larger initial brood sizes than unaffected families. Such high fecundity of carriers of a lethal recessive allele might reflect overdominance, potentially reducing purging and increasing allele persistence probability. We thereby demonstrate the phenotypic expression of a lethal recessive allele in a wild population of conservation concern, and provide a general framework for inferring allele distribution and persistence and informing management responses.

@article{charlierNGSbasedReverseGenetic2016,
	title = {{NGS}-based reverse genetic screen for common embryonic lethal mutations compromising fertility in livestock},
	volume = {26},
	issn = {1088-9051, 1549-5469},
	url = {http://genome.cshlp.org/lookup/doi/10.1101/gr.207076.116},
	doi = {10.1101/gr.207076.116},
	abstract = {We herein report the result of a large-scale, next generation sequencing (NGS)-based screen for embryonic lethal (EL) mutations in Belgian beef and New Zealand dairy cattle. We estimated by simulation that cattle might carry, on average, ∼0.5 recessive EL mutations. We mined exome sequence data from {\textgreater}600 animals, and identified 1377 stop-gain, 3139 frame-shift, 1341 splice-site, 22,939 disruptive missense, 62,399 benign missense, and 92,163 synonymous variants. We show that cattle have a comparable load of loss-of-function (LoF) variants (defined as stop-gain, frame-shift, or splice-site variants) as humans despite having a more variable exome. We genotyped {\textgreater}40,000 animals for up to 296 LoF and 3483 disruptive missense, breed-specific variants. We identified candidate EL mutations based on the observation of a significant depletion in homozygotes. We estimated the proportion of EL mutations at 15\% of tested LoF and 6\% of tested disruptive missense variants. We confirmed the EL nature of nine candidate variants by genotyping 200 carrier × carrier trios, and demonstrating the absence of homozygous offspring. The nine identified EL mutations segregate at frequencies ranging from 1.2\% to 6.6\% in the studied populations and collectively account for the mortality of ∼0.6\% of conceptuses. We show that EL mutations preferentially affect gene products fulfilling basic cellular functions. The resulting information will be useful to avoid at-risk matings, thereby improving fertility.},
	language = {en},
	number = {10},
	urldate = {2025-03-24},
	journal = {Genome Research},
	author = {Charlier, Carole and Li, Wanbo and Harland, Chad and Littlejohn, Mathew and Coppieters, Wouter and Creagh, Frances and Davis, Steve and Druet, Tom and Faux, Pierre and Guillaume, François and Karim, Latifa and Keehan, Mike and Kadri, Naveen Kumar and Tamma, Nico and Spelman, Richard and Georges, Michel},
	month = oct,
	year = {2016},
	pages = {1333--1341},
}

We herein report the result of a large-scale, next generation sequencing (NGS)-based screen for embryonic lethal (EL) mutations in Belgian beef and New Zealand dairy cattle. We estimated by simulation that cattle might carry, on average, ∼0.5 recessive EL mutations. We mined exome sequence data from \textgreater600 animals, and identified 1377 stop-gain, 3139 frame-shift, 1341 splice-site, 22,939 disruptive missense, 62,399 benign missense, and 92,163 synonymous variants. We show that cattle have a comparable load of loss-of-function (LoF) variants (defined as stop-gain, frame-shift, or splice-site variants) as humans despite having a more variable exome. We genotyped \textgreater40,000 animals for up to 296 LoF and 3483 disruptive missense, breed-specific variants. We identified candidate EL mutations based on the observation of a significant depletion in homozygotes. We estimated the proportion of EL mutations at 15% of tested LoF and 6% of tested disruptive missense variants. We confirmed the EL nature of nine candidate variants by genotyping 200 carrier × carrier trios, and demonstrating the absence of homozygous offspring. The nine identified EL mutations segregate at frequencies ranging from 1.2% to 6.6% in the studied populations and collectively account for the mortality of ∼0.6% of conceptuses. We show that EL mutations preferentially affect gene products fulfilling basic cellular functions. The resulting information will be useful to avoid at-risk matings, thereby improving fertility.

@article{kardosGenomicsAdvancesStudy2016,
	title = {Genomics advances the study of inbreeding depression in the wild},
	volume = {9},
	copyright = {http://creativecommons.org/licenses/by/4.0/},
	issn = {1752-4571, 1752-4571},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/eva.12414},
	doi = {10.1111/eva.12414},
	abstract = {Abstract
            Inbreeding depression (reduced fitness of individuals with related parents) has long been a major focus of ecology, evolution, and conservation biology. Despite decades of research, we still have a limited understanding of the strength, underlying genetic mechanisms, and demographic consequences of inbreeding depression in the wild. Studying inbreeding depression in natural populations has been hampered by the inability to precisely measure individual inbreeding. Fortunately, the rapidly increasing availability of high‐throughput sequencing data means it is now feasible to measure the inbreeding of any individual with high precision. Here, we review how genomic data are advancing our understanding of inbreeding depression in the wild. Recent results show that individual inbreeding and inbreeding depression can be measured more precisely with genomic data than via traditional pedigree analysis. Additionally, the availability of genomic data has made it possible to pinpoint loci with large effects contributing to inbreeding depression in wild populations, although this will continue to be a challenging task in many study systems due to low statistical power. Now that reliably measuring individual inbreeding is no longer a limitation, a major focus of future studies should be to more accurately quantify effects of inbreeding depression on population growth and viability.},
	language = {en},
	number = {10},
	urldate = {2025-03-23},
	journal = {Evolutionary Applications},
	author = {Kardos, Marty and Taylor, Helen R. and Ellegren, Hans and Luikart, Gordon and Allendorf, Fred W.},
	month = dec,
	year = {2016},
	pages = {1205--1218},
}

Abstract Inbreeding depression (reduced fitness of individuals with related parents) has long been a major focus of ecology, evolution, and conservation biology. Despite decades of research, we still have a limited understanding of the strength, underlying genetic mechanisms, and demographic consequences of inbreeding depression in the wild. Studying inbreeding depression in natural populations has been hampered by the inability to precisely measure individual inbreeding. Fortunately, the rapidly increasing availability of high‐throughput sequencing data means it is now feasible to measure the inbreeding of any individual with high precision. Here, we review how genomic data are advancing our understanding of inbreeding depression in the wild. Recent results show that individual inbreeding and inbreeding depression can be measured more precisely with genomic data than via traditional pedigree analysis. Additionally, the availability of genomic data has made it possible to pinpoint loci with large effects contributing to inbreeding depression in wild populations, although this will continue to be a challenging task in many study systems due to low statistical power. Now that reliably measuring individual inbreeding is no longer a limitation, a major focus of future studies should be to more accurately quantify effects of inbreeding depression on population growth and viability.

@article{sutterNoEvidenceFemale2016,
	title = {No evidence for female discrimination against male house mice carrying a selfish genetic element},
	volume = {62},
	issn = {1674-5507, 2396-9814},
	url = {https://academic.oup.com/cz/article-lookup/doi/10.1093/cz/zow063},
	doi = {10.1093/cz/zow063},
	language = {en},
	number = {6},
	urldate = {2025-03-23},
	journal = {Current Zoology},
	author = {Sutter, Andreas and Lindholm, Anna K.},
	month = dec,
	year = {2016},
	pages = {675--685},
}

@article{hedrickUnderstandingInbreedingDepression2016,
	title = {Understanding {Inbreeding} {Depression}, {Purging}, and {Genetic} {Rescue}},
	volume = {31},
	issn = {01695347},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0169534716301586},
	doi = {10.1016/j.tree.2016.09.005},
	language = {en},
	number = {12},
	urldate = {2025-03-19},
	journal = {Trends in Ecology \& Evolution},
	author = {Hedrick, Philip W. and Garcia-Dorado, Aurora},
	month = dec,
	year = {2016},
	pages = {940--952},
}

@article{speedRelatednessPostgenomicEra2015,
	title = {Relatedness in the post-genomic era: is it still useful?},
	volume = {16},
	issn = {1471-0056, 1471-0064},
	shorttitle = {Relatedness in the post-genomic era},
	url = {https://www.nature.com/articles/nrg3821},
	doi = {10.1038/nrg3821},
	language = {en},
	number = {1},
	urldate = {2025-03-31},
	journal = {Nature Reviews Genetics},
	author = {Speed, Doug and Balding, David J.},
	month = jan,
	year = {2015},
	pages = {33--44},
}

@article{ferrariRiskExploitationCommunal2015,
	title = {The risk of exploitation during communal nursing in house mice, {Mus} musculus domesticus},
	volume = {110},
	issn = {00033472},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0003347215003498},
	doi = {10.1016/j.anbehav.2015.09.018},
	language = {en},
	urldate = {2025-03-30},
	journal = {Animal Behaviour},
	author = {Ferrari, Manuela and Lindholm, Anna K. and König, Barbara},
	month = dec,
	year = {2015},
	pages = {133--143},
}

@article{haddadHabitatFragmentationIts2015a,
	title = {Habitat fragmentation and its lasting impact on {Earth}’s ecosystems},
	volume = {1},
	issn = {2375-2548},
	url = {https://www.science.org/doi/10.1126/sciadv.1500052},
	doi = {10.1126/sciadv.1500052},
	abstract = {Urgent need for conservation and restoration measures to improve landscape connectivity.
          , 
            We conducted an analysis of global forest cover to reveal that 70\% of remaining forest is within 1 km of the forest’s edge, subject to the degrading effects of fragmentation. A synthesis of fragmentation experiments spanning multiple biomes and scales, five continents, and 35 years demonstrates that habitat fragmentation reduces biodiversity by 13 to 75\% and impairs key ecosystem functions by decreasing biomass and altering nutrient cycles. Effects are greatest in the smallest and most isolated fragments, and they magnify with the passage of time. These findings indicate an urgent need for conservation and restoration measures to improve landscape connectivity, which will reduce extinction rates and help maintain ecosystem services.},
	language = {en},
	number = {2},
	urldate = {2025-03-30},
	journal = {Science Advances},
	author = {Haddad, Nick M. and Brudvig, Lars A. and Clobert, Jean and Davies, Kendi F. and Gonzalez, Andrew and Holt, Robert D. and Lovejoy, Thomas E. and Sexton, Joseph O. and Austin, Mike P. and Collins, Cathy D. and Cook, William M. and Damschen, Ellen I. and Ewers, Robert M. and Foster, Bryan L. and Jenkins, Clinton N. and King, Andrew J. and Laurance, William F. and Levey, Douglas J. and Margules, Chris R. and Melbourne, Brett A. and Nicholls, A. O. and Orrock, John L. and Song, Dan-Xia and Townshend, John R.},
	month = mar,
	year = {2015},
	pages = {e1500052},
}

Urgent need for conservation and restoration measures to improve landscape connectivity. , We conducted an analysis of global forest cover to reveal that 70% of remaining forest is within 1 km of the forest’s edge, subject to the degrading effects of fragmentation. A synthesis of fragmentation experiments spanning multiple biomes and scales, five continents, and 35 years demonstrates that habitat fragmentation reduces biodiversity by 13 to 75% and impairs key ecosystem functions by decreasing biomass and altering nutrient cycles. Effects are greatest in the smallest and most isolated fragments, and they magnify with the passage of time. These findings indicate an urgent need for conservation and restoration measures to improve landscape connectivity, which will reduce extinction rates and help maintain ecosystem services.

@article{dobryninGenomicLegacyAfrican2015,
	title = {Genomic legacy of the {African} cheetah, {Acinonyx} jubatus},
	volume = {16},
	issn = {1474-760X},
	url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0837-4},
	doi = {10.1186/s13059-015-0837-4},
	language = {en},
	number = {1},
	urldate = {2025-03-27},
	journal = {Genome Biology},
	author = {Dobrynin, Pavel and Liu, Shiping and Tamazian, Gaik and Xiong, Zijun and Yurchenko, Andrey A. and Krasheninnikova, Ksenia and Kliver, Sergey and Schmidt-Küntzel, Anne and Koepfli, Klaus-Peter and Johnson, Warren and Kuderna, Lukas F.K. and García-Pérez, Raquel and Manuel, Marc De and Godinez, Ricardo and Komissarov, Aleksey and Makunin, Alexey and Brukhin, Vladimir and Qiu, Weilin and Zhou, Long and Li, Fang and Yi, Jian and Driscoll, Carlos and Antunes, Agostinho and Oleksyk, Taras K. and Eizirik, Eduardo and Perelman, Polina and Roelke, Melody and Wildt, David and Diekhans, Mark and Marques-Bonet, Tomas and Marker, Laurie and Bhak, Jong and Wang, Jun and Zhang, Guojie and O’Brien, Stephen J.},
	month = dec,
	year = {2015},
	pages = {277},
}

@article{sandersonBandedMongoosesAvoid2015,
	title = {Banded mongooses avoid inbreeding when mating with members of the same natal group},
	volume = {24},
	copyright = {http://creativecommons.org/licenses/by/4.0/},
	issn = {0962-1083, 1365-294X},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/mec.13253},
	doi = {10.1111/mec.13253},
	abstract = {Inbreeding and inbreeding avoidance are key factors in the evolution of animal societies, influencing dispersal and reproductive strategies which can affect relatedness structure and helping behaviours. In cooperative breeding systems, individuals typically avoid inbreeding through reproductive restraint and/or dispersing to breed outside their natal group. However, where groups contain multiple potential mates of varying relatedness, strategies of kin recognition and mate choice may be favoured. Here, we investigate male mate choice and female control of paternity in the banded mongoose (Mungos mungo), a cooperatively breeding mammal where both sexes are often philopatric and mating between relatives is known to occur. We find evidence suggestive of inbreeding depression in banded mongooses, indicating a benefit to avoiding breeding with relatives. Successfully breeding pairs were less related than expected under random mating, which appeared to be driven by both male choice and female control of paternity. Male banded mongooses actively guard females to gain access to mating opportunities, and this guarding behaviour is preferentially directed towards less closely related females. Guard–female relatedness did not affect the guard’s probability of gaining reproductive success. However, where mate-guards are unsuccessful, they lose paternity to males that are less related to the females than themselves. Together, our results suggest that both sexes of banded mongoose use kin discrimination to avoid inbreeding. Although this strategy appears to be rare among cooperative breeders, it may be more prominent in species where relatedness to potential mates is variable, and/or where opportunities for dispersal and mating outside of the group are limited.},
	language = {en},
	number = {14},
	urldate = {2025-03-26},
	journal = {Molecular Ecology},
	author = {Sanderson, Jennifer L. and Wang, Jinliang and Vitikainen, Emma I. K. and Cant, Michael A. and Nichols, Hazel J.},
	month = jul,
	year = {2015},
	pages = {3738--3751},
}

Inbreeding and inbreeding avoidance are key factors in the evolution of animal societies, influencing dispersal and reproductive strategies which can affect relatedness structure and helping behaviours. In cooperative breeding systems, individuals typically avoid inbreeding through reproductive restraint and/or dispersing to breed outside their natal group. However, where groups contain multiple potential mates of varying relatedness, strategies of kin recognition and mate choice may be favoured. Here, we investigate male mate choice and female control of paternity in the banded mongoose (Mungos mungo), a cooperatively breeding mammal where both sexes are often philopatric and mating between relatives is known to occur. We find evidence suggestive of inbreeding depression in banded mongooses, indicating a benefit to avoiding breeding with relatives. Successfully breeding pairs were less related than expected under random mating, which appeared to be driven by both male choice and female control of paternity. Male banded mongooses actively guard females to gain access to mating opportunities, and this guarding behaviour is preferentially directed towards less closely related females. Guard–female relatedness did not affect the guard’s probability of gaining reproductive success. However, where mate-guards are unsuccessful, they lose paternity to males that are less related to the females than themselves. Together, our results suggest that both sexes of banded mongoose use kin discrimination to avoid inbreeding. Although this strategy appears to be rare among cooperative breeders, it may be more prominent in species where relatedness to potential mates is variable, and/or where opportunities for dispersal and mating outside of the group are limited.

