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\n\n \n \n 2023\n \n \n (3)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Reproductive variance can drive behavioral dynamics.\n \n \n \n \n\n\n \n Wang, G.; Su, Q.; Wang, L.; and Plotkin, J. B.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences, 120(12): e2216218120. March 2023.\n \n\n\n\n
\n\n\n\n \n \n![\"Reproductive](\"//bibbase.org/img/filetypes/link.svg\"\n\t "\\"Paper\\"\n\t")
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\n\n\n@article{wang_reproductive_2023,\n\ttitle = {Reproductive variance can drive behavioral dynamics},\n\tvolume = {120},\n\tissn = {0027-8424, 1091-6490},\n\turl = {https://pnas.org/doi/10.1073/pnas.2216218120},\n\tdoi = {10.1073/pnas.2216218120},\n\tabstract = {The concept of fitness is central to evolution, but it quantifies only the expected number of offspring an individual will produce. The actual number of offspring is also subject to demographic stochasticity—that is, randomness associated with birth and death processes. In nature, individuals who are more fecund tend to have greater variance in their offspring number. Here, we develop a model for the evolution of two types competing in a population of nonconstant size. The fitness of each type is determined by pairwise interactions in a prisoner’s dilemma game, and the variance in offspring number depends upon its mean. Although defectors are preferred by natural selection in classical population models, since they always have greater fitness than cooperators, we show that sufficiently large offspring variance can reverse the direction of evolution and favor cooperation. Large offspring variance produces qualitatively new dynamics for other types of social interactions, as well, which cannot arise in populations with a fixed size or with a Poisson offspring distribution.},\n\tlanguage = {en},\n\tnumber = {12},\n\turldate = {2023-04-17},\n\tjournal = {Proceedings of the National Academy of Sciences},\n\tauthor = {Wang, Guocheng and Su, Qi and Wang, Long and Plotkin, Joshua B.},\n\tmonth = mar,\n\tyear = {2023},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {e2216218120},\n\tfile = {Wang et al. - 2023 - Reproductive variance can drive behavioral dynamic.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\5DXGFT3K\\\\Wang et al. - 2023 - Reproductive variance can drive behavioral dynamic.pdf:application/pdf},\n}\n\n\n\n The concept of fitness is central to evolution, but it quantifies only the expected number of offspring an individual will produce. The actual number of offspring is also subject to demographic stochasticity—that is, randomness associated with birth and death processes. In nature, individuals who are more fecund tend to have greater variance in their offspring number. Here, we develop a model for the evolution of two types competing in a population of nonconstant size. The fitness of each type is determined by pairwise interactions in a prisoner’s dilemma game, and the variance in offspring number depends upon its mean. Although defectors are preferred by natural selection in classical population models, since they always have greater fitness than cooperators, we show that sufficiently large offspring variance can reverse the direction of evolution and favor cooperation. Large offspring variance produces qualitatively new dynamics for other types of social interactions, as well, which cannot arise in populations with a fixed size or with a Poisson offspring distribution.\n
\n\n\n\n \n\n \n \n \n \n \n Coupled environmental and demographic fluctuations shape the evolution of cooperative antimicrobial resistance.\n \n \n \n\n\n \n Hernández-Navarro, L.; Asker, M.; Rucklidge, A. M.; and Mobilia, M\n\n\n \n\n\n\n e-print: TBC. 2023.\n \n\n\n\n
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\n\n\n\n@article{LARM23,\n\ttitle = {Coupled environmental and demographic fluctuations shape the evolution of cooperative antimicrobial resistance},\n\tjournal = {e-print: TBC},\n\tauthor = {Hernández-Navarro, L. and Asker, M. and Rucklidge, A. M. and Mobilia, M},\n\tyear = {2023},\n\tkeywords = {⛔ No INSPIRE recid found},\n}\n\n\n\n \n\n \n \n \n \n \n Evolutionary dynamics in a varying environment: Continuous versus discrete noise.\n \n \n \n\n\n \n Taitelbaum, A.; West, R.; Mobilia, M.; and Assaf, M.\n\n\n \n\n\n\n , 5(2): L022004. 2023.\n \n\n\n\n
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\n\n\n\n@article{taitelbaum2023evolutionary,\n\ttitle = {Evolutionary dynamics in a varying environment: {Continuous} versus discrete noise},\n\tvolume = {5},\n\tnumber = {2},\n\tauthor = {Taitelbaum, Ami and West, Robert and Mobilia, Mauro and Assaf, Michael},\n\tyear = {2023},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {L022004},\n}\n\n\n\n
\n\n \n \n 2022\n \n \n (4)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Moran dynamics in spatially heterogeneous environments with periodic fitness distribution.\n \n \n \n \n\n\n \n Nemati, H.; Ejtehadi, M. R.; and Kaveh, K.\n\n\n \n\n\n\n arXiv:2202.04501 [physics, q-bio]. February 2022.\n arXiv: 2202.04501\n\n\n\n
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\n\n\n@article{nemati_moran_2022,\n\ttitle = {Moran dynamics in spatially heterogeneous environments with periodic fitness distribution},\n\turl = {http://arxiv.org/abs/2202.04501},\n\tabstract = {Local environmental interactions are a major factor in determining the success of a new mutant in structured populations. Spatial variations of concentration of a resource change the fitness of competing strategies locally and thus can drastically change the outcome of evolutionary process in unintuitive ways. Environmental interactions can be asymmetric, i.e. the same local resource value affects the fitness of strategies differently. The question is how such local environmental variations in network population structures change the condition for selection and fixation probability of an advantageous (or deleterious) mutant. We consider linear graph structure and focus on the case where resources have a spatial periodic pattern. Our model covers several biologically relevant cases. We numerically calculate fixation probability and fixation time for a Moran birth-death process as fitness heterogeneity and period vary. The fixation probability is affected by not only the level of fitness heterogeneity, but also spatial scale of resource variations set by period of distribution \\$T\\$. For most (weak) asymmetric environmental interactions the chance of success of a mutant increases with heterogeneity. We identify conditions for which a previously deleterious mutant (in a uniform environment) becomes beneficial as fitness heterogeneity is increased. We observe cases where the fixation probability of both mutant and resident types are less than their neutral value, \\$1/N\\$, simultaneously. This corresponds to potential coexistence of resident and mutant types. Finally, we discuss the effect of 'fitness shift' where the fitness function of two types has a phase difference. This happens when there are more than one type of resources in the environment. We observe significant increase (or decrease) in the fixation probability of the mutant as a result of such phase shift.},\n\tlanguage = {en},\n\turldate = {2022-02-10},\n\tjournal = {arXiv:2202.04501 [physics, q-bio]},\n\tauthor = {Nemati, Hossein and Ejtehadi, Mohammad Reza and Kaveh, Kamran},\n\tmonth = feb,\n\tyear = {2022},\n\tnote = {arXiv: 2202.04501},\n\tkeywords = {unread, on website},\n\tfile = {Nemati et al. - 2022 - Moran dynamics in spatially heterogeneous environm.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\2ZPU4GWJ\\\\Nemati et al. - 2022 - Moran dynamics in spatially heterogeneous environm.pdf:application/pdf},\n}\n\n\n\n Local environmental interactions are a major factor in determining the success of a new mutant in structured populations. Spatial variations of concentration of a resource change the fitness of competing strategies locally and thus can drastically change the outcome of evolutionary process in unintuitive ways. Environmental interactions can be asymmetric, i.e. the same local resource value affects the fitness of strategies differently. The question is how such local environmental variations in network population structures change the condition for selection and fixation probability of an advantageous (or deleterious) mutant. We consider linear graph structure and focus on the case where resources have a spatial periodic pattern. Our model covers several biologically relevant cases. We numerically calculate fixation probability and fixation time for a Moran birth-death process as fitness heterogeneity and period vary. The fixation probability is affected by not only the level of fitness heterogeneity, but also spatial scale of resource variations set by period of distribution $T$. For most (weak) asymmetric environmental interactions the chance of success of a mutant increases with heterogeneity. We identify conditions for which a previously deleterious mutant (in a uniform environment) becomes beneficial as fitness heterogeneity is increased. We observe cases where the fixation probability of both mutant and resident types are less than their neutral value, $1/N$, simultaneously. This corresponds to potential coexistence of resident and mutant types. Finally, we discuss the effect of 'fitness shift' where the fitness function of two types has a phase difference. This happens when there are more than one type of resources in the environment. We observe significant increase (or decrease) in the fixation probability of the mutant as a result of such phase shift.\n
\n\n\n\n \n\n \n \n \n \n \n \n Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis.\n \n \n \n \n\n\n \n Murray, C. J.; Ikuta, K. S.; Sharara, F.; Swetschinski, L.; Aguilar, G. R.; Gray, A.; Han, C.; Bisignano, C.; Rao, P.; Wool, E.; Johnson, S. C.; Browne, A. J.; Chipeta, M. G.; Fell, F.; Hackett, S.; Haines-Woodhouse, G.; Hamadani, B. H. K.; Kumaran, E. A. P.; McManigal, B.; Agarwal, R.; Akech, S.; Albertson, S.; Amuasi, J.; Andrews, J.; Aravkin, A.; Ashley, E.; Bailey, F.; Baker, S.; Basnyat, B.; Bekker, A.; Bender, R.; Bethou, A.; Bielicki, J.; Boonkasidecha, S.; Bukosia, J.; Carvalheiro, C.; Castañeda-Orjuela, C.; Chansamouth, V.; Chaurasia, S.; Chiurchiù, S.; Chowdhury, F.; Cook, A. J.; Cooper, B.; Cressey, T. R.; Criollo-Mora, E.; Cunningham, M.; Darboe, S.; Day, N. P. J.; Luca, M. D.; Dokova, K.; Dramowski, A.; Dunachie, S. J.; Eckmanns, T.; Eibach, D.; Emami, A.; Feasey, N.; Fisher-Pearson, N.; Forrest, K.; Garrett, D.; Gastmeier, P.; Giref, A. Z.; Greer, R. C.; Gupta, V.; Haller, S.; Haselbeck, A.; Hay, S. I.; Holm, M.; Hopkins, S.; Iregbu, K. C.; Jacobs, J.; Jarovsky, D.; Javanmardi, F.; Khorana, M.; Kissoon, N.; Kobeissi, E.; Kostyanev, T.; Krapp, F.; Krumkamp, R.; Kumar, A.; Kyu, H. H.; Lim, C.; Limmathurotsakul, D.; Loftus, M. J.; Lunn, M.; Ma, J.; Mturi, N.; Munera-Huertas, T.; Musicha, P.; Mussi-Pinhata, M. M.; Nakamura, T.; Nanavati, R.; Nangia, S.; Newton, P.; Ngoun, C.; Novotney, A.; Nwakanma, D.; Obiero, C. W.; Olivas-Martinez, A.; Olliaro, P.; Ooko, E.; Ortiz-Brizuela, E.; Peleg, A. Y.; Perrone, C.; Plakkal, N.; Ponce-de-Leon, A.; Raad, M.; Ramdin, T.; Riddell, A.; Roberts, T.; Robotham, J. V.; Roca, A.; Rudd, K. E.; Russell, N.; Schnall, J.; Scott, J. A. G.; Shivamallappa, M.; Sifuentes-Osornio, J.; Steenkeste, N.; Stewardson, A. J.; Stoeva, T.; Tasak, N.; Thaiprakong, A.; Thwaites, G.; Turner, C.; Turner, P.; Doorn, H. R. v.; Velaphi, S.; Vongpradith, A.; Vu, H.; Walsh, T.; Waner, S.; Wangrangsimakul, T.; Wozniak, T.; Zheng, P.; Sartorius, B.; Lopez, A. D.; Stergachis, A.; Moore, C.; Dolecek, C.; and Naghavi, M.\n\n\n \n\n\n\n The Lancet, 399(10325): 629–655. February 2022.\n Publisher: Elsevier\n\n\n\n