@article{firmanGameticInteractionsPromote2015,
	title = {Gametic interactions promote inbreeding avoidance in house mice},
	volume = {18},
	issn = {1461-023X, 1461-0248},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/ele.12471},
	doi = {10.1111/ele.12471},
	abstract = {Abstract
            
              Reproduction among related individuals is generally maladaptive. Inbreeding imposes significant costs on individual reproductive success, and can decrease population fitness. Theory predicts that polyandrous females can avoid inbreeding by exploiting paternity‐biasing mechanisms that enable differential sperm ‘use’. Evidence of sperm selection is difficult to demonstrate because patterns of non‐random paternity can be generated by a variety of different mechanisms. Here, using
              in vitro
              fertilisation in mice, we provide evidence of sperm selection at the gametic level. We mixed the sperm of sibling and non‐sibling males, and observed a fertilisation bias towards the sperm of non‐sibling males. The number of motile sperm and sperm swimming performance did not differ between competitors among the replicate assays. Therefore, our result can only be ascribed to egg‐driven sperm selection against related sperm. We conclude that the expression or secretion of gametic proteins could provide the molecular basis for this mechanism of cryptic female choice.},
	language = {en},
	number = {9},
	urldate = {2025-03-25},
	journal = {Ecology Letters},
	author = {Firman, Renée C. and Simmons, Leigh W.},
	editor = {Hosken, David},
	month = sep,
	year = {2015},
	pages = {937--943},
}

Abstract Reproduction among related individuals is generally maladaptive. Inbreeding imposes significant costs on individual reproductive success, and can decrease population fitness. Theory predicts that polyandrous females can avoid inbreeding by exploiting paternity‐biasing mechanisms that enable differential sperm ‘use’. Evidence of sperm selection is difficult to demonstrate because patterns of non‐random paternity can be generated by a variety of different mechanisms. Here, using in vitro fertilisation in mice, we provide evidence of sperm selection at the gametic level. We mixed the sperm of sibling and non‐sibling males, and observed a fertilisation bias towards the sperm of non‐sibling males. The number of motile sperm and sperm swimming performance did not differ between competitors among the replicate assays. Therefore, our result can only be ascribed to egg‐driven sperm selection against related sperm. We conclude that the expression or secretion of gametic proteins could provide the molecular basis for this mechanism of cryptic female choice.

@article{pauschHomozygousHaplotypeDeficiency2015,
	title = {Homozygous haplotype deficiency reveals deleterious mutations compromising reproductive and rearing success in cattle},
	volume = {16},
	issn = {1471-2164},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1483-7},
	doi = {10.1186/s12864-015-1483-7},
	language = {en},
	number = {1},
	urldate = {2025-03-25},
	journal = {BMC Genomics},
	author = {Pausch, Hubert and Schwarzenbacher, Hermann and Burgstaller, Johann and Flisikowski, Krzysztof and Wurmser, Christine and Jansen, Sandra and Jung, Simone and Schnieke, Angelika and Wittek, Thomas and Fries, Ruedi},
	month = dec,
	year = {2015},
	pages = {312},
}

@article{pilakoutaParentalCareBuffers2015,
	title = {Parental care buffers against inbreeding depression in burying beetles},
	volume = {112},
	issn = {0027-8424, 1091-6490},
	url = {https://pnas.org/doi/full/10.1073/pnas.1500658112},
	doi = {10.1073/pnas.1500658112},
	abstract = {Significance
            When relatives mate, their inbred offspring often suffer a reduction in fitness-related traits known as “inbreeding depression.” Environmental stresses such as starvation and competition can exacerbate these fitness costs of inbreeding. However, caring parents could mitigate the fitness costs of inbreeding by neutralizing the effects of these environmental stresses. We tested the hypothesis that maternal care can buffer against inbreeding depression in the offspring in burying beetles. Indeed, the female's presence led to a higher increase in larval survival in inbred than in outbred broods, and it increased the lifespan of inbred but not outbred adults. Our findings suggest that parental care can moderate the severity of inbreeding depression, possibly affecting how parental care strategies and inbreeding avoidance mechanisms evolve.
          , 
            
              When relatives mate, their inbred offspring often suffer a reduction in fitness-related traits known as “inbreeding depression.” There is mounting evidence that inbreeding depression can be exacerbated by environmental stresses such as starvation, predation, parasitism, and competition. Parental care may play an important role as a buffer against inbreeding depression in the offspring by alleviating these environmental stresses. Here, we examine the effect of parental care on the fitness costs of inbreeding in the burying beetle
              Nicrophorus vespilloides
              , an insect with facultative parental care. We used a 2 × 2 factorial design with the following factors: (
              i
              ) the presence or absence of a caring female parent during larval development and (
              ii
              ) inbred or outbred offspring. We examined the joint influence of maternal care and inbreeding status on fitness-related offspring traits to test the hypothesis that maternal care improves the performance of inbred offspring more than that of outbred offspring. Indeed, the female's presence led to a higher increase in larval survival in inbred than in outbred broods. Receiving care at the larval stage also increased the lifespan of inbred but not outbred adults, suggesting that the beneficial buffering effects of maternal care can persist long after the offspring have become independent. Our results show that parental care has the potential to moderate the severity of inbreeding depression, which in turn may favor inbreeding tolerance and influence the evolution of mating systems and other inbreeding-avoidance mechanisms.},
	language = {en},
	number = {26},
	urldate = {2025-03-23},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Pilakouta, Natalie and Jamieson, Seonaidh and Moorad, Jacob A. and Smiseth, Per T.},
	month = jun,
	year = {2015},
	pages = {8031--8035},
}

Significance When relatives mate, their inbred offspring often suffer a reduction in fitness-related traits known as “inbreeding depression.” Environmental stresses such as starvation and competition can exacerbate these fitness costs of inbreeding. However, caring parents could mitigate the fitness costs of inbreeding by neutralizing the effects of these environmental stresses. We tested the hypothesis that maternal care can buffer against inbreeding depression in the offspring in burying beetles. Indeed, the female's presence led to a higher increase in larval survival in inbred than in outbred broods, and it increased the lifespan of inbred but not outbred adults. Our findings suggest that parental care can moderate the severity of inbreeding depression, possibly affecting how parental care strategies and inbreeding avoidance mechanisms evolve. , When relatives mate, their inbred offspring often suffer a reduction in fitness-related traits known as “inbreeding depression.” There is mounting evidence that inbreeding depression can be exacerbated by environmental stresses such as starvation, predation, parasitism, and competition. Parental care may play an important role as a buffer against inbreeding depression in the offspring by alleviating these environmental stresses. Here, we examine the effect of parental care on the fitness costs of inbreeding in the burying beetle Nicrophorus vespilloides , an insect with facultative parental care. We used a 2 × 2 factorial design with the following factors: ( i ) the presence or absence of a caring female parent during larval development and ( ii ) inbred or outbred offspring. We examined the joint influence of maternal care and inbreeding status on fitness-related offspring traits to test the hypothesis that maternal care improves the performance of inbred offspring more than that of outbred offspring. Indeed, the female's presence led to a higher increase in larval survival in inbred than in outbred broods. Receiving care at the larval stage also increased the lifespan of inbred but not outbred adults, suggesting that the beneficial buffering effects of maternal care can persist long after the offspring have become independent. Our results show that parental care has the potential to moderate the severity of inbreeding depression, which in turn may favor inbreeding tolerance and influence the evolution of mating systems and other inbreeding-avoidance mechanisms.

@article{haddadHabitatFragmentationIts2015,
	title = {Habitat fragmentation and its lasting impact on {Earth}’s ecosystems},
	volume = {1},
	issn = {2375-2548},
	url = {https://www.science.org/doi/10.1126/sciadv.1500052},
	doi = {10.1126/sciadv.1500052},
	abstract = {Urgent need for conservation and restoration measures to improve landscape connectivity.
          , 
            We conducted an analysis of global forest cover to reveal that 70\% of remaining forest is within 1 km of the forest’s edge, subject to the degrading effects of fragmentation. A synthesis of fragmentation experiments spanning multiple biomes and scales, five continents, and 35 years demonstrates that habitat fragmentation reduces biodiversity by 13 to 75\% and impairs key ecosystem functions by decreasing biomass and altering nutrient cycles. Effects are greatest in the smallest and most isolated fragments, and they magnify with the passage of time. These findings indicate an urgent need for conservation and restoration measures to improve landscape connectivity, which will reduce extinction rates and help maintain ecosystem services.},
	language = {en},
	number = {2},
	urldate = {2025-03-23},
	journal = {Science Advances},
	author = {Haddad, Nick M. and Brudvig, Lars A. and Clobert, Jean and Davies, Kendi F. and Gonzalez, Andrew and Holt, Robert D. and Lovejoy, Thomas E. and Sexton, Joseph O. and Austin, Mike P. and Collins, Cathy D. and Cook, William M. and Damschen, Ellen I. and Ewers, Robert M. and Foster, Bryan L. and Jenkins, Clinton N. and King, Andrew J. and Laurance, William F. and Levey, Douglas J. and Margules, Chris R. and Melbourne, Brett A. and Nicholls, A. O. and Orrock, John L. and Song, Dan-Xia and Townshend, John R.},
	month = mar,
	year = {2015},
	pages = {e1500052},
}

Urgent need for conservation and restoration measures to improve landscape connectivity. , We conducted an analysis of global forest cover to reveal that 70% of remaining forest is within 1 km of the forest’s edge, subject to the degrading effects of fragmentation. A synthesis of fragmentation experiments spanning multiple biomes and scales, five continents, and 35 years demonstrates that habitat fragmentation reduces biodiversity by 13 to 75% and impairs key ecosystem functions by decreasing biomass and altering nutrient cycles. Effects are greatest in the smallest and most isolated fragments, and they magnify with the passage of time. These findings indicate an urgent need for conservation and restoration measures to improve landscape connectivity, which will reduce extinction rates and help maintain ecosystem services.

@article{manserFemaleHouseMice2015,
	title = {Female house mice avoid fertilization by \textit{t} haplotype incompatible males in a mate choice experiment},
	volume = {28},
	issn = {1010-061X, 1420-9101},
	url = {https://academic.oup.com/jeb/article/28/1/54-64/7379822},
	doi = {10.1111/jeb.12525},
	abstract = {Abstract
            
              The
              t
              haplotype in house mice is a well‐known selfish genetic element with detrimental, nonadditive fitness consequences to its carriers: recessive lethal mutations cause
              t
              /
              t
              homozygotes to perish
              in utero
              . Given the severe genetic incompatibility imposed by the
              t
              haplotype, we predict females to avoid fertilization by
              t
              haplotype incompatible males. Indeed, some of the strongest evidence for compatibility mate choice is related to the
              t
              haplotype in house mice. However, all previous evidence for compatibility mate choice in this system is based on olfactory preference. It is so far unknown how general these preferences are and whether they are relevant in an actual mating context. Here, we assess female compatibility mate choice related to
              t
              haplotypes in a setting that – for the first time – allowed females to directly interact and mate with males. This approach enabled us to analyse female behaviour during the testing period, and the resulting paternity success and fitness consequences of a given choice. We show that genetic incompatibilities arising from the
              t
              haplotype had severe indirect fitness consequences and
              t
              females avoided fertilization by
              t
              incompatible males. The results are inconclusive whether this avoidance of
              t
              fertilization by
              t
              females was caused by pre‐ or post‐copulatory processes.},
	language = {en},
	number = {1},
	urldate = {2025-03-23},
	journal = {Journal of Evolutionary Biology},
	author = {Manser, A. and König, B. and Lindholm, A. K.},
	month = jan,
	year = {2015},
	pages = {54--64},
}

Abstract The t haplotype in house mice is a well‐known selfish genetic element with detrimental, nonadditive fitness consequences to its carriers: recessive lethal mutations cause t / t homozygotes to perish in utero . Given the severe genetic incompatibility imposed by the t haplotype, we predict females to avoid fertilization by t haplotype incompatible males. Indeed, some of the strongest evidence for compatibility mate choice is related to the t haplotype in house mice. However, all previous evidence for compatibility mate choice in this system is based on olfactory preference. It is so far unknown how general these preferences are and whether they are relevant in an actual mating context. Here, we assess female compatibility mate choice related to t haplotypes in a setting that – for the first time – allowed females to directly interact and mate with males. This approach enabled us to analyse female behaviour during the testing period, and the resulting paternity success and fitness consequences of a given choice. We show that genetic incompatibilities arising from the t haplotype had severe indirect fitness consequences and t females avoided fertilization by t incompatible males. The results are inconclusive whether this avoidance of t fertilization by t females was caused by pre‐ or post‐copulatory processes.

@article{konigSystemAutomaticRecording2015,
	title = {A system for automatic recording of social behavior in a free-living wild house mouse population},
	volume = {3},
	issn = {2050-3385},
	url = {http://www.animalbiotelemetry.com/content/3/1/39},
	doi = {10.1186/s40317-015-0069-0},
	number = {1},
	journal = {Animal Biotelemetry},
	author = {König, Barbara and Lindholm, Anna K. and Lopes, Patricia C. and Dobay, Akos and Steinert, Sally and Buschmann, Frank Jens-Uwe},
	month = dec,
	year = {2015},
	keywords = {AniLoc, Cooperation, Demography, FNSA, House mice, Population ecology, RFID technology, Relatedness, Social networks, aniloc, cooperation, demography, house mice, population ecology, relatedness, rfid technology, social},
	pages = {39},
}

@article{farineConstructingConductingInterpreting2015,
	title = {Constructing, conducting and interpreting animal social network analysis},
	volume = {84},
	copyright = {http://creativecommons.org/licenses/by/4.0/},
	issn = {0021-8790, 1365-2656},
	url = {https://besjournals.onlinelibrary.wiley.com/doi/10.1111/1365-2656.12418},
	doi = {10.1111/1365-2656.12418},
	abstract = {Summary Animal social networks are descriptions of social structure which, aside from their intrinsic interest for understanding sociality, can have significant bearing across many fields of biology. Network analysis provides a flexible toolbox for testing a broad range of hypotheses, and for describing the social system of species or populations in a quantitative and comparable manner. However, it requires careful consideration of underlying assumptions, in particular differentiating real from observed networks and controlling for inherent biases that are common in social data. We provide a practical guide for using this framework to analyse animal social systems and test hypotheses. First, we discuss key considerations when defining nodes and edges, and when designing methods for collecting data. We discuss different approaches for inferring social networks from these data and displaying them. We then provide an overview of methods for quantifying properties of nodes and networks, as well as for testing hypotheses concerning network structure and network processes. Finally, we provide information about assessing the power and accuracy of an observed network. Alongside this manuscript, we provide appendices containing background information on common programming routines and worked examples of how to perform network analysis using the r programming language. We conclude by discussing some of the major current challenges in social network analysis and interesting future directions. In particular, we highlight the under‐exploited potential of experimental manipulations on social networks to address research questions.},
	language = {en},
	number = {5},
	urldate = {2025-02-19},
	journal = {Journal of Animal Ecology},
	author = {Farine, Damien R. and Whitehead, Hal},
	editor = {Altizer, Sonia},
	month = sep,
	year = {2015},
	pages = {1144--1163},
}

Summary Animal social networks are descriptions of social structure which, aside from their intrinsic interest for understanding sociality, can have significant bearing across many fields of biology. Network analysis provides a flexible toolbox for testing a broad range of hypotheses, and for describing the social system of species or populations in a quantitative and comparable manner. However, it requires careful consideration of underlying assumptions, in particular differentiating real from observed networks and controlling for inherent biases that are common in social data. We provide a practical guide for using this framework to analyse animal social systems and test hypotheses. First, we discuss key considerations when defining nodes and edges, and when designing methods for collecting data. We discuss different approaches for inferring social networks from these data and displaying them. We then provide an overview of methods for quantifying properties of nodes and networks, as well as for testing hypotheses concerning network structure and network processes. Finally, we provide information about assessing the power and accuracy of an observed network. Alongside this manuscript, we provide appendices containing background information on common programming routines and worked examples of how to perform network analysis using the r programming language. We conclude by discussing some of the major current challenges in social network analysis and interesting future directions. In particular, we highlight the under‐exploited potential of experimental manipulations on social networks to address research questions.

@article{yunVariationStrengthInbreeding2014,
	title = {Variation in the strength of inbreeding depression across environments: {Effects} of stress and density dependence: {INBREEDING} {DEPRESSION}, {DENSITY}-{DEPENDENCE}, {AND} {STRESS}},
	volume = {68},
	copyright = {http://doi.wiley.com/10.1002/tdm\_license\_1.1},
	issn = {00143820},
	shorttitle = {Variation in the strength of inbreeding depression across environments},
	url = {https://academic.oup.com/evolut/article/68/12/3599/6852556},
	doi = {10.1111/evo.12527},
	language = {en},
	number = {12},
	urldate = {2025-03-30},
	journal = {Evolution},
	author = {Yun, Li and Agrawal, Aneil F.},
	month = dec,
	year = {2014},
	pages = {3599--3606},
}

@article{leroyInbreedingDepressionLivestock2014,
	title = {Inbreeding depression in livestock species: review and meta‐analysis},
	volume = {45},
	copyright = {http://onlinelibrary.wiley.com/termsAndConditions\#vor},
	issn = {0268-9146, 1365-2052},
	shorttitle = {Inbreeding depression in livestock species},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/age.12178},
	doi = {10.1111/age.12178},
	abstract = {Summary
            Inbreeding, by virtue of its consequence on traits of interest, is a topic of major interest for geneticists and animal breeders. Based on meta‐analysis conducted on 57 studies and seven livestock species considering a wide variety of selected traits, it was estimated that inbreeding depression corresponds to on average a decrease of 0.137 percent of the mean of a trait per 1 percent of inbreeding. The decrease was larger for production traits (reduction of 0.351\%) than for other trait categories. For populations raised as purebreds, inbreeding depression may impact the economic income of breeders. There is a need for studies assessing the existence of an inbreeding purge phenomenon as well as the impact of inbreeding on adaptation capacities of livestock species. Promises brought by the development of dense genotyping as well as functional genomics will increase the capacities to improve our understanding and management of the phenomenon.},
	language = {en},
	number = {5},
	urldate = {2025-03-19},
	journal = {Animal Genetics},
	author = {Leroy, G.},
	month = oct,
	year = {2014},
	pages = {618--628},
}

Summary Inbreeding, by virtue of its consequence on traits of interest, is a topic of major interest for geneticists and animal breeders. Based on meta‐analysis conducted on 57 studies and seven livestock species considering a wide variety of selected traits, it was estimated that inbreeding depression corresponds to on average a decrease of 0.137 percent of the mean of a trait per 1 percent of inbreeding. The decrease was larger for production traits (reduction of 0.351%) than for other trait categories. For populations raised as purebreds, inbreeding depression may impact the economic income of breeders. There is a need for studies assessing the existence of an inbreeding purge phenomenon as well as the impact of inbreeding on adaptation capacities of livestock species. Promises brought by the development of dense genotyping as well as functional genomics will increase the capacities to improve our understanding and management of the phenomenon.

@article{kivelaMultilayerNetworks2014,
	title = {Multilayer networks},
	volume = {2},
	issn = {2051-1310, 2051-1329},
	url = {https://academic.oup.com/comnet/article-lookup/doi/10.1093/comnet/cnu016},
	doi = {10.1093/comnet/cnu016},
	language = {en},
	number = {3},
	urldate = {2025-02-12},
	journal = {Journal of Complex Networks},
	author = {Kivela, M. and Arenas, A. and Barthelemy, M. and Gleeson, J. P. and Moreno, Y. and Porter, M. A.},
	month = sep,
	year = {2014},
	pages = {203--271},
}

@article{boccalettiStructureDynamicsMultilayer2014,
	title = {The structure and dynamics of multilayer networks},
	volume = {544},
	issn = {03701573},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0370157314002105},
	doi = {10.1016/j.physrep.2014.07.001},
	language = {en},
	number = {1},
	urldate = {2025-02-12},
	journal = {Physics Reports},
	author = {Boccaletti, S. and Bianconi, G. and Criado, R. and Del Genio, C.I. and Gómez-Gardeñes, J. and Romance, M. and Sendiña-Nadal, I. and Wang, Z. and Zanin, M.},
	month = nov,
	year = {2014},
	pages = {1--122},
}

@article{lambiotteRandomWalksMarkov2014,
	title = {Random {Walks}, {Markov} {Processes} and the {Multiscale} {Modular} {Organization} of {Complex} {Networks}},
	volume = {1},
	issn = {2327-4697},
	url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=7010026},
	doi = {10.1109/TNSE.2015.2391998},
	abstract = {Most methods proposed to uncover communities in complex networks rely on combinatorial graph properties. Usually an edge-counting quality function, such as modularity, is optimized over all partitions of the graph compared against a null random graph model. Here we introduce a systematic dynamical framework to design and analyze a wide variety of quality functions for community detection. The quality of a partition is measured by its Markov Stability, a time-parametrized function defined in terms of the statistical properties of a Markov process taking place on the graph. The Markov process provides a dynamical sweeping across all scales in the graph, and the time scale is an intrinsic parameter that uncovers communities at different resolutions. This dynamic-based community detection leads to a compound optimization, which favours communities of comparable centrality (as defined by the stationary distribution), and provides a unifying framework for spectral algorithms, as well as different heuristics for community detection, including versions of modularity and Potts model. Our dynamic framework creates a systematic link between different stochastic dynamics and their corresponding notions of optimal communities under distinct (node and edge) centralities.We show that the Markov Stability can be computed efficiently to find multi-scale community structure in large networks.},
	number = {2},
	journal = {IEEE Transactions on Network Science and Engineering},
	author = {Lambiotte, Renaud and Delvenne, Jean-Charles and Barahona, Mauricio},
	month = jul,
	year = {2014},
	keywords = {Communities, Complex networks, FNSA, Graph theory, Multiscale structures, Optimization, centrality, community detection, graph theory, multiscale structure, optimization, partition stability, random walks, ★},
	pages = {76--90},
}

Most methods proposed to uncover communities in complex networks rely on combinatorial graph properties. Usually an edge-counting quality function, such as modularity, is optimized over all partitions of the graph compared against a null random graph model. Here we introduce a systematic dynamical framework to design and analyze a wide variety of quality functions for community detection. The quality of a partition is measured by its Markov Stability, a time-parametrized function defined in terms of the statistical properties of a Markov process taking place on the graph. The Markov process provides a dynamical sweeping across all scales in the graph, and the time scale is an intrinsic parameter that uncovers communities at different resolutions. This dynamic-based community detection leads to a compound optimization, which favours communities of comparable centrality (as defined by the stationary distribution), and provides a unifying framework for spectral algorithms, as well as different heuristics for community detection, including versions of modularity and Potts model. Our dynamic framework creates a systematic link between different stochastic dynamics and their corresponding notions of optimal communities under distinct (node and edge) centralities.We show that the Markov Stability can be computed efficiently to find multi-scale community structure in large networks.

@article{peixotoHierarchicalBlockStructures2014,
	title = {Hierarchical {Block} {Structures} and {High}-{Resolution} {Model} {Selection} in {Large} {Networks}},
	volume = {4},
	issn = {2160-3308},
	url = {http://link.aps.org/doi/10.1103/PhysRevX.4.011047},
	doi = {10.1103/PhysRevX.4.011047},
	abstract = {Discovering and characterizing the large-scale topological features in empirical networks are crucial steps in understanding how complex systems function. However, most existing methods used to obtain the modular structure of networks suffer from serious problems, such as being oblivious to the statistical evidence supporting the discovered patterns, which results in the inability to separate actual structure from noise. In addition to this, one also observes a resolution limit on the size of communities, where smaller but well-defined clusters are not detectable when the network becomes large. This phenomenon occurs not only for the very popular approach of modularity optimization, which lacks built-in statistical validation, but also for more principled methods based on statistical inference and model selection, which do incorporate statistical validation in a formally correct way. Here we construct a nested generative model that, through a complete description of the entire network hierarchy at multiple scales, is capable of avoiding this limitation, and enables the detection of modular structure at levels far beyond those possible with current approaches. Even with this increased resolution, the method is based on the principle of parsimony, and is capable of separating signal from noise, and thus will not lead to the identification of spurious modules even on sparse networks. Furthermore, it fully generalizes other approaches in that it is not restricted to purely assortative mixing patterns, directed or undirected graphs, and ad hoc hierarchical structures such as binary trees. Despite its general character, the approach is tractable, and can be combined with advanced techniques of community detection to yield an efficient algorithm that scales well for very large networks.},
	number = {1},
	journal = {Physical Review X},
	author = {Peixoto, Tiago P.},
	month = mar,
	year = {2014},
	keywords = {Complex systems, Interdisciplinary physics, Statistical physics},
	pages = {011047},
}

Discovering and characterizing the large-scale topological features in empirical networks are crucial steps in understanding how complex systems function. However, most existing methods used to obtain the modular structure of networks suffer from serious problems, such as being oblivious to the statistical evidence supporting the discovered patterns, which results in the inability to separate actual structure from noise. In addition to this, one also observes a resolution limit on the size of communities, where smaller but well-defined clusters are not detectable when the network becomes large. This phenomenon occurs not only for the very popular approach of modularity optimization, which lacks built-in statistical validation, but also for more principled methods based on statistical inference and model selection, which do incorporate statistical validation in a formally correct way. Here we construct a nested generative model that, through a complete description of the entire network hierarchy at multiple scales, is capable of avoiding this limitation, and enables the detection of modular structure at levels far beyond those possible with current approaches. Even with this increased resolution, the method is based on the principle of parsimony, and is capable of separating signal from noise, and thus will not lead to the identification of spurious modules even on sparse networks. Furthermore, it fully generalizes other approaches in that it is not restricted to purely assortative mixing patterns, directed or undirected graphs, and ad hoc hierarchical structures such as binary trees. Despite its general character, the approach is tractable, and can be combined with advanced techniques of community detection to yield an efficient algorithm that scales well for very large networks.