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\n\n\n\n@article{murray_global_2022,\n\ttitle = {Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis},\n\tvolume = {399},\n\tissn = {0140-6736, 1474-547X},\n\tshorttitle = {Global burden of bacterial antimicrobial resistance in 2019},\n\turl = {https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(21)02724-0/fulltext},\n\tdoi = {10.1016/S0140-6736(21)02724-0},\n\tlanguage = {English},\n\tnumber = {10325},\n\turldate = {2022-03-15},\n\tjournal = {The Lancet},\n\tauthor = {Murray, Christopher JL and Ikuta, Kevin Shunji and Sharara, Fablina and Swetschinski, Lucien and Aguilar, Gisela Robles and Gray, Authia and Han, Chieh and Bisignano, Catherine and Rao, Puja and Wool, Eve and Johnson, Sarah C. and Browne, Annie J. and Chipeta, Michael Give and Fell, Frederick and Hackett, Sean and Haines-Woodhouse, Georgina and Hamadani, Bahar H. Kashef and Kumaran, Emmanuelle A. P. and McManigal, Barney and Agarwal, Ramesh and Akech, Samuel and Albertson, Samuel and Amuasi, John and Andrews, Jason and Aravkin, Aleskandr and Ashley, Elizabeth and Bailey, Freddie and Baker, Stephen and Basnyat, Buddha and Bekker, Adrie and Bender, Rose and Bethou, Adhisivam and Bielicki, Julia and Boonkasidecha, Suppawat and Bukosia, James and Carvalheiro, Cristina and Castañeda-Orjuela, Carlos and Chansamouth, Vilada and Chaurasia, Suman and Chiurchiù, Sara and Chowdhury, Fazle and Cook, Aislinn J. and Cooper, Ben and Cressey, Tim R. and Criollo-Mora, Elia and Cunningham, Matthew and Darboe, Saffiatou and Day, Nicholas P. J. and Luca, Maia De and Dokova, Klara and Dramowski, Angela and Dunachie, Susanna J. and Eckmanns, Tim and Eibach, Daniel and Emami, Amir and Feasey, Nicholas and Fisher-Pearson, Natasha and Forrest, Karen and Garrett, Denise and Gastmeier, Petra and Giref, Ababi Zergaw and Greer, Rachel Claire and Gupta, Vikas and Haller, Sebastian and Haselbeck, Andrea and Hay, Simon I. and Holm, Marianne and Hopkins, Susan and Iregbu, Kenneth C. and Jacobs, Jan and Jarovsky, Daniel and Javanmardi, Fatemeh and Khorana, Meera and Kissoon, Niranjan and Kobeissi, Elsa and Kostyanev, Tomislav and Krapp, Fiorella and Krumkamp, Ralf and Kumar, Ajay and Kyu, Hmwe Hmwe and Lim, Cherry and Limmathurotsakul, Direk and Loftus, Michael James and Lunn, Miles and Ma, Jianing and Mturi, Neema and Munera-Huertas, Tatiana and Musicha, Patrick and Mussi-Pinhata, Marisa Marcia and Nakamura, Tomoka and Nanavati, Ruchi and Nangia, Sushma and Newton, Paul and Ngoun, Chanpheaktra and Novotney, Amanda and Nwakanma, Davis and Obiero, Christina W. and Olivas-Martinez, Antonio and Olliaro, Piero and Ooko, Ednah and Ortiz-Brizuela, Edgar and Peleg, Anton Yariv and Perrone, Carlo and Plakkal, Nishad and Ponce-de-Leon, Alfredo and Raad, Mathieu and Ramdin, Tanusha and Riddell, Amy and Roberts, Tamalee and Robotham, Julie Victoria and Roca, Anna and Rudd, Kristina E. and Russell, Neal and Schnall, Jesse and Scott, John Anthony Gerard and Shivamallappa, Madhusudhan and Sifuentes-Osornio, Jose and Steenkeste, Nicolas and Stewardson, Andrew James and Stoeva, Temenuga and Tasak, Nidanuch and Thaiprakong, Areerat and Thwaites, Guy and Turner, Claudia and Turner, Paul and Doorn, H. Rogier van and Velaphi, Sithembiso and Vongpradith, Avina and Vu, Huong and Walsh, Timothy and Waner, Seymour and Wangrangsimakul, Tri and Wozniak, Teresa and Zheng, Peng and Sartorius, Benn and Lopez, Alan D. and Stergachis, Andy and Moore, Catrin and Dolecek, Christiane and Naghavi, Mohsen},\n\tmonth = feb,\n\tyear = {2022},\n\tpmid = {35065702},\n\tnote = {Publisher: Elsevier},\n\tkeywords = {unread, ⛔ No INSPIRE recid found},\n\tpages = {629--655},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\LCFE27SP\\\\Murray et al. - 2022 - Global burden of bacterial antimicrobial resistanc.pdf:application/pdf;Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\W7A63ABC\\\\fulltext.html:text/html},\n}\n\n\n\n \n\n \n \n \n \n \n Extending the Monod model of microbal growth with memory.\n \n \n \n\n\n \n Amirian, M. M.; Irwin, A. J.; and Finkel, Z. V.\n\n\n \n\n\n\n Frontiers in Marine Science, 9. 2022.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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\n\n\n\n@article{amirian_extending_2022,\n\ttitle = {Extending the {Monod} model of microbal growth with memory},\n\tvolume = {9},\n\tjournal = {Frontiers in Marine Science},\n\tauthor = {Amirian, Mohammad M. and Irwin, Andrew J. and Finkel, Zoe V.},\n\tyear = {2022},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tfile = {Amirian et al. - 2022 - Extending the Monod model of microbal growth with .pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\CXG5GSQC\\\\Amirian et al. - 2022 - Extending the Monod model of microbal growth with .pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Quantitative characteristics of stabilizing and equalizing mechanisms.\n \n \n \n\n\n \n West, R.; and Shnerb, N. M.\n\n\n \n\n\n\n American Naturalist, 88: E160. 2022.\n \n\n\n\n
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\n\n\n\n@article{West22,\n\ttitle = {Quantitative characteristics of stabilizing and equalizing mechanisms},\n\tvolume = {88},\n\tdoi = {10.1086/720665},\n\tjournal = {American Naturalist},\n\tauthor = {West, R. and Shnerb, N. M.},\n\tyear = {2022},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {E160},\n\tfile = {West and Shnerb - 2022 - Quantitative characteristics of stabilizing and eq.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\NMIPNU2M\\\\West and Shnerb - 2022 - Quantitative characteristics of stabilizing and eq.pdf:application/pdf},\n}\n\n\n\n
\n\n \n \n 2021\n \n \n (7)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Exclusion of the fittest predicts microbial community diversity in fluctuating environments.\n \n \n \n \n\n\n \n Shibasaki, S.; Mobilia, M.; and Mitri, S.\n\n\n \n\n\n\n Journal of The Royal Society Interface, 18(183): 20210613. 2021.\n Publisher: Royal Society\n\n\n\n
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\n\n\n@article{shibasaki_exclusion_2021,\n\ttitle = {Exclusion of the fittest predicts microbial community diversity in fluctuating environments},\n\tvolume = {18},\n\turl = {https://royalsocietypublishing.org/doi/10.1098/rsif.2021.0613},\n\tdoi = {10.1098/rsif.2021.0613},\n\tabstract = {Microorganisms live in environments that inevitably fluctuate between mild and harsh conditions. As harsh conditions may cause extinctions, the rate at which fluctuations occur can shape microbial communities and their diversity, but we still lack an intuition on how. Here, we build a mathematical model describing two microbial species living in an environment where substrate supplies randomly switch between abundant and scarce. We then vary the rate of switching as well as different properties of the interacting species, and measure the probability of the weaker species driving the stronger one extinct. We find that this probability increases with the strength of demographic noise under harsh conditions and peaks at either low, high, or intermediate switching rates depending on both species’ ability to withstand the harsh environment. This complex relationship shows why finding patterns between environmental fluctuations and diversity has historically been difficult. In parameter ranges where the fittest species was most likely to be excluded, however, the beta diversity in larger communities also peaked. In sum, how environmental fluctuations affect interactions between a few species pairs predicts their effect on the beta diversity of the whole community.},\n\tnumber = {183},\n\turldate = {2022-02-25},\n\tjournal = {Journal of The Royal Society Interface},\n\tauthor = {Shibasaki, Shota and Mobilia, Mauro and Mitri, Sara},\n\tyear = {2021},\n\tnote = {Publisher: Royal Society},\n\tkeywords = {⛔ No INSPIRE recid found, on website, read},\n\tpages = {20210613},\n\tfile = {Full Text:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\HZGMTR3H\\\\Shibasaki et al. - Exclusion of the fittest predicts microbial commun.pdf:application/pdf},\n}\n\n\n\n Microorganisms live in environments that inevitably fluctuate between mild and harsh conditions. As harsh conditions may cause extinctions, the rate at which fluctuations occur can shape microbial communities and their diversity, but we still lack an intuition on how. Here, we build a mathematical model describing two microbial species living in an environment where substrate supplies randomly switch between abundant and scarce. We then vary the rate of switching as well as different properties of the interacting species, and measure the probability of the weaker species driving the stronger one extinct. We find that this probability increases with the strength of demographic noise under harsh conditions and peaks at either low, high, or intermediate switching rates depending on both species’ ability to withstand the harsh environment. This complex relationship shows why finding patterns between environmental fluctuations and diversity has historically been difficult. In parameter ranges where the fittest species was most likely to be excluded, however, the beta diversity in larger communities also peaked. In sum, how environmental fluctuations affect interactions between a few species pairs predicts their effect on the beta diversity of the whole community.\n
\n\n\n\n \n\n \n \n \n \n \n \n Carrying Capacity of Spatially Distributed Metapopulations.\n \n \n \n \n\n\n \n Zhang, B.; DeAngelis, D. L.; and Ni, W.\n\n\n \n\n\n\n Trends in Ecology & Evolution, 36(2): 164–173. February 2021.\n Publisher: Elsevier\n\n\n\n
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\n\n\n\n@article{zhang_carrying_2021,\n\ttitle = {Carrying {Capacity} of {Spatially} {Distributed} {Metapopulations}},\n\tvolume = {36},\n\tissn = {0169-5347},\n\turl = {https://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(20)30285-8},\n\tdoi = {10.1016/j.tree.2020.10.007},\n\tlanguage = {English},\n\tnumber = {2},\n\turldate = {2022-09-27},\n\tjournal = {Trends in Ecology \\& Evolution},\n\tauthor = {Zhang, Bo and DeAngelis, Donald L. and Ni, Wei-Ming},\n\tmonth = feb,\n\tyear = {2021},\n\tpmid = {33129588},\n\tnote = {Publisher: Elsevier},\n\tkeywords = {unread, ⛔ No INSPIRE recid found},\n\tpages = {164--173},\n\tfile = {Full Text:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\B4GNFK58\\\\Zhang et al. - 2021 - Carrying Capacity of Spatially Distributed Metapop.pdf:application/pdf;Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\95EADPPT\\\\Zhang et al. - 2021 - Carrying Capacity of Spatially Distributed Metapop.pdf:application/pdf;Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\38GQEL2V\\\\S0169-5347(20)30285-8.html:text/html},\n}\n\n\n\n \n\n \n \n \n \n \n \n Species coexistence and temporal environmental fluctuations: a quantitative comparison between stochastic and seasonal variations.\n \n \n \n \n\n\n \n Meyer, I.; Steinmetz, B.; and Shnerb, N. M.\n\n\n \n\n\n\n April 2021.\n Pages: 2021.04.20.440706 Section: New Results\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n\n