@article{pinter-wollmanDynamicsAnimalSocial2014,
	title = {The dynamics of animal social networks: analytical, conceptual, and theoretical advances},
	volume = {25},
	issn = {1045-2249, 1465-7279},
	shorttitle = {The dynamics of animal social networks},
	url = {https://academic.oup.com/beheco/article-lookup/doi/10.1093/beheco/art047},
	doi = {10.1093/beheco/art047},
	abstract = {Social network analysis provides a broad and complex perspective on animal sociality that is widely applicable to almost any species. Recent applications demonstrate the utility of network analysis for advancing our understanding of the dynamics, selection pressures, development, and evolution of complex social systems. However, most studies of animal social networks rely primarily on a descriptive approach. To propel the field of animal social networks beyond exploratory analyses and to facilitate the integration of quantitative methods that allow for the testing of ecologically and evolutionarily relevant hypotheses, we review methodological and conceptual advances in network science, which are underutilized in studies of animal sociality. First, we highlight how the use of statistical modeling and triadic motifs analysis can advance our understanding of the processes that structure networks. Second, we discuss how the consideration of temporal changes and spatial constraints can shed light on the dynamics of social networks. Third, we consider how the study of variation at multiple scales can potentially transform our understanding of the structure and function of animal networks. We direct readers to analytical tools that facilitate the adoption of these new concepts and methods. Our goal is to provide behavioral ecologists with a toolbox of current methods that can stimulate novel insights into the ecological influences and evolutionary pressures structuring networks and advance our understanding of the proximate and ultimate processes that drive animal sociality.},
	language = {en},
	number = {2},
	urldate = {2025-02-19},
	journal = {Behavioral Ecology},
	author = {Pinter-Wollman, N. and Hobson, E. A. and Smith, J. E. and Edelman, A. J. and Shizuka, D. and De Silva, S. and Waters, J. S. and Prager, S. D. and Sasaki, T. and Wittemyer, G. and Fewell, J. and McDonald, D. B.},
	month = mar,
	year = {2014},
	pages = {242--255},
}

Social network analysis provides a broad and complex perspective on animal sociality that is widely applicable to almost any species. Recent applications demonstrate the utility of network analysis for advancing our understanding of the dynamics, selection pressures, development, and evolution of complex social systems. However, most studies of animal social networks rely primarily on a descriptive approach. To propel the field of animal social networks beyond exploratory analyses and to facilitate the integration of quantitative methods that allow for the testing of ecologically and evolutionarily relevant hypotheses, we review methodological and conceptual advances in network science, which are underutilized in studies of animal sociality. First, we highlight how the use of statistical modeling and triadic motifs analysis can advance our understanding of the processes that structure networks. Second, we discuss how the consideration of temporal changes and spatial constraints can shed light on the dynamics of social networks. Third, we consider how the study of variation at multiple scales can potentially transform our understanding of the structure and function of animal networks. We direct readers to analytical tools that facilitate the adoption of these new concepts and methods. Our goal is to provide behavioral ecologists with a toolbox of current methods that can stimulate novel insights into the ecological influences and evolutionary pressures structuring networks and advance our understanding of the proximate and ultimate processes that drive animal sociality.

@article{szulkinInbreedingAvoidanceTolerance2013a,
	title = {Inbreeding avoidance, tolerance, or preference in animals?},
	volume = {28},
	copyright = {https://www.elsevier.com/tdm/userlicense/1.0/},
	issn = {01695347},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0169534712002893},
	doi = {10.1016/j.tree.2012.10.016},
	language = {en},
	number = {4},
	urldate = {2025-03-31},
	journal = {Trends in Ecology \& Evolution},
	author = {Szulkin, Marta and Stopher, Katie V. and Pemberton, Josephine M. and Reid, Jane M.},
	month = apr,
	year = {2013},
	pages = {205--211},
}

@article{szulkinInbreedingAvoidanceTolerance2013,
	title = {Inbreeding avoidance, tolerance, or preference in animals?},
	volume = {28},
	copyright = {https://www.elsevier.com/tdm/userlicense/1.0/},
	issn = {01695347},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0169534712002893},
	doi = {10.1016/j.tree.2012.10.016},
	language = {en},
	number = {4},
	urldate = {2025-03-31},
	journal = {Trends in Ecology \& Evolution},
	author = {Szulkin, Marta and Stopher, Katie V. and Pemberton, Josephine M. and Reid, Jane M.},
	month = apr,
	year = {2013},
	pages = {205--211},
}

@article{lindholmMateChoiceGenetic2013,
	title = {Mate choice for genetic compatibility in the house mouse},
	volume = {3},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2045-7758, 2045-7758},
	url = {https://onlinelibrary.wiley.com/doi/10.1002/ece3.534},
	doi = {10.1002/ece3.534},
	abstract = {Abstract
            
              In house mice, genetic compatibility is influenced by the
              t
              haplotype, a driving selfish genetic element with a recessive lethal allele, imposing fundamental costs on mate choice decisions. Here, we evaluate the cost of genetic incompatibility and its implication for mate choice in a wild house mice population. In laboratory reared mice, we detected no fertility (number of embryos) or fecundity (ability to conceive) costs of the
              t
              , and yet we found a high cost of genetic incompatibility: heterozygote crosses produced 40\% smaller birth litter sizes because of prenatal mortality. Surprisingly, transmission of
              t
              in crosses using +/
              t
              males was influenced by female genotype, consistent with postcopulatory female choice for + sperm in +/
              t
              females. Analysis of paternity patterns in a wild population of house mice showed that +/
              t
              females were more likely than +/+ females to have offspring sired by +/+ males, and unlike +/+ females, paternity of their offspring was not influenced by +/
              t
              male frequency, further supporting mate choice for genetic compatibility. As the major histocompatibility complex (
              MHC
              ) is physically linked to the
              t
              , we investigated whether females could potentially use variation at the
              MHC
              to identify male genotype at the sperm or individual level. A unique
              MHC
              haplotype is linked to the
              t
              haplotype. This
              MHC
              haplotype could allow the recognition of
              t
              and enable pre‐ and postcopulatory mate choice for genetic compatibility. Alternatively, the
              MHC
              itself could be the target of mate choice for genetic compatibility. We predict that mate choice for genetic compatibility will be difficult to find in many systems, as only weak fertilization biases were found despite an exceptionally high cost of genetic incompatibility.},
	language = {en},
	number = {5},
	urldate = {2025-03-23},
	journal = {Ecology and Evolution},
	author = {Lindholm, Anna K. and Musolf, Kerstin and Weidt, Andrea and König, Barbara},
	month = may,
	year = {2013},
	pages = {1231--1247},
}

Abstract In house mice, genetic compatibility is influenced by the t haplotype, a driving selfish genetic element with a recessive lethal allele, imposing fundamental costs on mate choice decisions. Here, we evaluate the cost of genetic incompatibility and its implication for mate choice in a wild house mice population. In laboratory reared mice, we detected no fertility (number of embryos) or fecundity (ability to conceive) costs of the t , and yet we found a high cost of genetic incompatibility: heterozygote crosses produced 40% smaller birth litter sizes because of prenatal mortality. Surprisingly, transmission of t in crosses using +/ t males was influenced by female genotype, consistent with postcopulatory female choice for + sperm in +/ t females. Analysis of paternity patterns in a wild population of house mice showed that +/ t females were more likely than +/+ females to have offspring sired by +/+ males, and unlike +/+ females, paternity of their offspring was not influenced by +/ t male frequency, further supporting mate choice for genetic compatibility. As the major histocompatibility complex ( MHC ) is physically linked to the t , we investigated whether females could potentially use variation at the MHC to identify male genotype at the sperm or individual level. A unique MHC haplotype is linked to the t haplotype. This MHC haplotype could allow the recognition of t and enable pre‐ and postcopulatory mate choice for genetic compatibility. Alternatively, the MHC itself could be the target of mate choice for genetic compatibility. We predict that mate choice for genetic compatibility will be difficult to find in many systems, as only weak fertilization biases were found despite an exceptionally high cost of genetic incompatibility.

@article{brettoHypergraphTheory2013,
	title = {Hypergraph theory},
	volume = {1},
	journal = {An introduction. Mathematical Engineering. Cham: Springer},
	publisher = {Springer},
	author = {Bretto, Alain},
	year = {2013},
}

@article{bianconiStatisticalMechanicsMultiplex2013,
	title = {Statistical mechanics of multiplex networks: {Entropy} and overlap},
	volume = {87},
	copyright = {http://link.aps.org/licenses/aps-default-license},
	issn = {1539-3755, 1550-2376},
	shorttitle = {Statistical mechanics of multiplex networks},
	url = {https://link.aps.org/doi/10.1103/PhysRevE.87.062806},
	doi = {10.1103/PhysRevE.87.062806},
	language = {en},
	number = {6},
	urldate = {2025-02-12},
	journal = {Physical Review E},
	author = {Bianconi, Ginestra},
	month = jun,
	year = {2013},
	pages = {062806},
}

@article{robinsonAssortativeMatingRelatedness2012,
	title = {Assortative mating for relatedness in a large naturally occurring population of \textit{{Drosophila} melanogaster}},
	volume = {25},
	issn = {1010-061X, 1420-9101},
	url = {https://academic.oup.com/jeb/article/25/4/716-725/7318247},
	doi = {10.1111/j.1420-9101.2012.02466.x},
	abstract = {New theoretical work on kin selection and inclusive fitness benefits predicts that individuals will sometimes choose close or intermediate relatives as mates to maximize their fitness. However, empirical examples supporting such predictions are rare. In this study, we look for such evidence in a natural population of Drosophila melanogaster. We compared mating and nonmating individuals to test whether mating was nonrandom with respect to relatedness. Consistent with optimal inbreeding, males were more closely related to their mate than to randomly sampled females. However, all individuals collected mating showed higher relatedness and males were not significantly more related to their mate than to other mating females. We also found a negative relationship between relatedness and fecundity. Our results are consistent with the hypothesis that inclusive fitness benefits may drive inbreeding tolerance despite direct costs to fitness; however, an experimental approach is needed to investigate the link between mate preference and relatedness.},
	language = {en},
	number = {4},
	urldate = {2025-03-31},
	journal = {Journal of Evolutionary Biology},
	author = {Robinson, S. P. and Kennington, W. J. and Simmons, L. W.},
	month = apr,
	year = {2012},
	pages = {716--725},
}

New theoretical work on kin selection and inclusive fitness benefits predicts that individuals will sometimes choose close or intermediate relatives as mates to maximize their fitness. However, empirical examples supporting such predictions are rare. In this study, we look for such evidence in a natural population of Drosophila melanogaster. We compared mating and nonmating individuals to test whether mating was nonrandom with respect to relatedness. Consistent with optimal inbreeding, males were more closely related to their mate than to randomly sampled females. However, all individuals collected mating showed higher relatedness and males were not significantly more related to their mate than to other mating females. We also found a negative relationship between relatedness and fecundity. Our results are consistent with the hypothesis that inclusive fitness benefits may drive inbreeding tolerance despite direct costs to fitness; however, an experimental approach is needed to investigate the link between mate preference and relatedness.

@incollection{konigComplexSocialEnvironment2012,
	title = {The complex social environment of female house mice ({Mus} domesticus)},
	booktitle = {Evolution of the {House} {Mouse}},
	publisher = {Cambridge University Press},
	author = {König, Barbara and Lindholm, Anna K},
	year = {2012},
	pages = {114--134},
}

@article{cheptouEnvironmentdependentInbreedingDepression2011,
	title = {Environment‐dependent inbreeding depression: its ecological and evolutionary significance},
	volume = {189},
	copyright = {http://onlinelibrary.wiley.com/termsAndConditions\#vor},
	issn = {0028-646X, 1469-8137},
	shorttitle = {Environment‐dependent inbreeding depression},
	url = {https://nph.onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2010.03541.x},
	doi = {10.1111/j.1469-8137.2010.03541.x},
	abstract = {Summary
            Inbreeding depression is a major evolutionary and ecological force that influences population dynamics and the evolution of inbreeding‐avoidance traits such as mating systems and dispersal. There is now compelling evidence that inbreeding depression is environment‐dependent. Here, we discuss ecological and evolutionary consequences of environment‐dependent inbreeding depression. The environmental dependence of inbreeding depression may be caused by environment‐dependent phenotypic expression, environment‐dependent dominance, and environment‐dependent natural selection. The existence of environment‐dependent inbreeding depression challenges classical models of inbreeding as caused by unconditionally deleterious alleles, and suggests that balancing selection may shape inbreeding depression in natural populations; loci associated with inbreeding depression in some environments may even contribute to adaptation to others. Environment‐dependent inbreeding depression also has important, often neglected, ecological and evolutionary consequences: it can influence the demography of marginal or colonizing populations and alter adaptive optima of mating systems, dispersal, and their associated traits. Incorporating the environmental dependence of inbreeding depression into theoretical models and empirical studies is necessary for understanding the genetic and ecological basis of inbreeding depression and its consequences in natural populations.
            
              
                
                  
                  
                  
                  
                    
                      
                      Contents
                      
                    
                  
                  
                    
                      
                      Summary
                      395
                    
                    
                      I.
                      
                        Introduction
                      
                      396
                    
                    
                      II.
                      
                        What is inbreeding depression?
                      
                      396
                    
                    
                      III.
                      
                        Causes of environment‐dependent inbreeding depression
                      
                      397
                    
                    
                      IV.
                      
                        Ecological and evolutionary consequences of environment‐dependent inbreeding depression
                      
                      401
                    
                    
                      V.
                      
                        Feedbacks when inbreeding depression influences the environment
                      
                      404
                    
                    
                      VI.
                      