\n\n\n@misc{meyer_species_2021,\n\ttitle = {Species coexistence and temporal environmental fluctuations: a quantitative comparison between stochastic and seasonal variations},\n\tcopyright = {© 2021, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NoDerivs 4.0 International), CC BY-ND 4.0, as described at http://creativecommons.org/licenses/by-nd/4.0/},\n\tshorttitle = {Species coexistence and temporal environmental fluctuations},\n\turl = {https://www.biorxiv.org/content/10.1101/2021.04.20.440706v1},\n\tdoi = {10.1101/2021.04.20.440706},\n\tabstract = {Temporal environmental variations may promote diversity in communities of competing populations. Here we compare the effect of environmental stochasticity with the effect of periodic (e.g., seasonal) cycles, using analytic solutions and individual-based Monte-Carlo simulations. Even when stochasticity facilitates coexistence it still allows for rare sequences of bad years that may drive a population to extinction, therefore the stabilizing effect of periodic variations is stronger. Correspondingly, the mean time to extinction grows exponentially with community size in periodic environment and switch to power-law dependence under stochastic fluctuations. On the other hand, the number of temporal niches in periodic environment is typically lower, so as diversity increases stochastic temporal variations may support higher species richness.},\n\tlanguage = {en},\n\turldate = {2023-03-21},\n\tpublisher = {bioRxiv},\n\tauthor = {Meyer, Immanuel and Steinmetz, Bnaya and Shnerb, Nadav M.},\n\tmonth = apr,\n\tyear = {2021},\n\tnote = {Pages: 2021.04.20.440706\nSection: New Results},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\F3WWFPCY\\\\Meyer et al. - 2021 - Species coexistence and temporal environmental flu.pdf:application/pdf},\n}\n\n\n\n Temporal environmental variations may promote diversity in communities of competing populations. Here we compare the effect of environmental stochasticity with the effect of periodic (e.g., seasonal) cycles, using analytic solutions and individual-based Monte-Carlo simulations. Even when stochasticity facilitates coexistence it still allows for rare sequences of bad years that may drive a population to extinction, therefore the stabilizing effect of periodic variations is stronger. Correspondingly, the mean time to extinction grows exponentially with community size in periodic environment and switch to power-law dependence under stochastic fluctuations. On the other hand, the number of temporal niches in periodic environment is typically lower, so as diversity increases stochastic temporal variations may support higher species richness.\n
\n\n\n\n \n\n \n \n \n \n \n Roadmap on biology in time varying environments.\n \n \n \n\n\n \n Murugan, A.; Husain, K.; and Rust et al. , M. J.\n\n\n \n\n\n\n Physical Biology, 18: 041502. 2021.\n \n\n\n\n
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\n\n\n\n@article{Murugan21,\n\ttitle = {Roadmap on biology in time varying environments},\n\tvolume = {18},\n\tjournal = {Physical Biology},\n\tauthor = {Murugan, A. and Husain, K. and Rust \\textit{et al.}, M. J.},\n\tyear = {2021},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {041502},\n\tfile = {Murugan et al. - 2021 - Roadmap on biology in time varying environments.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\UYAET6UE\\\\Murugan et al. - 2021 - Roadmap on biology in time varying environments.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Fluctuating environments maintain genetic diversity through neutral fitness effects and balancing selection.\n \n \n \n\n\n \n Abdul-Rahman, F.; Tranchina, D.; and Gresham, D.\n\n\n \n\n\n\n Molecular Biology and Evolution, 38: msab173. 2021.\n \n\n\n\n
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\n\n\n\n@article{Abdul21,\n\ttitle = {Fluctuating environments maintain genetic diversity through neutral fitness effects and balancing selection},\n\tvolume = {38},\n\tjournal = {Molecular Biology and Evolution},\n\tauthor = {Abdul-Rahman, F. and Tranchina, D. and Gresham, D.},\n\tyear = {2021},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {msab173},\n\tfile = {Abdul-Rahman et al. - 2021 - Fluctuating environments maintain genetic diversit.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\VUHVIJND\\\\Abdul-Rahman et al. - 2021 - Fluctuating environments maintain genetic diversit.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Environmental fluctuations and their effects on microbial communities, populations and individuals.\n \n \n \n\n\n \n Nguyen, T.; Lara-Gutiérrez, J.; and R., S.\n\n\n \n\n\n\n Fems Microbiology Reviews, 45: fuaa068. 2021.\n \n\n\n\n
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\n\n\n\n@article{Nguyen21,\n\ttitle = {Environmental fluctuations and their effects on microbial communities, populations and individuals},\n\tvolume = {45},\n\tjournal = {Fems Microbiology Reviews},\n\tauthor = {Nguyen, T. and Lara-Gutiérrez, J. and R., Stocker},\n\tyear = {2021},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {fuaa068},\n\tfile = {Nguyen et al. - 2021 - Environmental fluctuations and their effects on mi.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\JPMRU8DL\\\\Nguyen et al. - 2021 - Environmental fluctuations and their effects on mi.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Species coexistence and temporal environmental fluctuations: a quantitative comparison between stochastic and seasonal variations.\n \n \n \n\n\n \n Meyer, I.; Steinmetz, B.; and Shnerb, N. M.\n\n\n \n\n\n\n 2021.\n \n\n\n\n
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\n\n\n\n@misc{meyer_species_2021,\n\ttitle = {Species coexistence and temporal environmental fluctuations: a quantitative comparison between stochastic and seasonal variations},\n\tauthor = {Meyer, Immanuel and Steinmetz, Bnaya and Shnerb, Nadav M.},\n\tyear = {2021},\n\tkeywords = {⛔ No INSPIRE recid found},\n}\n\n\n\n
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\n \n \n\n \n \n \n \n \n \n Fixation properties of rock-paper-scissors games in fluctuating populations.\n \n \n \n \n\n\n \n West, R.; and Mobilia, M.\n\n\n \n\n\n\n Journal of Theoretical Biology, 491: 110135. April 2020.\n \n\n\n\n
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\n\n\n\n@article{west_fixation_2020,\n\ttitle = {Fixation properties of rock-paper-scissors games in fluctuating populations},\n\tvolume = {491},\n\tissn = {00225193},\n\turl = {https://linkinghub.elsevier.com/retrieve/pii/S0022519319305041},\n\tdoi = {10.1016/j.jtbi.2019.110135},\n\tlanguage = {en},\n\turldate = {2022-02-03},\n\tjournal = {Journal of Theoretical Biology},\n\tauthor = {West, Robert and Mobilia, Mauro},\n\tmonth = apr,\n\tyear = {2020},\n\tkeywords = {unread, ⛔ No INSPIRE recid found},\n\tpages = {110135},\n\tfile = {West and Mobilia - 2020 - Fixation properties of rock-paper-scissors games i.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\SQ9I6EGD\\\\West and Mobilia - 2020 - Fixation properties of rock-paper-scissors games i.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n \n Resist or perish: fate of a microbial population subjected to a periodic presence of antimicrobial.\n \n \n \n \n\n\n \n Marrec, L.; and Bitbol, A.\n\n\n \n\n\n\n PLOS Computational Biology, 16(4): e1007798. April 2020.\n arXiv:1911.06425 [physics, q-bio]\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{marrec_resist_2020,\n\ttitle = {Resist or perish: fate of a microbial population subjected to a periodic presence of antimicrobial},\n\tvolume = {16},\n\tissn = {1553-7358},\n\tshorttitle = {Resist or perish},\n\turl = {http://arxiv.org/abs/1911.06425},\n\tdoi = {10.1371/journal.pcbi.1007798},\n\tabstract = {The evolution of antimicrobial resistance can be strongly affected by variations of antimicrobial concentration. Here, we study the impact of periodic alternations of absence and presence of antimicrobial on resistance evolution in a microbial population, using a stochastic model that includes variations of both population composition and size, and fully incorporates stochastic population extinctions. We show that fast alternations of presence and absence of antimicrobial are inefficient to eradicate the microbial population and strongly favor the establishment of resistance, unless the antimicrobial increases enough the death rate. We further demonstrate that if the period of alternations is longer than a threshold value, the microbial population goes extinct upon the first addition of antimicrobial, if it is not rescued by resistance. We express the probability that the population is eradicated upon the first addition of antimicrobial, assuming rare mutations. Rescue by resistance can happen either if resistant mutants preexist, or if they appear after antimicrobial is added to the environment. Importantly, the latter case is fully prevented by perfect biostatic antimicrobials that completely stop division of sensitive microorganisms. By contrast, we show that the parameter regime where treatment is efficient is larger for biocidal drugs than for biostatic drugs. This sheds light on the respective merits of different antimicrobial modes of action.},\n\tnumber = {4},\n\turldate = {2022-09-27},\n\tjournal = {PLOS Computational Biology},\n\tauthor = {Marrec, Loïc and Bitbol, Anne-Florence},\n\tmonth = apr,\n\tyear = {2020},\n\tnote = {arXiv:1911.06425 [physics, q-bio]},\n\tkeywords = {unread, ⛔ No INSPIRE recid found},\n\tpages = {e1007798},\n\tfile = {arXiv.org Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\NILK3827\\\\1911.html:text/html;Marrec and Bitbol - 2020 - Resist or perish fate of a microbial population s.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\VLD2SVJJ\\\\Marrec and Bitbol - 2020 - Resist or perish fate of a microbial population s.pdf:application/pdf},\n}\n\n\n\n The evolution of antimicrobial resistance can be strongly affected by variations of antimicrobial concentration. Here, we study the impact of periodic alternations of absence and presence of antimicrobial on resistance evolution in a microbial population, using a stochastic model that includes variations of both population composition and size, and fully incorporates stochastic population extinctions. We show that fast alternations of presence and absence of antimicrobial are inefficient to eradicate the microbial population and strongly favor the establishment of resistance, unless the antimicrobial increases enough the death rate. We further demonstrate that if the period of alternations is longer than a threshold value, the microbial population goes extinct upon the first addition of antimicrobial, if it is not rescued by resistance. We express the probability that the population is eradicated upon the first addition of antimicrobial, assuming rare mutations. Rescue by resistance can happen either if resistant mutants preexist, or if they appear after antimicrobial is added to the environment. Importantly, the latter case is fully prevented by perfect biostatic antimicrobials that completely stop division of sensitive microorganisms. By contrast, we show that the parameter regime where treatment is efficient is larger for biocidal drugs than for biostatic drugs. This sheds light on the respective merits of different antimicrobial modes of action.\n
\n\n\n\n \n\n \n \n \n \n \n \n Dynamics of bacterial populations under the feast-famine cycles.\n \n \n \n \n\n\n \n Himeoka, Y.; and Mitarai, N.\n\n\n \n\n\n\n Physical Review Research, 2(1): 013372. March 2020.\n arXiv:1910.05673 [physics, q-bio]\n\n\n\n
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\n\n\n@article{himeoka_dynamics_2020,\n\ttitle = {Dynamics of bacterial populations under the feast-famine cycles},\n\tvolume = {2},\n\tissn = {2643-1564},\n\turl = {http://arxiv.org/abs/1910.05673},\n\tdoi = {10.1103/PhysRevResearch.2.013372},\n\tabstract = {Bacterial populations in natural conditions are expected to experience stochastic environmental fluctuations, and in addition, environments are affected by bacterial activities since they consume substrates and excrete various chemicals. We here study possible outcomes of population dynamics and evolution under the repeated cycle of substrate-rich conditions and starvation, called the "feast-famine cycle", by a simple stochastic model with the trade-off relationship between the growth rate and the growth yield or the death rate. In the model, the feast (substrate-rich) period is led by a stochastic substrate addition event, while the famine (starvation) period is evoked because bacteria use the supplied substrate. Under the repeated feast-famine cycle, the bacterial population tends to increase the growth rate, even though that tends to decrease the total population size due to the trade-off. Analysis of the model shows that the ratio between the growth rate and the death rate becomes the effective fitness of the population. Hence, the functional form of the trade-off between the growth and death rate determines if the bacterial population eventually goes extinct as an evolutionary consequence. We then show that the increase of the added substrate in the feast period can drive the extinction faster. Overall, the model sheds light on non-trivial possible outcomes under repeated feast-famine cycles.},\n\tnumber = {1},\n\turldate = {2023-03-14},\n\tjournal = {Physical Review Research},\n\tauthor = {Himeoka, Yusuke and Mitarai, Namiko},\n\tmonth = mar,\n\tyear = {2020},\n\tnote = {arXiv:1910.05673 [physics, q-bio]},\n\tkeywords = {Quantitative Biology - Populations and Evolution, Physics - Biological Physics, ⛔ No INSPIRE recid found},\n\tpages = {013372},\n\tfile = {APS Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\APQFALZS\\\\PhysRevResearch.2.html:text/html;arXiv.org Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\F4ZDZJW3\\\\1910.html:text/html;Full Text:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\6GKLHC5J\\\\Himeoka and Mitarai - 2020 - Dynamics of bacterial populations under the feast-.pdf:application/pdf},\n}\n\n\n\n Bacterial populations in natural conditions are expected to experience stochastic environmental fluctuations, and in addition, environments are affected by bacterial activities since they consume substrates and excrete various chemicals. We here study possible outcomes of population dynamics and evolution under the repeated cycle of substrate-rich conditions and starvation, called the \"feast-famine cycle\", by a simple stochastic model with the trade-off relationship between the growth rate and the growth yield or the death rate. In the model, the feast (substrate-rich) period is led by a stochastic substrate addition event, while the famine (starvation) period is evoked because bacteria use the supplied substrate. Under the repeated feast-famine cycle, the bacterial population tends to increase the growth rate, even though that tends to decrease the total population size due to the trade-off. Analysis of the model shows that the ratio between the growth rate and the death rate becomes the effective fitness of the population. Hence, the functional form of the trade-off between the growth and death rate determines if the bacterial population eventually goes extinct as an evolutionary consequence. We then show that the increase of the added substrate in the feast period can drive the extinction faster. Overall, the model sheds light on non-trivial possible outcomes under repeated feast-famine cycles.\n
\n\n\n\n \n\n \n \n \n \n \n \n Evolutionary dynamics in fluctuating environment.\n \n \n \n \n\n\n \n Meyer, I.; and Shnerb, N. M.\n\n\n \n\n\n\n Physical Review Research, 2(2): 023308. June 2020.\n Publisher: American Physical Society\n\n\n\n
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\n\n\n@article{meyer_evolutionary_2020,\n\ttitle = {Evolutionary dynamics in fluctuating environment},\n\tvolume = {2},\n\turl = {https://link.aps.org/doi/10.1103/PhysRevResearch.2.023308},\n\tdoi = {10.1103/PhysRevResearch.2.023308},\n\tabstract = {Temporal environmental variations are ubiquitous in nature, yet most of the theoretical works in population genetics and evolution assume fixed environment. Here we analyze the effect of variations in selection sign, selection intensity, and population size on the fate of a mutant type. Using Kimura's diffusion approximation we present simple formulas for effective population size and effective selection, and use it to calculate the chance of ultimate fixation, the time to fixation, and the time to absorption (either fixation or loss). For simple models, in which the number of environmental states is relatively small, the effective parameters are obtained analytically. For more complicated models, where the monitoring of the weights of all microstates is complicated, we present a semianalytic solution whose parameters are obtained from short numerical experiments. Our analysis shows perfect agreement with numerical solutions for neutral, beneficial, and deleterious mutant, under periodic and stochastic environmental variations and different competition modes.},\n\tnumber = {2},\n\turldate = {2023-03-21},\n\tjournal = {Physical Review Research},\n\tauthor = {Meyer, Immanuel and Shnerb, Nadav M.},\n\tmonth = jun,\n\tyear = {2020},\n\tnote = {Publisher: American Physical Society},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {023308},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\S7IK7EGQ\\\\Meyer and Shnerb - 2020 - Evolutionary dynamics in fluctuating environment.pdf:application/pdf},\n}\n\n\n\n Temporal environmental variations are ubiquitous in nature, yet most of the theoretical works in population genetics and evolution assume fixed environment. Here we analyze the effect of variations in selection sign, selection intensity, and population size on the fate of a mutant type. Using Kimura's diffusion approximation we present simple formulas for effective population size and effective selection, and use it to calculate the chance of ultimate fixation, the time to fixation, and the time to absorption (either fixation or loss). For simple models, in which the number of environmental states is relatively small, the effective parameters are obtained analytically. For more complicated models, where the monitoring of the weights of all microstates is complicated, we present a semianalytic solution whose parameters are obtained from short numerical experiments. Our analysis shows perfect agreement with numerical solutions for neutral, beneficial, and deleterious mutant, under periodic and stochastic environmental variations and different competition modes.\n
\n\n\n\n \n\n \n \n \n \n \n \n Phenotypic memory drives population growth and extinction risk in a noisy environment.\n \n \n \n \n\n\n \n Rescan, M.; Grulois, D.; Ortega-Aboud, E.; and Chevin, L.\n\n\n \n\n\n\n Nature Ecology & Evolution, 4(2): 193–201. January 2020.\n \n\n\n\n
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\n\n\n@article{rescan_phenotypic_2020,\n\ttitle = {Phenotypic memory drives population growth and extinction risk in a noisy environment},\n\tvolume = {4},\n\tissn = {2397-334X},\n\turl = {https://www.nature.com/articles/s41559-019-1089-6},\n\tdoi = {10.1038/s41559-019-1089-6},\n\tabstract = {Random environmental fluctuations pose major threats to wild populations. As patterns of environmental noise are themselves altered by global change, there is a growing need to identify general mechanisms underlying their effects on population dynamics. This notably requires understanding and predicting population responses to the colour of environmental noise, in other words its temporal autocorrelation pattern. Here, we show experimentally that environmental autocorrelation has a large influence on population dynamics and extinction rates, which can be predicted accurately provided that a memory of past environment is accounted for. We exposed nearly 1,000 lines of the microalgae Dunaliella salina to randomly fluctuating salinity, with autocorrelation ranging from negative to highly positive. We found lower population growth, and twice as many extinctions, under lower autocorrelation. These responses closely matched predictions based on a tolerance curve with environmental memory, showing that non-genetic inheritance can be a major driver of population dynamics in randomly fluctuating environments. Exposing experimental lines of microalgae to random fluctuations in salinity, the authors show that environmental autocorrelation strongly influences population growth and extinction risk, with accurate predictions only possible when the impact of past environments is taken into account.},\n\tlanguage = {en},\n\tnumber = {2},\n\turldate = {2023-04-04},\n\tjournal = {Nature Ecology \\& Evolution},\n\tauthor = {Rescan, Marie and Grulois, Daphné and Ortega-Aboud, Enrique and Chevin, Luis-Miguel},\n\tmonth = jan,\n\tyear = {2020},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {193--201},\n\tfile = {Accepted Version:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\IJWWKTNW\\\\Rescan et al. - 2020 - Phenotypic memory drives population growth and ext.pdf:application/pdf},\n}\n\n\n\n Random environmental fluctuations pose major threats to wild populations. As patterns of environmental noise are themselves altered by global change, there is a growing need to identify general mechanisms underlying their effects on population dynamics. This notably requires understanding and predicting population responses to the colour of environmental noise, in other words its temporal autocorrelation pattern. Here, we show experimentally that environmental autocorrelation has a large influence on population dynamics and extinction rates, which can be predicted accurately provided that a memory of past environment is accounted for. We exposed nearly 1,000 lines of the microalgae Dunaliella salina to randomly fluctuating salinity, with autocorrelation ranging from negative to highly positive. We found lower population growth, and twice as many extinctions, under lower autocorrelation. These responses closely matched predictions based on a tolerance curve with environmental memory, showing that non-genetic inheritance can be a major driver of population dynamics in randomly fluctuating environments. Exposing experimental lines of microalgae to random fluctuations in salinity, the authors show that environmental autocorrelation strongly influences population growth and extinction risk, with accurate predictions only possible when the impact of past environments is taken into account.\n
\n\n\n\n \n\n \n \n \n \n \n Evolutionary games with environmental feedbacks.\n \n \n \n\n\n \n Tilman, A.; Plotkin, J.; and Akcay, E.\n\n\n \n\n\n\n Nature Communications, 11: 915. 2020.\n \n\n\n\n
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\n\n\n\n@article{Tilman20,\n\ttitle = {Evolutionary games with environmental feedbacks},\n\tvolume = {11},\n\tjournal = {Nature Communications},\n\tauthor = {Tilman, A.R. and Plotkin, J.B. and Akcay, E.},\n\tyear = {2020},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {915},\n\tfile = {Tilman et al. - 2020 - Evolutionary games with environmental feedbacks.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\2I2AX4DK\\\\Tilman et al. - 2020 - Evolutionary games with environmental feedbacks.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Changes in microbiome confer multigenerational host resistance after sub-toxic pesticide exposure.\n \n \n \n\n\n \n Wang, G.; Berdy, B. M.; Velasquez, O.; Jovanovic, N.; Alkhalifa, S.; Minbiole, K. P. C; and Brucker, R. M.\n\n\n \n\n\n\n Cell host & microbe, 27: 213. 2020.\n \n\n\n\n