                        Conclusions and future directions
                      
                      405
                    
                    
                      
                      
                        Acknowledgements
                      
                      406
                    
                    
                      
                      
                        References
                      
                      406},
	language = {en},
	number = {2},
	urldate = {2025-03-30},
	journal = {New Phytologist},
	author = {Cheptou, Pierre‐Olivier and Donohue, Kathleen},
	month = jan,
	year = {2011},
	pages = {395--407},
}

Summary Inbreeding depression is a major evolutionary and ecological force that influences population dynamics and the evolution of inbreeding‐avoidance traits such as mating systems and dispersal. There is now compelling evidence that inbreeding depression is environment‐dependent. Here, we discuss ecological and evolutionary consequences of environment‐dependent inbreeding depression. The environmental dependence of inbreeding depression may be caused by environment‐dependent phenotypic expression, environment‐dependent dominance, and environment‐dependent natural selection. The existence of environment‐dependent inbreeding depression challenges classical models of inbreeding as caused by unconditionally deleterious alleles, and suggests that balancing selection may shape inbreeding depression in natural populations; loci associated with inbreeding depression in some environments may even contribute to adaptation to others. Environment‐dependent inbreeding depression also has important, often neglected, ecological and evolutionary consequences: it can influence the demography of marginal or colonizing populations and alter adaptive optima of mating systems, dispersal, and their associated traits. Incorporating the environmental dependence of inbreeding depression into theoretical models and empirical studies is necessary for understanding the genetic and ecological basis of inbreeding depression and its consequences in natural populations. Contents Summary 395 I. Introduction 396 II. What is inbreeding depression? 396 III. Causes of environment‐dependent inbreeding depression 397 IV. Ecological and evolutionary consequences of environment‐dependent inbreeding depression 401 V. Feedbacks when inbreeding depression influences the environment 404 VI. Conclusions and future directions 405 Acknowledgements 406 References 406

@article{kellerQuantificationInbreedingDue2011,
	title = {Quantification of inbreeding due to distant ancestors and {Its} detection using dense single nucleotide polymorphism data},
	volume = {189},
	copyright = {https://academic.oup.com/journals/pages/open\_access/funder\_policies/chorus/standard\_publication\_model},
	issn = {1943-2631},
	url = {https://academic.oup.com/genetics/article/189/1/237/6064009},
	doi = {10.1534/genetics.111.130922},
	abstract = {Abstract
            Inbreeding depression, which refers to reduced fitness among offspring of related parents, has traditionally been studied using pedigrees. In practice, pedigree information is difficult to obtain, potentially unreliable, and rarely assessed for inbreeding arising from common ancestors who lived more than a few generations ago. Recently, there has been excitement about using SNP data to estimate inbreeding (F) arising from distant common ancestors in apparently “outbred” populations. Statistical power to detect inbreeding depression using SNP data depends on the actual variation in inbreeding in a population, the accuracy of detecting that with marker data, the effect size, and the sample size. No one has yet investigated what variation in F is expected in SNP data as a function of population size, and it is unclear which estimate of F is optimal for detecting inbreeding depression. In the present study, we use theory, simulated genetic data, and real genetic data to find the optimal estimate of F, to quantify the likely variation in F in populations of various sizes, and to estimate the power to detect inbreeding depression. We find that F estimated from runs of homozygosity (Froh), which reflects shared ancestry of genetic haplotypes, retains variation in even large populations (e.g., SD = 0.5\% when Ne = 10,000) and is likely to be the most powerful method of detecting inbreeding effects from among several alternative estimates of F. However, large samples (e.g., 12,000–65,000) will be required to detect inbreeding depression for likely effect sizes, and so studies using Froh to date have probably been underpowered.},
	language = {en},
	number = {1},
	urldate = {2025-03-22},
	journal = {Genetics},
	author = {Keller, Matthew C and Visscher, Peter M and Goddard, Michael E},
	month = sep,
	year = {2011},
	pages = {237--249},
}

Abstract Inbreeding depression, which refers to reduced fitness among offspring of related parents, has traditionally been studied using pedigrees. In practice, pedigree information is difficult to obtain, potentially unreliable, and rarely assessed for inbreeding arising from common ancestors who lived more than a few generations ago. Recently, there has been excitement about using SNP data to estimate inbreeding (F) arising from distant common ancestors in apparently “outbred” populations. Statistical power to detect inbreeding depression using SNP data depends on the actual variation in inbreeding in a population, the accuracy of detecting that with marker data, the effect size, and the sample size. No one has yet investigated what variation in F is expected in SNP data as a function of population size, and it is unclear which estimate of F is optimal for detecting inbreeding depression. In the present study, we use theory, simulated genetic data, and real genetic data to find the optimal estimate of F, to quantify the likely variation in F in populations of various sizes, and to estimate the power to detect inbreeding depression. We find that F estimated from runs of homozygosity (Froh), which reflects shared ancestry of genetic haplotypes, retains variation in even large populations (e.g., SD = 0.5% when Ne = 10,000) and is likely to be the most powerful method of detecting inbreeding effects from among several alternative estimates of F. However, large samples (e.g., 12,000–65,000) will be required to detect inbreeding depression for likely effect sizes, and so studies using Froh to date have probably been underpowered.

@article{manserPolyandryDecreaseSelfish2011,
	title = {Polyandry and the decrease of a selfish genetic element in a wild mouse population},
	volume = {65},
	copyright = {http://doi.wiley.com/10.1002/tdm\_license\_1.1},
	issn = {00143820},
	shorttitle = {{POLYANDRY} {AND} {THE} {DECREASE} {OF} {A} {SELFISH} {GENETIC} {ELEMENT} {IN} {A} {WILD} {HOUSE} {MOUSE} {POPULATION}},
	url = {https://academic.oup.com/evolut/article/65/9/2435/6854778},
	doi = {10.1111/j.1558-5646.2011.01336.x},
	language = {en},
	number = {9},
	urldate = {2025-03-19},
	journal = {Evolution},
	author = {Manser, Andri and Lindholm, Anna K. and König, Barbara and Bagheri, Homayoun C.},
	month = sep,
	year = {2011},
	pages = {2435--2447},
}

@article{angeloniMetaanalysisAssociationPopulation2011,
	title = {Meta-analysis on the association of population size and life history with inbreeding depression in plants},
	volume = {144},
	copyright = {https://www.elsevier.com/tdm/userlicense/1.0/},
	issn = {00063207},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0006320710003733},
	doi = {10.1016/j.biocon.2010.08.016},
	language = {en},
	number = {1},
	urldate = {2025-03-19},
	journal = {Biological Conservation},
	author = {Angeloni, Francesco and Ouborg, N. Joop and Leimu, Roosa},
	month = jan,
	year = {2011},
	pages = {35--43},
}

@article{rosvallMultilevelCompressionRandom2011,
	title = {Multilevel {Compression} of {Random} {Walks} on {Networks} {Reveals} {Hierarchical} {Organization} in {Large} {Integrated} {Systems}},
	volume = {6},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0018209},
	doi = {10.1371/journal.pone.0018209},
	abstract = {To comprehend the hierarchical organization of large integrated systems, we introduce the hierarchical map equation, which reveals multilevel structures in networks. In this information-theoretic approach, we exploit the duality between compression and pattern detection; by compressing a description of a random walker as a proxy for real flow on a network, we find regularities in the network that induce this system-wide flow. Finding the shortest multilevel description of the random walker therefore gives us the best hierarchical clustering of the network - the optimal number of levels and modular partition at each level - with respect to the dynamics on the network. With a novel search algorithm, we extract and illustrate the rich multilevel organization of several large social and biological networks. For example, from the global air traffic network we uncover countries and continents, and from the pattern of scientific communication we reveal more than 100 scientific fields organized in four major disciplines: life sciences, physical sciences, ecology and earth sciences, and social sciences. In general, we find shallow hierarchical structures in globally interconnected systems, such as neural networks, and rich multilevel organizations in systems with highly separated regions, such as road networks. © 2011 Rosvall, Bergstrom.},
	number = {4},
	journal = {PLoS ONE},
	author = {Rosvall, Martin and Bergstrom, Carl T.},
	editor = {Rapallo, Fabio},
	month = apr,
	year = {2011},
	pages = {e18209},
}

To comprehend the hierarchical organization of large integrated systems, we introduce the hierarchical map equation, which reveals multilevel structures in networks. In this information-theoretic approach, we exploit the duality between compression and pattern detection; by compressing a description of a random walker as a proxy for real flow on a network, we find regularities in the network that induce this system-wide flow. Finding the shortest multilevel description of the random walker therefore gives us the best hierarchical clustering of the network - the optimal number of levels and modular partition at each level - with respect to the dynamics on the network. With a novel search algorithm, we extract and illustrate the rich multilevel organization of several large social and biological networks. For example, from the global air traffic network we uncover countries and continents, and from the pattern of scientific communication we reveal more than 100 scientific fields organized in four major disciplines: life sciences, physical sciences, ecology and earth sciences, and social sciences. In general, we find shallow hierarchical structures in globally interconnected systems, such as neural networks, and rich multilevel organizations in systems with highly separated regions, such as road networks. © 2011 Rosvall, Bergstrom.

@article{bittlesConsanguinityHumanEvolution2010,
	title = {Consanguinity, human evolution, and complex diseases},
	volume = {107},
	issn = {0027-8424, 1091-6490},
	url = {https://pnas.org/doi/full/10.1073/pnas.0906079106},
	doi = {10.1073/pnas.0906079106},
	abstract = {There is little information on inbreeding during the critical early years of human existence. However, given the small founding group sizes and restricted mate choices it seems inevitable that intrafamilial reproduction occurred and the resultant levels of inbreeding would have been substantial. Currently, couples related as second cousins or closer ( 
              F 
              ≥ 0.0156) and their progeny account for an estimated 10.4\% of the global population. The highest rates of consanguineous marriage occur in north and sub-Saharan Africa, the Middle East, and west, central, and south Asia. In these regions even couples who regard themselves as unrelated may exhibit high levels of homozygosity, because marriage within clan, tribe, caste, or biraderi boundaries has been a long-established tradition. Mortality in first-cousin progeny is ≈3.5\% higher than in nonconsanguineous offspring, although demographic, social, and economic factors can significantly influence the outcome. Improving socioeconomic conditions and better access to health care will impact the effects of consanguinity, with a shift from infant and childhood mortality to extended morbidity. At the same time, a range of primarily social factors, including urbanization, improved female education, and smaller family sizes indicate that the global prevalence of consanguineous unions will decline. This shift in marriage patterns will initially result in decreased homozygosity, accompanied by a reduction in the expression of recessive single-gene disorders. Although the roles of common and rare gene variants in the etiology of complex disease remain contentious, it would be expected that declining consanguinity would also be reflected in reduced prevalence of complex diseases, especially in population isolates.},
	language = {en},
	number = {suppl\_1},
	urldate = {2025-03-19},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Bittles, A. H. and Black, M. L.},
	month = jan,
	year = {2010},
	pages = {1779--1786},
}

There is little information on inbreeding during the critical early years of human existence. However, given the small founding group sizes and restricted mate choices it seems inevitable that intrafamilial reproduction occurred and the resultant levels of inbreeding would have been substantial. Currently, couples related as second cousins or closer ( F ≥ 0.0156) and their progeny account for an estimated 10.4% of the global population. The highest rates of consanguineous marriage occur in north and sub-Saharan Africa, the Middle East, and west, central, and south Asia. In these regions even couples who regard themselves as unrelated may exhibit high levels of homozygosity, because marriage within clan, tribe, caste, or biraderi boundaries has been a long-established tradition. Mortality in first-cousin progeny is ≈3.5% higher than in nonconsanguineous offspring, although demographic, social, and economic factors can significantly influence the outcome. Improving socioeconomic conditions and better access to health care will impact the effects of consanguinity, with a shift from infant and childhood mortality to extended morbidity. At the same time, a range of primarily social factors, including urbanization, improved female education, and smaller family sizes indicate that the global prevalence of consanguineous unions will decline. This shift in marriage patterns will initially result in decreased homozygosity, accompanied by a reduction in the expression of recessive single-gene disorders. Although the roles of common and rare gene variants in the etiology of complex disease remain contentious, it would be expected that declining consanguinity would also be reflected in reduced prevalence of complex diseases, especially in population isolates.

@article{agrawalEnvironmentalDuressEpistasis2010,
	title = {Environmental duress and epistasis: how does stress affect the strength of selection on new mutations?},
	volume = {25},
	copyright = {https://www.elsevier.com/tdm/userlicense/1.0/},
	issn = {01695347},
	shorttitle = {Environmental duress and epistasis},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0169534710001023},
	doi = {10.1016/j.tree.2010.05.003},
	language = {en},
	number = {8},
	urldate = {2025-03-19},
	journal = {Trends in Ecology \& Evolution},
	author = {Agrawal, Aneil F. and Whitlock, Michael C.},
	month = aug,
	year = {2010},
	pages = {450--458},
}

@article{snijdersIntroductionStochasticActorbased2010,
	title = {Introduction to stochastic actor-based models for network dynamics},
	volume = {32},
	copyright = {https://www.elsevier.com/tdm/userlicense/1.0/},
	issn = {03788733},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378873309000069},
	doi = {10.1016/j.socnet.2009.02.004},
	abstract = {Stochastic actor-based models are models for network dynamics that can represent a wide variety of influences on network change, and allow to estimate parameters expressing such influences, and test corresponding hypotheses. The nodes in the network represent social actors, and the collection of ties represents a social relation. The assumptions posit that the network evolves as a stochastic process ‘driven by the actors’, i.e., the model lends itself especially for representing theories about how actors change their outgoing ties. The probabilities of tie changes are in part endogenously determined, i.e., as a function of the current network structure itself, and in part exogenously, as a function of characteristics of the nodes (‘actor covariates’) and of characteristics of pairs of nodes (‘dyadic covariates’). In an extended form, stochastic actor-based models can be used to analyze longitudinal data on social networks jointly with changing attributes of the actors: dynamics of networks and behavior.},
	language = {en},
	number = {1},
	urldate = {2025-02-26},
	journal = {Social Networks},
	author = {Snijders, Tom A.B. and Van De Bunt, Gerhard G. and Steglich, Christian E.G.},
	month = jan,
	year = {2010},
	pages = {44--60},
}

Stochastic actor-based models are models for network dynamics that can represent a wide variety of influences on network change, and allow to estimate parameters expressing such influences, and test corresponding hypotheses. The nodes in the network represent social actors, and the collection of ties represents a social relation. The assumptions posit that the network evolves as a stochastic process ‘driven by the actors’, i.e., the model lends itself especially for representing theories about how actors change their outgoing ties. The probabilities of tie changes are in part endogenously determined, i.e., as a function of the current network structure itself, and in part exogenously, as a function of characteristics of the nodes (‘actor covariates’) and of characteristics of pairs of nodes (‘dyadic covariates’). In an extended form, stochastic actor-based models can be used to analyze longitudinal data on social networks jointly with changing attributes of the actors: dynamics of networks and behavior.