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\n\n\n\n@article{Wang20,\n\ttitle = {Changes in microbiome confer multigenerational host resistance after sub-toxic pesticide exposure},\n\tvolume = {27},\n\tjournal = {Cell host \\& microbe},\n\tauthor = {Wang, G.-H. and Berdy, B. M. and Velasquez, O. and Jovanovic, N. and Alkhalifa, S. and Minbiole, K. P. C and Brucker, R. M.},\n\tyear = {2020},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {213},\n\tfile = {Wang et al. - 2020 - Changes in microbiome confer multigenerational hos.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\H2LCNT5B\\\\Wang et al. - 2020 - Changes in microbiome confer multigenerational hos.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Gut microbiome toxicity: Connecting the environment and gut microbiome-associated diseases.\n \n \n \n\n\n \n Tu, P.; Chi, L.; Bodnar, W.; Zhang, Z.; Gao, B.; Bian, X.; Stewart, J.; Fry, R.; and Lu, K.\n\n\n \n\n\n\n Toxics, 8: 19. 2020.\n \n\n\n\n
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\n\n\n\n@article{Tu20,\n\ttitle = {Gut microbiome toxicity: {Connecting} the environment and gut microbiome-associated diseases},\n\tvolume = {8},\n\tjournal = {Toxics},\n\tauthor = {Tu, P. and Chi, L. and Bodnar, W. and Zhang, Z. and Gao, B. and Bian, X. and Stewart, J. and Fry, R. and Lu, K.},\n\tyear = {2020},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {19},\n\tfile = {Tu et al. - 2020 - Gut microbiome toxicity Connecting the environmen.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\TCNXKU84\\\\Tu et al. - 2020 - Gut microbiome toxicity Connecting the environmen.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Macroecological laws describe variation and diversity in microbial communities.\n \n \n \n\n\n \n Grilli, J.\n\n\n \n\n\n\n Nature Communications, 11: 4743. 2020.\n \n\n\n\n
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\n\n\n\n@article{Grilli20,\n\ttitle = {Macroecological laws describe variation and diversity in microbial communities},\n\tvolume = {11},\n\tjournal = {Nature Communications},\n\tauthor = {Grilli, J.},\n\tyear = {2020},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {4743},\n\tfile = {Grilli - 2020 - Macroecological laws describe variation and divers.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\FDSTEVDL\\\\Grilli - 2020 - Macroecological laws describe variation and divers.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n \n Population Dynamics in a Changing Environment: Random versus Periodic Switching.\n \n \n \n \n\n\n \n Taitelbaum, A.; West, R.; Assaf, M.; and Mobilia, M.\n\n\n \n\n\n\n Physical Review Letters, 125(4): 048105. July 2020.\n \n\n\n\n
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\n\n\n\n@article{taitelbaum_population_2020,\n\ttitle = {Population {Dynamics} in a {Changing} {Environment}: {Random} versus {Periodic} {Switching}},\n\tvolume = {125},\n\tissn = {0031-9007, 1079-7114},\n\tshorttitle = {Population {Dynamics} in a {Changing} {Environment}},\n\turl = {https://link.aps.org/doi/10.1103/PhysRevLett.125.048105},\n\tdoi = {10.1103/PhysRevLett.125.048105},\n\tlanguage = {en},\n\tnumber = {4},\n\turldate = {2023-06-29},\n\tjournal = {Physical Review Letters},\n\tauthor = {Taitelbaum, Ami and West, Robert and Assaf, Michael and Mobilia, Mauro},\n\tmonth = jul,\n\tyear = {2020},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {048105},\n\tfile = {Supplementary Material:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\ZIJE57RD\\\\Taitelbaum et al. - 2020 - Population Dynamics in a Changing Environment Ran.pdf:application/pdf;Taitelbaum et al. - 2020 - Population Dynamics in a Changing Environment Ran.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\8NSL7VI2\\\\Taitelbaum et al. - 2020 - Population Dynamics in a Changing Environment Ran.pdf:application/pdf},\n}\n\n\n\n
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\n \n \n\n \n \n \n \n \n \n Population-level mathematical modeling of antimicrobial resistance: a systematic review.\n \n \n \n \n\n\n \n Niewiadomska, A. M.; Jayabalasingham, B.; Seidman, J. C.; Willem, L.; Grenfell, B.; Spiro, D.; and Viboud, C.\n\n\n \n\n\n\n BMC Medicine, 17(1): 81. December 2019.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n
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Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n\n
\n\n\n@article{niewiadomska_population-level_2019,\n\ttitle = {Population-level mathematical modeling of antimicrobial resistance: a systematic review},\n\tvolume = {17},\n\tissn = {1741-7015},\n\tshorttitle = {Population-level mathematical modeling of antimicrobial resistance},\n\turl = {https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-019-1314-9},\n\tdoi = {10.1186/s12916-019-1314-9},\n\tabstract = {Background: Mathematical transmission models are increasingly used to guide public health interventions for infectious diseases, particularly in the context of emerging pathogens; however, the contribution of modeling to the growing issue of antimicrobial resistance (AMR) remains unclear. Here, we systematically evaluate publications on population-level transmission models of AMR over a recent period (2006–2016) to gauge the state of research and identify gaps warranting further work.\nMethods: We performed a systematic literature search of relevant databases to identify transmission studies of AMR in viral, bacterial, and parasitic disease systems. We analyzed the temporal, geographic, and subject matter trends, described the predominant medical and behavioral interventions studied, and identified central findings relating to key pathogens.\nResults: We identified 273 modeling studies; the majority of which ({\\textgreater} 70\\%) focused on 5 infectious diseases (human immunodeficiency virus (HIV), influenza virus, Plasmodium falciparum (malaria), Mycobacterium tuberculosis (TB), and methicillin-resistant Staphylococcus aureus (MRSA)). AMR studies of influenza and nosocomial pathogens were mainly set in industrialized nations, while HIV, TB, and malaria studies were heavily skewed towards developing countries. The majority of articles focused on AMR exclusively in humans (89\\%), either in community (58\\%) or healthcare (27\\%) settings. Model systems were largely compartmental (76\\%) and deterministic (66\\%). Only 43\\% of models were calibrated against epidemiological data, and few were validated against out-of-sample datasets (14\\%). The interventions considered were primarily the impact of different drug regimens, hygiene and infection control measures, screening, and diagnostics, while few studies addressed de novo resistance, vaccination strategies, economic, or behavioral changes to reduce antibiotic use in humans and animals.\nConclusions: The AMR modeling literature concentrates on disease systems where resistance has been longestablished, while few studies pro-actively address recent rise in resistance in new pathogens or explore upstream strategies to reduce overall antibiotic consumption. Notable gaps include research on emerging resistance in Enterobacteriaceae and Neisseria gonorrhoeae; AMR transmission at the animal-human interface, particularly in agricultural and veterinary settings; transmission between hospitals and the community; the role of environmental factors in AMR transmission; and the potential of vaccines to combat AMR.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2022-09-15},\n\tjournal = {BMC Medicine},\n\tauthor = {Niewiadomska, Anna Maria and Jayabalasingham, Bamini and Seidman, Jessica C. and Willem, Lander and Grenfell, Bryan and Spiro, David and Viboud, Cecile},\n\tmonth = dec,\n\tyear = {2019},\n\tkeywords = {unread, ⛔ No INSPIRE recid found},\n\tpages = {81},\n\tfile = {Niewiadomska et al. - 2019 - Population-level mathematical modeling of antimicr.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\X52HXQVR\\\\Niewiadomska et al. - 2019 - Population-level mathematical modeling of antimicr.pdf:application/pdf},\n}\n\n\n\n Background: Mathematical transmission models are increasingly used to guide public health interventions for infectious diseases, particularly in the context of emerging pathogens; however, the contribution of modeling to the growing issue of antimicrobial resistance (AMR) remains unclear. Here, we systematically evaluate publications on population-level transmission models of AMR over a recent period (2006–2016) to gauge the state of research and identify gaps warranting further work. Methods: We performed a systematic literature search of relevant databases to identify transmission studies of AMR in viral, bacterial, and parasitic disease systems. We analyzed the temporal, geographic, and subject matter trends, described the predominant medical and behavioral interventions studied, and identified central findings relating to key pathogens. Results: We identified 273 modeling studies; the majority of which (\\textgreater 70%) focused on 5 infectious diseases (human immunodeficiency virus (HIV), influenza virus, Plasmodium falciparum (malaria), Mycobacterium tuberculosis (TB), and methicillin-resistant Staphylococcus aureus (MRSA)). AMR studies of influenza and nosocomial pathogens were mainly set in industrialized nations, while HIV, TB, and malaria studies were heavily skewed towards developing countries. The majority of articles focused on AMR exclusively in humans (89%), either in community (58%) or healthcare (27%) settings. Model systems were largely compartmental (76%) and deterministic (66%). Only 43% of models were calibrated against epidemiological data, and few were validated against out-of-sample datasets (14%). The interventions considered were primarily the impact of different drug regimens, hygiene and infection control measures, screening, and diagnostics, while few studies addressed de novo resistance, vaccination strategies, economic, or behavioral changes to reduce antibiotic use in humans and animals. Conclusions: The AMR modeling literature concentrates on disease systems where resistance has been longestablished, while few studies pro-actively address recent rise in resistance in new pathogens or explore upstream strategies to reduce overall antibiotic consumption. Notable gaps include research on emerging resistance in Enterobacteriaceae and Neisseria gonorrhoeae; AMR transmission at the animal-human interface, particularly in agricultural and veterinary settings; transmission between hospitals and the community; the role of environmental factors in AMR transmission; and the potential of vaccines to combat AMR.\n
\n\n\n\n \n\n \n \n \n \n \n \n The rate of environmental fluctuations shapes ecological dynamics in a two-species microbial system.\n \n \n \n \n\n\n \n Rodríguez-Verdugo, A.; Vulin, C.; and Ackermann, M.\n\n\n \n\n\n\n Ecology Letters, 22(5): 838–846. 2019.\n _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.13241\n\n\n\n