@article{ilmonenFemalesPreferScent2009,
	title = {Females prefer the scent of outbred males: good-genes-as-heterozygosity?},
	volume = {9},
	issn = {1471-2148},
	shorttitle = {Females prefer the scent of outbred males},
	url = {http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-9-104},
	doi = {10.1186/1471-2148-9-104},
	language = {en},
	number = {1},
	urldate = {2025-03-30},
	journal = {BMC Evolutionary Biology},
	author = {Ilmonen, Petteri and Stundner, Gloria and ThoSZ, Michaela and Penn, Dustin J.},
	year = {2009},
	pages = {104},
}

@article{szulkinDispersalMeansInbreeding2008,
	title = {Dispersal as a means of inbreeding avoidance in a wild bird population},
	volume = {275},
	issn = {0962-8452, 1471-2954},
	url = {https://royalsocietypublishing.org/doi/10.1098/rspb.2007.0989},
	doi = {10.1098/rspb.2007.0989},
	abstract = {The long-term study of animal populations facilitates detailed analysis of processes otherwise difficult to measure, and whose significance may appear only when a large sample size from many years is available for analysis. For example, inbreeding is a rare event in most natural populations, and therefore many years of data are needed to estimate its effect on fitness. A key behaviour hypothesized to play an important role in avoiding inbreeding is natal dispersal. However, the functional significance of natal dispersal with respect to inbreeding has been much debated but subject to very few empirical tests. We analysed 44 years of data from a wild great tit
              Parus major
              population involving over 5000 natal dispersal events within Wytham Woods, UK. Individuals breeding with a relative dispersed over several-fold shorter distances than those outbreeding; within the class of inbreeding birds, increased inbreeding was associated with reduced dispersal distance, for both males and females. This led to a 3.4-fold increase (2.3–5, 95\% CI) in the likelihood of close (
              f
              =0.25) inbreeding relative to the population average when individuals dispersed less than 200 m. In the light of our results, and published evidence showing little support for active inbreeding avoidance in vertebrates, we suggest that dispersal should be considered as a mechanism of prime importance for inbreeding avoidance in wild populations.},
	language = {en},
	number = {1635},
	urldate = {2025-03-30},
	journal = {Proceedings of the Royal Society B: Biological Sciences},
	author = {Szulkin, Marta and Sheldon, Ben C},
	month = mar,
	year = {2008},
	pages = {703--711},
}

The long-term study of animal populations facilitates detailed analysis of processes otherwise difficult to measure, and whose significance may appear only when a large sample size from many years is available for analysis. For example, inbreeding is a rare event in most natural populations, and therefore many years of data are needed to estimate its effect on fitness. A key behaviour hypothesized to play an important role in avoiding inbreeding is natal dispersal. However, the functional significance of natal dispersal with respect to inbreeding has been much debated but subject to very few empirical tests. We analysed 44 years of data from a wild great tit Parus major population involving over 5000 natal dispersal events within Wytham Woods, UK. Individuals breeding with a relative dispersed over several-fold shorter distances than those outbreeding; within the class of inbreeding birds, increased inbreeding was associated with reduced dispersal distance, for both males and females. This led to a 3.4-fold increase (2.3–5, 95% CI) in the likelihood of close ( f =0.25) inbreeding relative to the population average when individuals dispersed less than 200 m. In the light of our results, and published evidence showing little support for active inbreeding avoidance in vertebrates, we suggest that dispersal should be considered as a mechanism of prime importance for inbreeding avoidance in wild populations.

@article{wrightInbreedingInbreedingDepression2008,
	title = {Inbreeding, inbreeding depression and extinction},
	volume = {9},
	issn = {1572-9737},
	url = {https://doi.org/10.1007/s10592-007-9405-0},
	doi = {10.1007/s10592-007-9405-0},
	abstract = {Inbreeding is unavoidable in small, isolated populations and can cause substantial fitness reductions compared to outbred populations. This loss of fitness has been predicted to elevate extinction risk giving it substantial conservation significance. Inbreeding may result in reduced fitness for two reasons: an increased expression of deleterious recessive alleles (partial dominance hypothesis) or the loss of favourable heterozygote combinations (overdominance hypothesis). Because both these sources of inbreeding depression are dependent upon dominance variance, inbreeding depression is predicted to be greater in life history traits than in morphological traits. In this study we used replicate inbred and control lines of Drosophila simulans to address three questions:1) is inbreeding depression greater in life history than morphological traits? 2) which of the two hypotheses is the major underlying cause of inbreeding depression? 3) does inbreeding elevate population extinction risk? We found that inbreeding depression was significantly greater in life history traits compared to morphological traits, but were unable to find unequivocal support for either the overdominance or partial dominance hypotheses as the genetic basis of inbreeding depression. As predicted, inbred lines had a significantly greater extinction risk.},
	language = {en},
	number = {4},
	urldate = {2025-03-19},
	journal = {Conservation Genetics},
	author = {Wright, Lucy I. and Tregenza, Tom and Hosken, David J.},
	month = aug,
	year = {2008},
	keywords = {Dominance, Drosophila simulans, Extinction risk, Purging},
	pages = {833--843},
}

Inbreeding is unavoidable in small, isolated populations and can cause substantial fitness reductions compared to outbred populations. This loss of fitness has been predicted to elevate extinction risk giving it substantial conservation significance. Inbreeding may result in reduced fitness for two reasons: an increased expression of deleterious recessive alleles (partial dominance hypothesis) or the loss of favourable heterozygote combinations (overdominance hypothesis). Because both these sources of inbreeding depression are dependent upon dominance variance, inbreeding depression is predicted to be greater in life history traits than in morphological traits. In this study we used replicate inbred and control lines of Drosophila simulans to address three questions:1) is inbreeding depression greater in life history than morphological traits? 2) which of the two hypotheses is the major underlying cause of inbreeding depression? 3) does inbreeding elevate population extinction risk? We found that inbreeding depression was significantly greater in life history traits compared to morphological traits, but were unable to find unequivocal support for either the overdominance or partial dominance hypotheses as the genetic basis of inbreeding depression. As predicted, inbred lines had a significantly greater extinction risk.

@article{weySocialNetworkAnalysis2008,
	title = {Social network analysis of animal behaviour: a promising tool for the study of sociality},
	volume = {75},
	number = {2},
	journal = {Animal behaviour},
	publisher = {Elsevier},
	author = {Wey, Tina and Blumstein, Daniel T and Shen, Weiwei and Jordán, Ferenc},
	year = {2008},
	pages = {333--344},
}

@article{sherborneGeneticBasisInbreeding2007,
	title = {The genetic basis of inbreeding avoidance in house mice},
	volume = {17},
	copyright = {https://www.elsevier.com/tdm/userlicense/1.0/},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982207021380},
	doi = {10.1016/j.cub.2007.10.041},
	language = {en},
	number = {23},
	urldate = {2025-03-25},
	journal = {Current Biology},
	author = {Sherborne, Amy L. and Thom, Michael D. and Paterson, Steve and Jury, Francine and Ollier, William E.R. and Stockley, Paula and Beynon, Robert J. and Hurst, Jane L.},
	month = dec,
	year = {2007},
	pages = {2061--2066},
}

@article{dekkerSensitivityMRQAPTests2007,
	title = {Sensitivity of {MRQAP} {Tests} to {Collinearity} and {Autocorrelation} {Conditions}},
	volume = {72},
	copyright = {https://www.cambridge.org/core/terms},
	issn = {0033-3123, 1860-0980},
	url = {https://www.cambridge.org/core/product/identifier/S0033312300022444/type/journal_article},
	doi = {10.1007/s11336-007-9016-1},
	abstract = {Multiple regression quadratic assignment procedures (MRQAP) tests are permutation tests for multiple linear regression model coefficients for data organized in square matrices of relatedness among n objects. Such a data structure is typical in social network studies, where variables indicate some type of relation between a given set of actors. We present a new permutation method (called “double semipartialing”, or DSP) that complements the family of extant approaches to MRQAP tests. We assess the statistical bias (type I error rate) and statistical power of the set of five methods, including DSP, across a variety of conditions of network autocorrelation, of spuriousness (size of confounder effect), and of skewness in the data. These conditions are explored across three assumed data distributions: normal, gamma, and negative binomial. We find that the Freedman–Lane method and the DSP method are the most robust against a wide array of these conditions. We also find that all five methods perform better if the test statistic is pivotal. Finally, we find limitations of usefulness for MRQAP tests: All tests degrade under simultaneous conditions of extreme skewness and high spuriousness for gamma and negative binomial distributions.},
	language = {en},
	number = {4},
	urldate = {2025-02-19},
	journal = {Psychometrika},
	author = {Dekker, David and Krackhardt, David and Snijders, Tom A. B.},
	month = dec,
	year = {2007},
	pages = {563--581},
}

Multiple regression quadratic assignment procedures (MRQAP) tests are permutation tests for multiple linear regression model coefficients for data organized in square matrices of relatedness among n objects. Such a data structure is typical in social network studies, where variables indicate some type of relation between a given set of actors. We present a new permutation method (called “double semipartialing”, or DSP) that complements the family of extant approaches to MRQAP tests. We assess the statistical bias (type I error rate) and statistical power of the set of five methods, including DSP, across a variety of conditions of network autocorrelation, of spuriousness (size of confounder effect), and of skewness in the data. These conditions are explored across three assumed data distributions: normal, gamma, and negative binomial. We find that the Freedman–Lane method and the DSP method are the most robust against a wide array of these conditions. We also find that all five methods perform better if the test statistic is pivotal. Finally, we find limitations of usefulness for MRQAP tests: All tests degrade under simultaneous conditions of extreme skewness and high spuriousness for gamma and negative binomial distributions.

@article{fortunatoResolutionLimitCommunity2007,
	title = {Resolution limit in community detection},
	volume = {104},
	issn = {0027-8424},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0605965104},
	doi = {10.1073/pnas.0605965104},
	abstract = {Detecting community structure is fundamental for uncovering the links between structure and function in complex networks and for practical applications in many disciplines such as biology and sociology. A popular method now widely used relies on the optimization of a quantity called modularity, which is a quality index for a partition of a network into communities. We find that modularity optimization may fail to identify modules smaller than a scale which depends on the total size of the network and on the degree of interconnectedness of the modules, even in cases where modules are unambiguously defined. This finding is confirmed through several examples, both in artificial and in real social, biological, and technological networks, where we show that modularity optimization indeed does not resolve a large number of modules. A check of the modules obtained through modularity optimization is thus necessary, and we provide here key elements for the assessment of the reliability of this community detection method.},
	number = {1},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Fortunato, Santo and Barthelemy, M.},
	month = jan,
	year = {2007},
	pages = {36--41},
}

Detecting community structure is fundamental for uncovering the links between structure and function in complex networks and for practical applications in many disciplines such as biology and sociology. A popular method now widely used relies on the optimization of a quantity called modularity, which is a quality index for a partition of a network into communities. We find that modularity optimization may fail to identify modules smaller than a scale which depends on the total size of the network and on the degree of interconnectedness of the modules, even in cases where modules are unambiguously defined. This finding is confirmed through several examples, both in artificial and in real social, biological, and technological networks, where we show that modularity optimization indeed does not resolve a large number of modules. A check of the modules obtained through modularity optimization is thus necessary, and we provide here key elements for the assessment of the reliability of this community detection method.

@article{kokkoWhenNotAvoid2006,
	title = {When not to avoid inbreeding},
	volume = {60},
	copyright = {http://onlinelibrary.wiley.com/termsAndConditions\#vor},
	issn = {0014-3820, 1558-5646},
	url = {https://academic.oup.com/evolut/article/60/3/467/6756586},
	doi = {10.1111/j.0014-3820.2006.tb01128.x},
	language = {en},
	number = {3},
	urldate = {2025-03-30},
	journal = {Evolution},
	author = {Kokko, Hanna and Ots, Indrek},
	month = mar,
	year = {2006},
	pages = {467--475},
}

@article{croquetInbreedingDepressionGlobal2006,
	title = {Inbreeding {Depression} for {Global} and {Partial} {Economic} {Indexes}, {Production}, {Type}, and {Functional} {Traits}},
	volume = {89},
	copyright = {https://www.elsevier.com/tdm/userlicense/1.0/},
	issn = {00220302},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0022030206722974},
	doi = {10.3168/jds.S0022-0302(06)72297-4},
	language = {en},
	number = {6},
	urldate = {2025-03-25},
	journal = {Journal of Dairy Science},
	author = {Croquet, C. and Mayeres, P. and Gillon, A. and Vanderick, S. and Gengler, N.},
	month = jun,
	year = {2006},
	pages = {2257--2267},
}

@article{ogradyRealisticLevelsInbreeding2006,
	title = {Realistic levels of inbreeding depression strongly affect extinction risk in wild populations},
	volume = {133},
	copyright = {https://www.elsevier.com/tdm/userlicense/1.0/},
	issn = {00063207},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0006320706002126},
	doi = {10.1016/j.biocon.2006.05.016},
	language = {en},
	number = {1},
	urldate = {2025-03-19},
	journal = {Biological Conservation},
	author = {O’Grady, Julian J. and Brook, Barry W. and Reed, David H. and Ballou, Jonathan D. and Tonkyn, David W. and Frankham, Richard},
	month = nov,
	year = {2006},
	pages = {42--51},
}

@article{newmanModularityCommunityStructure2006,
	title = {Modularity and community structure in networks},
	volume = {103},
	issn = {0027-8424},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0601602103},
	doi = {10.1073/pnas.0601602103},
	abstract = {Many networks of interest in the sciences, including social networks, computer networks, and metabolic and regulatory networks, are found to divide naturally into communities or modules. The problem of detecting and characterizing this community structure is one of the outstanding issues in the study of networked systems. One highly effective approach is the optimization of the quality function known as "modularity" over the possible divisions of a network. Here I show that the modularity can be expressed in terms of the eigenvectors of a characteristic matrix for the network, which I call the modularity matrix, and that this expression leads to a spectral algorithm for community detection that returns results of demonstrably higher quality than competing methods in shorter running times. I illustrate the method with applications to several published network data sets.},
	number = {23},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Newman, M. E. J.},
	month = jun,
	year = {2006},
	pages = {8577--8582},
}

Many networks of interest in the sciences, including social networks, computer networks, and metabolic and regulatory networks, are found to divide naturally into communities or modules. The problem of detecting and characterizing this community structure is one of the outstanding issues in the study of networked systems. One highly effective approach is the optimization of the quality function known as "modularity" over the possible divisions of a network. Here I show that the modularity can be expressed in terms of the eigenvectors of a characteristic matrix for the network, which I call the modularity matrix, and that this expression leads to a spectral algorithm for community detection that returns results of demonstrably higher quality than competing methods in shorter running times. I illustrate the method with applications to several published network data sets.

@article{armbrusterInbreedingDepressionBenign2005,
	title = {Inbreeding depression in benign and stressful environments},
	volume = {95},
	copyright = {http://www.springer.com/tdm},
	issn = {0018-067X, 1365-2540},
	url = {https://www.nature.com/articles/6800721},
	doi = {10.1038/sj.hdy.6800721},
	language = {en},
	number = {3},
	urldate = {2025-03-22},
	journal = {Heredity},
	author = {Armbruster, P and Reed, D H},
	month = sep,
	year = {2005},
	pages = {235--242},
}

@article{newmanStructureFunctionComplex2003,
	title = {The {Structure} and {Function} of {Complex} {Networks}},
	volume = {45},
	issn = {1958-5969},
	url = {http://arxiv.org/abs/cond-mat/0303516},
	doi = {10.1137/S003614450342480},
	abstract = {Inspired by empirical studies of networked systems such as the Internet, social networks, and biological networks, researchers have in recent years developed a variety of techniques and models to help us understand or predict the behavior of these systems. Here we review developments in this field, including such concepts as the small-world effect, degree distributions, clustering, network correlations, random graph models, models of network growth and preferential attachment, and dynamical processes taking place on networks.},
	number = {2},
	journal = {SIAM REVIEW},
	author = {Newman, Mark E. J.},
	year = {2003},
	keywords = {05c75, 05c90, 94c15, Animals, Brain, Brain Mapping, Brain Mapping: methods, Brain: anatomy \& histology, Brain: physiology, Disordered Systems and Neural Networks, FNSA, Humans, Nerve Net, Nerve Net: anatomy \& histology, Nerve Net: physiology, Neural Pathways, Neural Pathways: anatomy \& histology, Neural Pathways: physiology, Neuroimaging, Neuroimaging: methods, Psychomotor Performance, Psychomotor Performance: physiology, Rest, Rest: physiology, Statistical Mechanics, ams subject classifications, complex systems, computer networks, graph theory, graphs, networks, percolation theory, pii, random, s0036144503424804, social networks},
	pages = {167--256},
}

Inspired by empirical studies of networked systems such as the Internet, social networks, and biological networks, researchers have in recent years developed a variety of techniques and models to help us understand or predict the behavior of these systems. Here we review developments in this field, including such concepts as the small-world effect, degree distributions, clustering, network correlations, random graph models, models of network growth and preferential attachment, and dynamical processes taking place on networks.

@article{kellerInbreedingEffectsWild2002,
	title = {Inbreeding effects in wild populations},
	volume = {17},
	copyright = {https://www.elsevier.com/tdm/userlicense/1.0/},
	issn = {01695347},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0169534702024898},
	doi = {10.1016/S0169-5347(02)02489-8},
	number = {5},
	urldate = {2025-03-25},
	journal = {Trends in Ecology \& Evolution},
	author = {Keller, Lukas F. and Waller, Donald M.},
	month = may,
	year = {2002},
	pages = {230--241},
}

@article{wangEstimatorPairwiseRelatedness2002,
	title = {An estimator for pairwise relatedness using molecular markers},
	volume = {160},
	number = {3},
	journal = {Genetics},
	publisher = {Oxford University Press},
	author = {Wang, Jinliang},
	year = {2002},
	pages = {1203--1215},
}

@article{macyFactorsActorsComputational2002,
	title = {From factors to actors: {Computational} sociology and agent-based modeling},
	volume = {28},
	number = {1},
	journal = {Annual review of sociology},
	publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA},
	author = {Macy, Michael W and Willer, Robert},
	year = {2002},
	pages = {143--166},
}

@article{meagherMaleMaleCompetition2000,
	title = {Male–male competition magnifies inbreeding depression in wild house mice},
	volume = {97},
	issn = {0027-8424, 1091-6490},
	url = {https://pnas.org/doi/full/10.1073/pnas.97.7.3324},
	doi = {10.1073/pnas.97.7.3324},
	abstract = {The detrimental effects of inbreeding on vertebrates are well documented for early stages of the life cycle in the laboratory. However, the consequences of inbreeding on long-term survival and reproductive success (Darwinian fitness) are uncertain for vertebrates in the wild. Here, we report direct experimental evidence for vertebrates that competition increases the harmful effects of inbreeding on offspring survival and reproduction. We compared the fitness of inbred (from full-sib matings) and outbred wild house mice (
              Mus domesticus
              ) in large, seminatural enclosures. Inbred males sired only one-fifth as many surviving offspring as outbred males because of their poor competitive ability and survivorship. In laboratory conditions, inbreeding had relatively minor effects on male reproductive success and no effect on survivorship. Seminatural conditions did not increase inbreeding depression for females, probably because females were not competing for any critical resources. The overall reduction in fitness from inbreeding was 57\%, which is 4.5 times as great as previous estimates from the laboratory. These results have important implications for medicine, conservation, evolutionary biology, and functional genomics.},
	language = {en},
	number = {7},
	urldate = {2025-03-22},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Meagher, Shawn and Penn, Dustin J. and Potts, Wayne K.},
	month = mar,
	year = {2000},
	pages = {3324--3329},
}

The detrimental effects of inbreeding on vertebrates are well documented for early stages of the life cycle in the laboratory. However, the consequences of inbreeding on long-term survival and reproductive success (Darwinian fitness) are uncertain for vertebrates in the wild. Here, we report direct experimental evidence for vertebrates that competition increases the harmful effects of inbreeding on offspring survival and reproduction. We compared the fitness of inbred (from full-sib matings) and outbred wild house mice ( Mus domesticus ) in large, seminatural enclosures. Inbred males sired only one-fifth as many surviving offspring as outbred males because of their poor competitive ability and survivorship. In laboratory conditions, inbreeding had relatively minor effects on male reproductive success and no effect on survivorship. Seminatural conditions did not increase inbreeding depression for females, probably because females were not competing for any critical resources. The overall reduction in fitness from inbreeding was 57%, which is 4.5 times as great as previous estimates from the laboratory. These results have important implications for medicine, conservation, evolutionary biology, and functional genomics.

@article{pennEvolutionMatingPreferences1999,
	title = {The evolution of mating preferences and major histocompatibility complex genes},
	volume = {153},
	issn = {0003-0147, 1537-5323},
	url = {https://www.journals.uchicago.edu/doi/10.1086/303166},
	doi = {10.1086/303166},
	language = {en},
	number = {2},
	urldate = {2025-03-25},
	journal = {The American Naturalist},
	author = {Penn, Dustin J. and Potts, Wayne K.},
	month = feb,
	year = {1999},
	pages = {145--164},
}

@article{crnokrakInbreedingDepressionWild1999,
	title = {Inbreeding depression in the wild},
	volume = {83},
	copyright = {http://www.springer.com/tdm},
	issn = {0018-067X, 1365-2540},
	url = {https://www.nature.com/articles/6885530},
	doi = {10.1038/sj.hdy.6885530},
	language = {en},
	number = {3},
	urldate = {2025-03-25},
	journal = {Heredity},
	author = {Crnokrak, Peter and Roff, Derek A},
	month = sep,
	year = {1999},
	pages = {260--270},
}

@book{falconerIntroductionQuantitativeGenetics1996,
	address = {Harlow},
	edition = {4. ed., [16. print.]},
	title = {Introduction to quantitative genetics},
	isbn = {978-0-582-24302-6},
	language = {eng},
	publisher = {Pearson, Prentice Hall},
	author = {Falconer, Douglas S. and Mackay, Trudy},
	year = {1996},
}

@article{eklundEffectsInbreedingAggression1996,
	title = {The effects of inbreeding on aggression in wild male house mice ({Mus} domesticus)},
	volume = {133},
	issn = {0005-7959, 1568-539X},
	url = {https://brill.com/view/journals/beh/133/11-12/article-p883_5.xml},
	doi = {10.1163/156853996X00297},
	abstract = {This study examined the effect of inbreeding on aggression levels and competitive ability in wild male house mice. Wild mice were bred in the laboratory to produce males of three levels of inbreeding: male offspring of unrelated parents, male offspring of first-cousin parents, and male offspring of full-sibling parents. Paired encounters were staged between males of the three offspring groups, when the males reached maturity. Less inbred males won more encounters and tended to have higher scores of aggression level than more inbred males. If competitive ability in the laboratory is related to competitive ability in nature, wild mice from this population may benefit from avoiding inbreeding and the consequent decrease in aggression levels and competitive ability.},
	number = {11-12},
	urldate = {2025-03-25},
	journal = {Behaviour},
	author = {Eklund, Amy},
	year = {1996},
	pages = {883--901},
}

This study examined the effect of inbreeding on aggression levels and competitive ability in wild male house mice. Wild mice were bred in the laboratory to produce males of three levels of inbreeding: male offspring of unrelated parents, male offspring of first-cousin parents, and male offspring of full-sibling parents. Paired encounters were staged between males of the three offspring groups, when the males reached maturity. Less inbred males won more encounters and tended to have higher scores of aggression level than more inbred males. If competitive ability in the laboratory is related to competitive ability in nature, wild mice from this population may benefit from avoiding inbreeding and the consequent decrease in aggression levels and competitive ability.

@article{millerInbreedingDepressionMore1994,
	title = {Is inbreeding depression more severe in a stressful environment?},
	volume = {13},
	copyright = {http://onlinelibrary.wiley.com/termsAndConditions\#vor},
	issn = {0733-3188, 1098-2361},
	url = {https://onlinelibrary.wiley.com/doi/10.1002/zoo.1430130302},
	doi = {10.1002/zoo.1430130302},
	abstract = {Abstract
            
              Successful reintroduction of endangered species depends in part on their ability to respond to changing environmental conditions. Population genetics theory suggests that inbred populations lacking genetic variability may be unable to respond effectively to environmental stress. There have been very few studies designed explicitly to investigate the phenomenon of inbreeding depression under environmental stress, particularly in the context of conservation genetics. Three separate experiments using
              Drosophila melanogaster
              were designed to explore this issue. No increase in the magnitude of inbreeding depression was detected in laboratory lines subjected to three generations of continuous full‐sib mating under temperature stress (28°C), lead stress (medium contaminated with 400 ppm Pb), or a combination of these stresses. Individual isofemale lines from a different population, however, did show significant increases in inbreeding depression when exposed to temperature stress for one generation of full‐sib mating following three generations of full‐sib inbreeding at 25°C. Further, chromosome‐2 homozygotes showed, on average, a significant increase in inbreeding depression under lead stress when in competition with corresponding chromosome‐2 heterozygotes compared to the same lines in a benign environment. Taken together, these results suggest that inbreeding depression is more severe under conditions of environmental stress and is more likely to be realized in an inter‐ or intraspecific competitive situation as can be experienced in the wild. Therefore, it is likely that reduced genetic variability through inbreeding is a much greater problem for recently reintroduced populations than it is for populations in a relatively benign zoo environment. © 1994 Wiley‐Liss, Inc.},
	language = {en},
	number = {3},
	urldate = {2025-03-22},
	journal = {Zoo Biology},
	author = {Miller, Philip S.},
	month = jan,
	year = {1994},
	pages = {195--208},
}

Abstract Successful reintroduction of endangered species depends in part on their ability to respond to changing environmental conditions. Population genetics theory suggests that inbred populations lacking genetic variability may be unable to respond effectively to environmental stress. There have been very few studies designed explicitly to investigate the phenomenon of inbreeding depression under environmental stress, particularly in the context of conservation genetics. Three separate experiments using Drosophila melanogaster were designed to explore this issue. No increase in the magnitude of inbreeding depression was detected in laboratory lines subjected to three generations of continuous full‐sib mating under temperature stress (28°C), lead stress (medium contaminated with 400 ppm Pb), or a combination of these stresses. Individual isofemale lines from a different population, however, did show significant increases in inbreeding depression when exposed to temperature stress for one generation of full‐sib mating following three generations of full‐sib inbreeding at 25°C. Further, chromosome‐2 homozygotes showed, on average, a significant increase in inbreeding depression under lead stress when in competition with corresponding chromosome‐2 heterozygotes compared to the same lines in a benign environment. Taken together, these results suggest that inbreeding depression is more severe under conditions of environmental stress and is more likely to be realized in an inter‐ or intraspecific competitive situation as can be experienced in the wild. Therefore, it is likely that reduced genetic variability through inbreeding is a much greater problem for recently reintroduced populations than it is for populations in a relatively benign zoo environment. © 1994 Wiley‐Liss, Inc.

@article{charlesworthMutationAccumulationFinite1993,
	title = {Mutation accumulation in finite outbreeding and inbreeding populations},
	volume = {61},
	copyright = {https://www.cambridge.org/core/terms},
	issn = {0016-6723, 1469-5073},
	url = {https://www.cambridge.org/core/product/identifier/S0016672300031086/type/journal_article},
	doi = {10.1017/S0016672300031086},
	abstract = {Summary 
            We have carried out an investigation of the effects of various parameters on the accumulation of deleterious mutant alleles in finite diploid populations. Two different processes contribute to mutation accumulation. In random-mating populations of very small size and with tight linkage, fixation of mutant alleles occurs at a high rate, but decreases with extremely tight linkage. With very restricted recombination, the numbers of low-frequency mutant alleles per genome in randommating populations increase over time independently of fixation (Muller's ratchet). Increased population size affects the ratchet less than the fixation process, and the decline in population fitness is dominated by the ratchet in populations of size greater than about 100, especially with high mutation rates. The effects of differences in the selection parameters (strength of selection, dominance coefficient), of multiplicative versus synergistic selection, and of different amounts of inbreeding, are complex, but can be interpreted in terms of opposing effects of selection on individual loci and associations between loci. Stronger selection slows the accumulation of mutations, though a faster decline in mean fitness sometimes results. Increasing dominance tends to have a similar effect to greater strength of selection. High inbreeding slows the ratchet, because the increased homozygous expression of mutant alleles in inbred populations has effects similar to stronger selection, and because with inbreeding there is a higher initial frequency of the least loaded class. Fixation of deleterious mutations is accelerated in highly inbred populations. Even with inbreeding, sexual populations larger than 100 will probably rarely experience mutation accumulation to the point that their survival is endangered because neither fixation nor the ratchet has effects of the magnitude seen in asexual populations. The effects of breeding system and rate of recombination on the rate of molecular evolution by the fixation of slightly deleterious alleles are discussed.},
	language = {en},
	number = {1},
	urldate = {2025-03-19},
	journal = {Genetical Research},
	author = {Charlesworth, D. and Morgan, M. T. and Charlesworth, B.},
	month = feb,
	year = {1993},
	pages = {39--56},
}

Summary We have carried out an investigation of the effects of various parameters on the accumulation of deleterious mutant alleles in finite diploid populations. Two different processes contribute to mutation accumulation. In random-mating populations of very small size and with tight linkage, fixation of mutant alleles occurs at a high rate, but decreases with extremely tight linkage. With very restricted recombination, the numbers of low-frequency mutant alleles per genome in randommating populations increase over time independently of fixation (Muller's ratchet). Increased population size affects the ratchet less than the fixation process, and the decline in population fitness is dominated by the ratchet in populations of size greater than about 100, especially with high mutation rates. The effects of differences in the selection parameters (strength of selection, dominance coefficient), of multiplicative versus synergistic selection, and of different amounts of inbreeding, are complex, but can be interpreted in terms of opposing effects of selection on individual loci and associations between loci. Stronger selection slows the accumulation of mutations, though a faster decline in mean fitness sometimes results. Increasing dominance tends to have a similar effect to greater strength of selection. High inbreeding slows the ratchet, because the increased homozygous expression of mutant alleles in inbred populations has effects similar to stronger selection, and because with inbreeding there is a higher initial frequency of the least loaded class. Fixation of deleterious mutations is accelerated in highly inbred populations. Even with inbreeding, sexual populations larger than 100 will probably rarely experience mutation accumulation to the point that their survival is endangered because neither fixation nor the ratchet has effects of the magnitude seen in asexual populations. The effects of breeding system and rate of recombination on the rate of molecular evolution by the fixation of slightly deleterious alleles are discussed.