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\n\n\n@article{rodriguez-verdugo_rate_2019,\n\ttitle = {The rate of environmental fluctuations shapes ecological dynamics in a two-species microbial system},\n\tvolume = {22},\n\tissn = {1461-0248},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ele.13241},\n\tdoi = {10.1111/ele.13241},\n\tabstract = {Species interactions change when the external conditions change. How these changes affect microbial community properties is an open question. We address this question using a two-species consortium in which species interactions change from exploitation to competition depending on the carbon source provided. We built a mathematical model and calibrated it using single-species growth measurements. This model predicted that low frequencies of change between carbon sources lead to species loss, while intermediate and high frequencies of change maintained both species. We experimentally confirmed these predictions by growing co-cultures in fluctuating environments. These findings complement more established concepts of a diversity peak at intermediate disturbance frequencies. They also provide a mechanistic understanding for how the dynamics at the community level emerges from single-species behaviours and interspecific interactions. Our findings suggest that changes in species interactions can profoundly impact the ecological dynamics and properties of microbial systems.},\n\tlanguage = {en},\n\tnumber = {5},\n\turldate = {2023-03-06},\n\tjournal = {Ecology Letters},\n\tauthor = {Rodríguez-Verdugo, Alejandra and Vulin, Clément and Ackermann, Martin},\n\tyear = {2019},\n\tnote = {\\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.13241},\n\tkeywords = {read, Acinetobacter johnsonii, cross-feeding, exploitation, mathematical modelling, population dynamics, Pseudomonas putida, rate of environmental change, resource competition, species interactions, synthetic communities, ⛔ No INSPIRE recid found},\n\tpages = {838--846},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\TEJ5I4UM\\\\Rodríguez-Verdugo et al. - 2019 - The rate of environmental fluctuations shapes ecol.pdf:application/pdf;Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\5A2INBK5\\\\ele.html:text/html},\n}\n\n\n\n Species interactions change when the external conditions change. How these changes affect microbial community properties is an open question. We address this question using a two-species consortium in which species interactions change from exploitation to competition depending on the carbon source provided. We built a mathematical model and calibrated it using single-species growth measurements. This model predicted that low frequencies of change between carbon sources lead to species loss, while intermediate and high frequencies of change maintained both species. We experimentally confirmed these predictions by growing co-cultures in fluctuating environments. These findings complement more established concepts of a diversity peak at intermediate disturbance frequencies. They also provide a mechanistic understanding for how the dynamics at the community level emerges from single-species behaviours and interspecific interactions. Our findings suggest that changes in species interactions can profoundly impact the ecological dynamics and properties of microbial systems.\n
\n\n\n\n \n\n \n \n \n \n \n \n Antimicrobial Resistance: Implications and Costs.\n \n \n \n \n\n\n \n Dadgostar, P.\n\n\n \n\n\n\n Infection and Drug Resistance, 12: 3903–3910. December 2019.\n \n\n\n\n
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\n\n\n@article{dadgostar_antimicrobial_2019,\n\ttitle = {Antimicrobial {Resistance}: {Implications} and {Costs}},\n\tvolume = {12},\n\tissn = {1178-6973},\n\tshorttitle = {Antimicrobial {Resistance}},\n\turl = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6929930/},\n\tdoi = {10.2147/IDR.S234610},\n\tabstract = {Antimicrobial resistance (AMR) has developed as one of the major urgent threats to public health causing serious issues to successful prevention and treatment of persistent diseases. In spite of different actions taken in recent decades to tackle this issue, the trends of global AMR demonstrate no signs of slowing down. Misusing and overusing different antibacterial agents in the health care setting as well as in the agricultural industry are considered the major reasons behind the emergence of antimicrobial resistance. In addition, the spontaneous evolution, mutation of bacteria, and passing the resistant genes through horizontal gene transfer are significant contributors to antimicrobial resistance. Many studies have demonstrated the disastrous financial consequences of AMR including extremely high healthcare costs due to an increase in hospital admissions and drug usage. The literature review, which included articles published after the year 2012, was performed using Scopus, PubMed and Google Scholar with the utilization of keyword searches. Results indicated that the multifactorial threat of antimicrobial resistance has resulted in different complex issues affecting countries across the globe. These impacts found in the sources are categorized into three different levels: patient, healthcare, and economic. Although gaps in knowledge about AMR and areas for improvement are obvious, there is not any clearly understood progress to put an end to the persistent trends of antimicrobial resistance.},\n\turldate = {2023-03-07},\n\tjournal = {Infection and Drug Resistance},\n\tauthor = {Dadgostar, Porooshat},\n\tmonth = dec,\n\tyear = {2019},\n\tpmid = {31908502},\n\tpmcid = {PMC6929930},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {3903--3910},\n\tfile = {PubMed Central Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\DMLD434C\\\\Dadgostar - 2019 - Antimicrobial Resistance Implications and Costs.pdf:application/pdf},\n}\n\n\n\n Antimicrobial resistance (AMR) has developed as one of the major urgent threats to public health causing serious issues to successful prevention and treatment of persistent diseases. In spite of different actions taken in recent decades to tackle this issue, the trends of global AMR demonstrate no signs of slowing down. Misusing and overusing different antibacterial agents in the health care setting as well as in the agricultural industry are considered the major reasons behind the emergence of antimicrobial resistance. In addition, the spontaneous evolution, mutation of bacteria, and passing the resistant genes through horizontal gene transfer are significant contributors to antimicrobial resistance. Many studies have demonstrated the disastrous financial consequences of AMR including extremely high healthcare costs due to an increase in hospital admissions and drug usage. The literature review, which included articles published after the year 2012, was performed using Scopus, PubMed and Google Scholar with the utilization of keyword searches. Results indicated that the multifactorial threat of antimicrobial resistance has resulted in different complex issues affecting countries across the globe. These impacts found in the sources are categorized into three different levels: patient, healthcare, and economic. Although gaps in knowledge about AMR and areas for improvement are obvious, there is not any clearly understood progress to put an end to the persistent trends of antimicrobial resistance.\n
\n\n\n\n \n\n \n \n \n \n \n Cooperation in microbial populations: Theory and experimental model systems.\n \n \n \n\n\n \n J. Cremer; A. Melbinger; K. Wienand; T. Henriquez; H. Jung; and E. Frey\n\n\n \n\n\n\n Journal of Molecular Biology, 431(23): 4599–4644. 2019.\n \n\n\n\n
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\n\n\n\n@article{cremer_cooperation_2019,\n\ttitle = {Cooperation in microbial populations: {Theory} and experimental model systems},\n\tvolume = {431},\n\tnumber = {23},\n\tjournal = {Journal of Molecular Biology},\n\tauthor = {{J. Cremer} and {A. Melbinger} and {K. Wienand} and {T. Henriquez} and {H. Jung} and {E. Frey}},\n\tyear = {2019},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {4599--4644},\n\tfile = {2019 - Cooperation in microbial populations Theory and e.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\BJFVJZH2\\\\2019 - Cooperation in microbial populations Theory and e.pdf:application/pdf},\n}\n\n\n
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\n \n \n\n \n \n \n \n \n \n Eco-evolutionary dynamics of a population with randomly switching carrying capacity.\n \n \n \n \n\n\n \n Wienand, K.; Frey, E.; and Mobilia, M.\n\n\n \n\n\n\n Journal of The Royal Society Interface, 15(145): 20180343. August 2018.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{wienand_eco-evolutionary_2018,\n\ttitle = {Eco-evolutionary dynamics of a population with randomly switching carrying capacity},\n\tvolume = {15},\n\tissn = {1742-5689, 1742-5662},\n\turl = {https://royalsocietypublishing.org/doi/10.1098/rsif.2018.0343},\n\tdoi = {10.1098/rsif.2018.0343},\n\tabstract = {Environmental variability greatly influences the eco-evolutionary dynamics of a population, i.e. it affects how its size and composition evolve. Here, we study a well-mixed population of finite and fluctuating size whose growth is limited by a randomly switching carrying capacity. This models the environmental fluctuations between states of resources abundance and scarcity. The population consists of two strains, one growing slightly faster than the other, competing under two scenarios: one in which competition is solely for resources, and one in which the slow (cooperating) strain produces a public good (PG) that benefits also the fast (free-riding) strain. We investigate how the coupling of demographic and environmental (external) noise affects the population's eco-evolutionary dynamics. By analytical and computational means, we study the correlations between the population size and its composition, and discuss the social-dilemma-like ‘eco-evolutionary game’ characterizing the PG production. We determine in what conditions it is best to produce a PG; when cooperating is beneficial but outcompeted by free riding, and when the PG production is detrimental for cooperators. Within a linear noise approximation to populations of varying size, we also accurately analyse the coupled effects of demographic and environmental noise on the size distribution.},\n\tlanguage = {en},\n\tnumber = {145},\n\turldate = {2022-02-03},\n\tjournal = {Journal of The Royal Society Interface},\n\tauthor = {Wienand, Karl and Frey, Erwin and Mobilia, Mauro},\n\tmonth = aug,\n\tyear = {2018},\n\tkeywords = {read, carrying capacity switching, fixation probability, random switching, varying population size, Moran model, public good, on website, ⛔ No INSPIRE recid found},\n\tpages = {20180343},\n\tfile = {Supplementary Material:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\C5MDSW9Y\\\\Wienand et al. - 2018 - Eco-evolutionary dynamics of a population with ran.pdf:application/pdf;Wienand et al. - 2018 - Eco-evolutionary dynamics of a population with ran.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\YR2EWM7E\\\\Wienand et al. - 2018 - Eco-evolutionary dynamics of a population with ran.pdf:application/pdf},\n}\n\n\n\n Environmental variability greatly influences the eco-evolutionary dynamics of a population, i.e. it affects how its size and composition evolve. Here, we study a well-mixed population of finite and fluctuating size whose growth is limited by a randomly switching carrying capacity. This models the environmental fluctuations between states of resources abundance and scarcity. The population consists of two strains, one growing slightly faster than the other, competing under two scenarios: one in which competition is solely for resources, and one in which the slow (cooperating) strain produces a public good (PG) that benefits also the fast (free-riding) strain. We investigate how the coupling of demographic and environmental (external) noise affects the population's eco-evolutionary dynamics. By analytical and computational means, we study the correlations between the population size and its composition, and discuss the social-dilemma-like ‘eco-evolutionary game’ characterizing the PG production. We determine in what conditions it is best to produce a PG; when cooperating is beneficial but outcompeted by free riding, and when the PG production is detrimental for cooperators. Within a linear noise approximation to populations of varying size, we also accurately analyse the coupled effects of demographic and environmental noise on the size distribution.\n
\n\n\n\n \n\n \n \n \n \n \n \n Antibiotic-induced population fluctuations and stochastic clearance of bacteria.\n \n \n \n \n\n\n \n Coates, J.; Park, B. R.; Le, D.; Şimşek, E.; Chaudhry, W.; and Kim, M.\n\n\n \n\n\n\n eLife, 7: e32976. March 2018.\n Publisher: eLife Sciences Publications, Ltd\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{coates_antibiotic-induced_2018,\n\ttitle = {Antibiotic-induced population fluctuations and stochastic clearance of bacteria},\n\tvolume = {7},\n\tissn = {2050-084X},\n\turl = {https://doi.org/10.7554/eLife.32976},\n\tdoi = {10.7554/eLife.32976},\n\tabstract = {Effective antibiotic use that minimizes treatment failures remains a challenge. A better understanding of how bacterial populations respond to antibiotics is necessary. Previous studies of large bacterial populations established the deterministic framework of pharmacodynamics. Here, characterizing the dynamics of population extinction, we demonstrated the stochastic nature of eradicating bacteria with antibiotics. Antibiotics known to kill bacteria (bactericidal) induced population fluctuations. Thus, at high antibiotic concentrations, the dynamics of bacterial clearance were heterogeneous. At low concentrations, clearance still occurred with a non-zero probability. These striking outcomes of population fluctuations were well captured by our probabilistic model. Our model further suggested a strategy to facilitate eradication by increasing extinction probability. We experimentally tested this prediction for antibiotic-susceptible and clinically-isolated resistant bacteria. This new knowledge exposes fundamental limits in our ability to predict bacterial eradication. Additionally, it demonstrates the potential of using antibiotic concentrations that were previously deemed inefficacious to eradicate bacteria.},\n\tjournal = {eLife},\n\tauthor = {Coates, Jessica and Park, Bo Ryoung and Le, Dai and Şimşek, Emrah and Chaudhry, Waqas and Kim, Minsu},\n\teditor = {Walczak, Aleksandra M},\n\tmonth = mar,\n\tyear = {2018},\n\tnote = {Publisher: eLife Sciences Publications, Ltd},\n\tkeywords = {unread, read, on website, ⛔ No INSPIRE recid found},\n\tpages = {e32976},\n\tfile = {Coates et al. - 2018 - Antibiotic-induced population fluctuations and sto.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\L6RGKHIG\\\\Coates et al. - 2018 - Antibiotic-induced population fluctuations and sto.pdf:application/pdf},\n}\n\n\n\n Effective antibiotic use that minimizes treatment failures remains a challenge. A better understanding of how bacterial populations respond to antibiotics is necessary. Previous studies of large bacterial populations established the deterministic framework of pharmacodynamics. Here, characterizing the dynamics of population extinction, we demonstrated the stochastic nature of eradicating bacteria with antibiotics. Antibiotics known to kill bacteria (bactericidal) induced population fluctuations. Thus, at high antibiotic concentrations, the dynamics of bacterial clearance were heterogeneous. At low concentrations, clearance still occurred with a non-zero probability. These striking outcomes of population fluctuations were well captured by our probabilistic model. Our model further suggested a strategy to facilitate eradication by increasing extinction probability. We experimentally tested this prediction for antibiotic-susceptible and clinically-isolated resistant bacteria. This new knowledge exposes fundamental limits in our ability to predict bacterial eradication. Additionally, it demonstrates the potential of using antibiotic concentrations that were previously deemed inefficacious to eradicate bacteria.\n
\n\n\n\n \n\n \n \n \n \n \n \n Quantifying the impact of a periodic presence of antimicrobial on resistance evolution in a homogeneous microbial population of fixed size.\n \n \n \n \n\n\n \n Marrec, L.; and Bitbol, A.\n\n\n \n\n\n\n Journal of Theoretical Biology, 457: 190–198. November 2018.\n arXiv:1803.03201 [physics, q-bio]\n\n\n\n
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\n\n\n@article{marrec_quantifying_2018,\n\ttitle = {Quantifying the impact of a periodic presence of antimicrobial on resistance evolution in a homogeneous microbial population of fixed size},\n\tvolume = {457},\n\tissn = {00225193},\n\turl = {http://arxiv.org/abs/1803.03201},\n\tdoi = {10.1016/j.jtbi.2018.08.040},\n\tabstract = {The evolution of antimicrobial resistance generally occurs in an environment where antimicrobial concentration is variable, which has dramatic consequences on the microorganisms' fitness landscape, and thus on the evolution of resistance. We investigate the effect of these time-varying patterns of selection within a stochastic model. We consider a homogeneous microbial population of fixed size subjected to periodic alternations of phases of absence and presence of an antimicrobial that stops growth. Combining analytical approaches and stochastic simulations, we quantify how the time necessary for fit resistant bacteria to take over the microbial population depends on the alternation period. We demonstrate that fast alternations strongly accelerate the evolution of resistance, reaching a plateau for sufficiently small periods. Furthermore, this acceleration is stronger in larger populations. For asymmetric alternations, featuring a different duration of the phases with and without antimicrobial, we shed light on the existence of a minimum for the time taken by the population to fully evolve resistance. The corresponding dramatic acceleration of the evolution of antimicrobial resistance likely occurs in realistic situations, and may have an important impact both in clinical and experimental situations.},\n\turldate = {2022-09-27},\n\tjournal = {Journal of Theoretical Biology},\n\tauthor = {Marrec, Loïc and Bitbol, Anne-Florence},\n\tmonth = nov,\n\tyear = {2018},\n\tnote = {arXiv:1803.03201 [physics, q-bio]},\n\tkeywords = {unread, ⛔ No INSPIRE recid found},\n\tpages = {190--198},\n\tfile = {arXiv Fulltext PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\25XN3MXY\\\\Marrec and Bitbol - 2018 - Quantifying the impact of a periodic presence of a.pdf:application/pdf;arXiv.org Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\QFDWXKEI\\\\1803.html:text/html},\n}\n\n\n\n The evolution of antimicrobial resistance generally occurs in an environment where antimicrobial concentration is variable, which has dramatic consequences on the microorganisms' fitness landscape, and thus on the evolution of resistance. We investigate the effect of these time-varying patterns of selection within a stochastic model. We consider a homogeneous microbial population of fixed size subjected to periodic alternations of phases of absence and presence of an antimicrobial that stops growth. Combining analytical approaches and stochastic simulations, we quantify how the time necessary for fit resistant bacteria to take over the microbial population depends on the alternation period. We demonstrate that fast alternations strongly accelerate the evolution of resistance, reaching a plateau for sufficiently small periods. Furthermore, this acceleration is stronger in larger populations. For asymmetric alternations, featuring a different duration of the phases with and without antimicrobial, we shed light on the existence of a minimum for the time taken by the population to fully evolve resistance. The corresponding dramatic acceleration of the evolution of antimicrobial resistance likely occurs in realistic situations, and may have an important impact both in clinical and experimental situations.\n
\n\n\n\n \n\n \n \n \n \n \n Fixation and absorption in a fluctuating environment.\n \n \n \n\n\n \n Danino, M.; and Shnerb, N. M.\n\n\n \n\n\n\n Journal of Theoretical Biology, 441: 84–92. March 2018.\n MAG ID: 2963213838\n\n\n\n
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\n\n\n@article{danino_fixation_2018,\n\ttitle = {Fixation and absorption in a fluctuating environment},\n\tvolume = {441},\n\tdoi = {10.1016/j.jtbi.2018.01.004},\n\tabstract = {Abstract A fundamental problem in the fields of population genetics, evolution, and community ecology, is the fate of a single mutant, or invader, introduced in a finite population of wild types. For a fixed-size community of N individuals, with Markovian, zero-sum dynamics driven by stochastic birth-death events, the mutant population eventually reaches either fixation or extinction. The classical analysis, provided by Kimura and his coworkers, is focused on the neutral case, [where the dynamics is only due to demographic stochasticity (drift)], and on time-independent selective forces (deleterious/beneficial mutation). However, both theoretical arguments and empirical analyses suggest that in many cases the selective forces fluctuate in time (temporal environmental stochasticity). Here we consider a generic model for a system with demographic noise and fluctuating selection. Our system is characterized by the time-averaged (log)-fitness s 0 and zero-mean fitness fluctuations. These fluctuations, in turn, are parameterized by their amplitude γ and their correlation time δ . We provide asymptotic (large N ) formulas for the chance of fixation, the mean time to fixation and the mean time to absorption. Our expressions interpolate correctly between the constant selection limit γ →0 and the time-averaged neutral case s 0 = 0 .},\n\tjournal = {Journal of Theoretical Biology},\n\tauthor = {Danino, Matan and Shnerb, Nadav M.},\n\tmonth = mar,\n\tyear = {2018},\n\tdoi = {10.1016/j.jtbi.2018.01.004},\n\tnote = {MAG ID: 2963213838},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {84--92},\n\tfile = {Danino and Shnerb - 2018 - Fixation and absorption in a fluctuating environme.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\UPQAEPGC\\\\Danino and Shnerb - 2018 - Fixation and absorption in a fluctuating environme.pdf:application/pdf},\n}\n\n\n\n Abstract A fundamental problem in the fields of population genetics, evolution, and community ecology, is the fate of a single mutant, or invader, introduced in a finite population of wild types. For a fixed-size community of N individuals, with Markovian, zero-sum dynamics driven by stochastic birth-death events, the mutant population eventually reaches either fixation or extinction. The classical analysis, provided by Kimura and his coworkers, is focused on the neutral case, [where the dynamics is only due to demographic stochasticity (drift)], and on time-independent selective forces (deleterious/beneficial mutation). However, both theoretical arguments and empirical analyses suggest that in many cases the selective forces fluctuate in time (temporal environmental stochasticity). Here we consider a generic model for a system with demographic noise and fluctuating selection. Our system is characterized by the time-averaged (log)-fitness s 0 and zero-mean fitness fluctuations. These fluctuations, in turn, are parameterized by their amplitude γ and their correlation time δ . We provide asymptotic (large N ) formulas for the chance of fixation, the mean time to fixation and the mean time to absorption. Our expressions interpolate correctly between the constant selection limit γ →0 and the time-averaged neutral case s 0 = 0 .\n