@article{besagGeneralizedMonteCarlo1989,
	title = {Generalized monte carlo significance tests},
	volume = {76},
	number = {4},
	journal = {Biometrika},
	publisher = {Oxford University Press},
	author = {Besag, Julian and Clifford, Peter},
	year = {1989},
	pages = {633--642},
}

@article{krackhardtPredictingNetworksNonparametric1988,
	title = {Predicting with networks: {Nonparametric} multiple regression analysis of dyadic data},
	volume = {10},
	copyright = {https://www.elsevier.com/tdm/userlicense/1.0/},
	issn = {03788733},
	shorttitle = {Predicting with networks},
	url = {https://linkinghub.elsevier.com/retrieve/pii/0378873388900044},
	doi = {10.1016/0378-8733(88)90004-4},
	language = {en},
	number = {4},
	urldate = {2025-02-26},
	journal = {Social Networks},
	author = {Krackhardt, David},
	month = dec,
	year = {1988},
	pages = {359--381},
}

@article{charlesworthInbreedingDepressionIts1987,
	title = {Inbreeding depression and its evolutionary consequences},
	volume = {18},
	issn = {0066-4162},
	url = {https://www.annualreviews.org/doi/10.1146/annurev.es.18.110187.001321},
	doi = {10.1146/annurev.es.18.110187.001321},
	language = {en},
	number = {1},
	urldate = {2025-03-19},
	journal = {Annual Review of Ecology and Systematics},
	author = {Charlesworth, D. and Charlesworth, B.},
	month = nov,
	year = {1987},
	pages = {237--268},
}

@article{maccluerPedigreeAnalysisComputer1986,
	title = {Pedigree analysis by computer simulation},
	volume = {5},
	copyright = {Copyright © 1986 Wiley-Liss, Inc., A Wiley Company},
	issn = {1098-2361},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/zoo.1430050209},
	doi = {10.1002/zoo.1430050209},
	abstract = {Computer simulation is a valuable tool in the genetic management of captive populations. It can be used to assess the extent of genetic variability in a colony, to predict the risk of future loss of variability, or to identify likely ancestral sources of traits of interest. “Gene dropping” is a simulation procedure in which hypothetical alleles are assigned to each colony founder, and a genotype is created for each descendant by Mendelian segregation of parental alleles. The gene dropping method is applied to analyses of four populations: (1) a colony of small South American marsupials, Monodelphis domestica; (2) Speke's gazelles, Gazella spekei; (3) Przewalski's horses, Equus przewalskii; and (4) American Standardbred horses.},
	language = {en},
	number = {2},
	urldate = {2025-03-26},
	journal = {Zoo Biology},
	author = {MacCluer, Jean W. and VandeBerg, John L. and Read, Bruce and Ryder, Oliver A.},
	year = {1986},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/zoo.1430050209},
	keywords = {gene dropping, genetic management},
	pages = {147--160},
}

Computer simulation is a valuable tool in the genetic management of captive populations. It can be used to assess the extent of genetic variability in a colony, to predict the risk of future loss of variability, or to identify likely ancestral sources of traits of interest. “Gene dropping” is a simulation procedure in which hypothetical alleles are assigned to each colony founder, and a genotype is created for each descendant by Mendelian segregation of parental alleles. The gene dropping method is applied to analyses of four populations: (1) a colony of small South American marsupials, Monodelphis domestica; (2) Speke's gazelles, Gazella spekei; (3) Przewalski's horses, Equus przewalskii; and (4) American Standardbred horses.

@article{landeEvolutionSelffertilizationInbreeding1985,
	title = {The evolution of self-fertilization and inbreeding depression in plants. {I}. {Genetic} models.},
	volume = {39},
	copyright = {http://onlinelibrary.wiley.com/termsAndConditions\#vor},
	issn = {0014-3820, 1558-5646},
	url = {https://academic.oup.com/evolut/article/39/1/24/6872321},
	doi = {10.1111/j.1558-5646.1985.tb04077.x},
	language = {en},
	number = {1},
	urldate = {2025-03-30},
	journal = {Evolution},
	author = {Lande, Russell and Schemske, Douglas W.},
	month = jan,
	year = {1985},
	pages = {24--40},
}

@article{harveyNullModelsEcology1983,
	title = {Null {Models} in {Ecology}},
	volume = {14},
	issn = {0066-4162},
	url = {https://www.annualreviews.org/doi/10.1146/annurev.es.14.110183.001201},
	doi = {10.1146/annurev.es.14.110183.001201},
	language = {en},
	number = {1},
	urldate = {2025-02-21},
	journal = {Annual Review of Ecology and Systematics},
	author = {Harvey, P H and Colwell, R K and Silvertown, J W and May, R M},
	month = nov,
	year = {1983},
	pages = {189--211},
}

@article{bengtssonAvoidingInbreedingWhat1978,
	title = {Avoiding inbreeding: at what cost?},
	volume = {73},
	copyright = {https://www.elsevier.com/tdm/userlicense/1.0/},
	issn = {00225193},
	shorttitle = {Avoiding inbreeding},
	url = {https://linkinghub.elsevier.com/retrieve/pii/0022519378901510},
	doi = {10.1016/0022-5193(78)90151-0},
	language = {en},
	number = {3},
	urldate = {2025-03-30},
	journal = {Journal of Theoretical Biology},
	author = {Bengtsson, B.O.},
	month = aug,
	year = {1978},
	pages = {439--444},
}

@article{freemanCentralitySocialNetworks1978,
	title = {Centrality in social networks conceptual clarification},
	volume = {1},
	number = {3},
	journal = {Social Networks},
	publisher = {Elsevier},
	author = {Freeman, Linton C},
	year = {1978},
	pages = {215--239},
}

@article{hamiltonDispersalStableHabitats1977,
	title = {Dispersal in stable habitats},
	volume = {269},
	copyright = {http://www.springer.com/tdm},
	issn = {0028-0836, 1476-4687},
	url = {https://www.nature.com/articles/269578a0},
	doi = {10.1038/269578a0},
	language = {en},
	number = {5629},
	urldate = {2025-03-30},
	journal = {Nature},
	author = {Hamilton, W. D. and May, Robert M.},
	month = oct,
	year = {1977},
	pages = {578--581},
}

@article{makarFormateAssayBody1975,
	title = {Formate assay in body fluids: application in methanol poisoning},
	volume = {13},
	issn = {0006-2944},
	shorttitle = {Formate assay in body fluids},
	doi = {10.1016/0006-2944(75)90147-7},
	language = {eng},
	number = {2},
	journal = {Biochemical Medicine},
	author = {Makar, A. B. and McMartin, K. E. and Palese, M. and Tephly, T. R.},
	month = jun,
	year = {1975},
	keywords = {Aldehyde Oxidoreductases, Animals, Body Fluids, Carbon Dioxide, Formates, Haplorhini, Humans, Hydrogen-Ion Concentration, Kinetics, Methanol, Methods, Pseudomonas},
	pages = {117--126},
}

@article{silenAcidbaseBalanceAmphibian1975,
	title = {Acid-base balance in amphibian gastric mucosa},
	volume = {229},
	issn = {0002-9513},
	doi = {10.1152/ajplegacy.1975.229.3.721},
	abstract = {It has been established that H+ secretion can be maintained in frog stomach in the absence of exogenous CO2 by using a nutrient bathing fluid containing 25 mM H2PO4 (pH approximately equal to 4.5) or by lowering the pH of a nonbuffered nutrient solution to about 3.0-3.6. Exogenous CO2 in the presence of these nutrient solutions uniformly caused a marked decrease in H+ secretion, PD, adn short-circuit current (Isc) and an increase in transmucosal resistance (R). Elevation of nutrient [k+] to 83 mM reduced R significantly but transiently without change in H+ when nutrient pH less than 5.0, whereas R returned to base line and H+ increased when nutrient pH greater than 5.0. Acidification of the nutrient medium in the presence of exogenous CO2 results in inhibition of the secretory pump, probably by decreasing intracellular pH, and also interferes with conductance at the nutrient membrane. Removal of exogenous CO2 from standard bicarbonate nutrient solution reduced by 50\% the H+, PD, and Isc without change in R; K+-free nutrient solutions reverse these changes in Isc and PD but not in H+. The dropping PD and rising R induced by K+-free nutrient solutions in 5\% CO2 - 95\% O2 are returned toward normal by 100\% O2. Our findings support an important role for exogenous CO2 in maintaining normal acid-base balance in frog mucosa by acting as an acidifying agent.},
	language = {eng},
	number = {3},
	journal = {The American Journal of Physiology},
	author = {Silen, W. and Machen, T. E. and Forte, J. G.},
	month = sep,
	year = {1975},
	keywords = {Acid-Base Equilibrium, Animals, Anura, Bicarbonates, Carbon Dioxide, Electrophysiology, Gastric Mucosa, Hydrogen-Ion Concentration, Phosphates, Potassium, Rana catesbeiana, Solutions},
	pages = {721--730},
}

It has been established that H+ secretion can be maintained in frog stomach in the absence of exogenous CO2 by using a nutrient bathing fluid containing 25 mM H2PO4 (pH approximately equal to 4.5) or by lowering the pH of a nonbuffered nutrient solution to about 3.0-3.6. Exogenous CO2 in the presence of these nutrient solutions uniformly caused a marked decrease in H+ secretion, PD, adn short-circuit current (Isc) and an increase in transmucosal resistance (R). Elevation of nutrient [k+] to 83 mM reduced R significantly but transiently without change in H+ when nutrient pH less than 5.0, whereas R returned to base line and H+ increased when nutrient pH greater than 5.0. Acidification of the nutrient medium in the presence of exogenous CO2 results in inhibition of the secretory pump, probably by decreasing intracellular pH, and also interferes with conductance at the nutrient membrane. Removal of exogenous CO2 from standard bicarbonate nutrient solution reduced by 50% the H+, PD, and Isc without change in R; K+-free nutrient solutions reverse these changes in Isc and PD but not in H+. The dropping PD and rising R induced by K+-free nutrient solutions in 5% CO2 - 95% O2 are returned toward normal by 100% O2. Our findings support an important role for exogenous CO2 in maintaining normal acid-base balance in frog mucosa by acting as an acidifying agent.

@article{barthelAggregationBloodPlatelets1975,
	title = {Aggregation of blood platelets by adrenaline and its uptake},
	volume = {24},
	issn = {0006-2952},
	doi = {10.1016/0006-2952(75)90415-3},
	language = {eng},
	number = {20},
	journal = {Biochemical Pharmacology},
	author = {Barthel, W. and Markwardt, F.},
	month = oct,
	year = {1975},
	keywords = {Animals, Blood Platelets, Dihydroergotamine, Drug Interactions, Epinephrine, In Vitro Techniques, Lysergic Acid Diethylamide, Platelet Aggregation, Rabbits},
	pages = {1903--1904},
}

@article{marniemiRadiochemicalAssayGlutathione1975,
	title = {Radiochemical assay of glutathione {S}-epoxide transferase and its enhancement by phenobarbital in rat liver in vivo},
	volume = {24},
	issn = {0006-2952},
	doi = {10.1016/0006-2952(75)90080-5},
	language = {eng},
	number = {17},
	journal = {Biochemical Pharmacology},
	author = {Marniemi, J. and Parkki, M. G.},
	month = sep,
	year = {1975},
	keywords = {Animals, Carrier Proteins, Epoxy Compounds, Glutathione, Glutathione Transferase, Hydrogen-Ion Concentration, Liver, Male, Methylcholanthrene, Phenobarbital, Rats, Stimulation, Chemical, Styrenes},
	pages = {1569--1572},
}

@article{beauchampImprovedIndexCentrality1965,
	title = {An improved index of centrality},
	volume = {10},
	number = {2},
	journal = {Behavioral science},
	publisher = {Wiley Online Library},
	author = {Beauchamp, Murray A},
	year = {1965},
	pages = {161--163},
}

@article{katzNewStatusIndex1953,
	title = {A new status index derived from sociometric analysis},
	volume = {18},
	number = {1},
	journal = {Psychometrika},
	publisher = {Springer-Verlag},
	author = {Katz, Leo},
	year = {1953},
	pages = {39--43},
}

@book{darwinEffectsCrossSelffertilization1876,
	address = {London},
	title = {The effects of cross and self-fertilization in the vegetable kingdom},
	publisher = {John Murray},
	author = {Darwin, Charles},
	year = {1876},
}

@misc{MiceResearch_proposal_2403,
	title = {Mice {Research}\_proposal\_2403},
	url = {https://docs.google.com/document/u/0/d/1WG9t_tDRLG3Fe9lf3Sml4KpwV2XDdH5eJtDtwox4Y5I/edit?fromCopy=true&ct=2&usp=embed_facebook},
	abstract = {Current state of research in the field Inbreeding is a widespread problem. The average decline in population size of wild mammals, bird, fish, reptiles and amphibians is more than 70\% over the last 50 years, based on long term monitoring of nearly 5,500 species (WWF Living Planet Report 2024 A Sy...},
	language = {en-GB},
	urldate = {2025-03-24},
	journal = {Google Docs},
}

Current state of research in the field Inbreeding is a widespread problem. The average decline in population size of wild mammals, bird, fish, reptiles and amphibians is more than 70% over the last 50 years, based on long term monitoring of nearly 5,500 species (WWF Living Planet Report 2024 A Sy...