\n\n\n\n \n\n \n \n \n \n \n Stability of two-species communities: Drift, environmental stochasticity, storage effect and selection.\n \n \n \n\n\n \n Danino, M.; Kessler, D. A.; and Shnerb, N. M.\n\n\n \n\n\n\n Theoretical Population Biology, 119: 57–71. February 2018.\n MAG ID: 2963890507\n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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\n\n\n@article{danino_stability_2018,\n\ttitle = {Stability of two-species communities: {Drift}, environmental stochasticity, storage effect and selection.},\n\tvolume = {119},\n\tdoi = {10.1016/j.tpb.2017.11.003},\n\tabstract = {The dynamics of two competing species in a finite size community is one of the most studied problems in population genetics and community ecology. Stochastic fluctuations lead, inevitably, to the extinction of one of the species, but the relevant timescale depends on the underlying dynamics. The persistence time of the community has been calculated both for neutral models, where the only driving force of the system is drift (demographic stochasticity), and for models with strong selection. Following recent analyses that stress the importance of environmental stochasticity in empirical systems, we present here a general theory of the persistence time of a two-species community where drift, environmental variations and time independent selective advantage are all taken into account.},\n\tjournal = {Theoretical Population Biology},\n\tauthor = {Danino, Matan and Kessler, David A. and Shnerb, Nadav M.},\n\tmonth = feb,\n\tyear = {2018},\n\tdoi = {10.1016/j.tpb.2017.11.003},\n\tpmid = {29175607},\n\tnote = {MAG ID: 2963890507},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {57--71},\n\tfile = {Danino et al. - 2018 - Stability of two-species communities Drift, envir.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\L6D2LHEG\\\\Danino et al. - 2018 - Stability of two-species communities Drift, envir.pdf:application/pdf},\n}\n\n\n\n The dynamics of two competing species in a finite size community is one of the most studied problems in population genetics and community ecology. Stochastic fluctuations lead, inevitably, to the extinction of one of the species, but the relevant timescale depends on the underlying dynamics. The persistence time of the community has been calculated both for neutral models, where the only driving force of the system is drift (demographic stochasticity), and for models with strong selection. Following recent analyses that stress the importance of environmental stochasticity in empirical systems, we present here a general theory of the persistence time of a two-species community where drift, environmental variations and time independent selective advantage are all taken into account.\n
\n\n\n\n \n\n \n \n \n \n \n \n Frequency- and Amplitude-Dependent Microbial Population Dynamics during Cycles of Feast and Famine.\n \n \n \n \n\n\n \n Merritt, J.; and Kuehn, S.\n\n\n \n\n\n\n Physical Review Letters, 121(9): 098101. August 2018.\n Publisher: American Physical Society\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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\n\n\n@article{merritt_frequency-_2018,\n\ttitle = {Frequency- and {Amplitude}-{Dependent} {Microbial} {Population} {Dynamics} during {Cycles} of {Feast} and {Famine}},\n\tvolume = {121},\n\turl = {https://link.aps.org/doi/10.1103/PhysRevLett.121.098101},\n\tdoi = {10.1103/PhysRevLett.121.098101},\n\tabstract = {In nature microbial populations are subject to fluctuating nutrient levels. Nutrient fluctuations are important for evolutionary and ecological dynamics in microbial communities since they impact growth rates, population sizes, and biofilm formation. Here we use automated continuous-culture devices and high-throughput imaging to show that when populations of Escherichia coli are subjected to cycles of nutrient excess (feasts) and scarcity (famine) their abundance dynamics during famines depend on the frequency and amplitude of feasts. We show that frequency and amplitude dependent dynamics in planktonic populations arise from nutrient and history dependent rates of aggregation and dispersal. A phenomenological model recapitulates our experimental observations. Our results show that the statistical properties of environmental fluctuations have substantial impacts on spatial structure in bacterial populations driving large changes in abundance dynamics.},\n\tnumber = {9},\n\turldate = {2023-03-14},\n\tjournal = {Physical Review Letters},\n\tauthor = {Merritt, Jason and Kuehn, Seppe},\n\tmonth = aug,\n\tyear = {2018},\n\tnote = {Publisher: American Physical Society},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {098101},\n\tfile = {APS Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\K9W2AVPU\\\\PhysRevLett.121.html:text/html;Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\DFNIBMI5\\\\Merritt and Kuehn - 2018 - Frequency- and Amplitude-Dependent Microbial Popul.pdf:application/pdf},\n}\n\n\n\n In nature microbial populations are subject to fluctuating nutrient levels. Nutrient fluctuations are important for evolutionary and ecological dynamics in microbial communities since they impact growth rates, population sizes, and biofilm formation. Here we use automated continuous-culture devices and high-throughput imaging to show that when populations of Escherichia coli are subjected to cycles of nutrient excess (feasts) and scarcity (famine) their abundance dynamics during famines depend on the frequency and amplitude of feasts. We show that frequency and amplitude dependent dynamics in planktonic populations arise from nutrient and history dependent rates of aggregation and dispersal. A phenomenological model recapitulates our experimental observations. Our results show that the statistical properties of environmental fluctuations have substantial impacts on spatial structure in bacterial populations driving large changes in abundance dynamics.\n
\n\n\n\n \n\n \n \n \n \n \n Stochastic population dynamics in spatially extended predator-prey systems.\n \n \n \n\n\n \n Dobramysl, U.; Mobilia, M.; Pleimling, M.; and Täuber, U. C.\n\n\n \n\n\n\n Journal of Physics A: Mathematical and Theoretical, 51: 063001. 2018.\n \n\n\n\n
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\n\n\n\n@article{Dobra18,\n\ttitle = {Stochastic population dynamics in spatially extended predator-prey systems},\n\tvolume = {51},\n\tjournal = {Journal of Physics A: Mathematical and Theoretical},\n\tauthor = {Dobramysl, U. and Mobilia, M. and Pleimling, M. and Täuber, U. C.},\n\tyear = {2018},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {063001},\n\tfile = {Dobramysl et al. - 2018 - Stochastic population dynamics in spatially extend.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\SH6GH4LM\\\\Dobramysl et al. - 2018 - Stochastic population dynamics in spatially extend.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Chesson’s coexistence theory.\n \n \n \n\n\n \n Barabás, G.; D'Andrea, R.; and Stump, S.\n\n\n \n\n\n\n Ecological Monographs, 88: 1. 2018.\n \n\n\n\n
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\n\n\n\n@article{Barabas18,\n\ttitle = {Chesson’s coexistence theory},\n\tvolume = {88},\n\tjournal = {Ecological Monographs},\n\tauthor = {Barabás, G. and D'Andrea, R. and Stump, S.M.},\n\tyear = {2018},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {1},\n\tfile = {Barabás et al. - 2018 - Chesson’s coexistence theory.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\K9QZQSEB\\\\Barabás et al. - 2018 - Chesson’s coexistence theory.pdf:application/pdf},\n}\n\n\n\n
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\n \n \n\n \n \n \n \n \n \n Species coexistence in a neutral dynamics with environmental noise.\n \n \n \n \n\n\n \n Hidalgo, J.; Suweis, S.; and Maritan, A.\n\n\n \n\n\n\n Journal of Theoretical Biology, 413: 1–10. January 2017.\n arXiv:1609.00520 [q-bio]\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{hidalgo_species_2017,\n\ttitle = {Species coexistence in a neutral dynamics with environmental noise},\n\tvolume = {413},\n\tissn = {00225193},\n\turl = {http://arxiv.org/abs/1609.00520},\n\tdoi = {10.1016/j.jtbi.2016.11.002},\n\tabstract = {Environmental fluctuations have important consequences in the organization of ecological communities, and understanding how such variability influences the biodiversity of an ecosystem is a major question in ecology. In this paper, we analyze the case of two species competing for the resources within the framework of the neutral theory where we introduce environmental noise, devoting special attention on how such variability modulates species fitness. The environment is dichotomous and stochastically alternates between periods favoring one of the species while disfavoring the other one, preserving neutrality on the long term. We study two different scenarios: in the first one species fitness varies linearly with the environment, and in the second one the effective fitness is re-scaled by the total fitness of the individuals competing for the same resource. We find that, in the former case environmental fluctuations always reduce the time of species coexistence, whereas such a time can be enhanced or reduced in the latter case, depending on the correlation time of the environment. This phenomenon can be understood as a direct consequence of the Chesson’s storage effect.},\n\tlanguage = {en},\n\turldate = {2022-05-16},\n\tjournal = {Journal of Theoretical Biology},\n\tauthor = {Hidalgo, Jorge and Suweis, Samir and Maritan, Amos},\n\tmonth = jan,\n\tyear = {2017},\n\tnote = {arXiv:1609.00520 [q-bio]},\n\tkeywords = {unread, ⛔ No INSPIRE recid found},\n\tpages = {1--10},\n\tfile = {Hidalgo et al. - 2017 - Species coexistence in a neutral dynamics with env.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\GQJU8SCR\\\\Hidalgo et al. - 2017 - Species coexistence in a neutral dynamics with env.pdf:application/pdf},\n}\n\n\n\n Environmental fluctuations have important consequences in the organization of ecological communities, and understanding how such variability influences the biodiversity of an ecosystem is a major question in ecology. In this paper, we analyze the case of two species competing for the resources within the framework of the neutral theory where we introduce environmental noise, devoting special attention on how such variability modulates species fitness. The environment is dichotomous and stochastically alternates between periods favoring one of the species while disfavoring the other one, preserving neutrality on the long term. We study two different scenarios: in the first one species fitness varies linearly with the environment, and in the second one the effective fitness is re-scaled by the total fitness of the individuals competing for the same resource. We find that, in the former case environmental fluctuations always reduce the time of species coexistence, whereas such a time can be enhanced or reduced in the latter case, depending on the correlation time of the environment. This phenomenon can be understood as a direct consequence of the Chesson’s storage effect.\n
\n\n\n\n \n\n \n \n \n \n \n \n Evolution of a Fluctuating Population in a Randomly Switching Environment.\n \n \n \n \n\n\n \n Wienand, K.; Frey, E.; and Mobilia, M.\n\n\n \n\n\n\n Physical Review Letters, 119(15): 158301. October 2017.\n Publisher: American Physical Society\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{wienand_evolution_2017,\n\ttitle = {Evolution of a {Fluctuating} {Population} in a {Randomly} {Switching} {Environment}},\n\tvolume = {119},\n\turl = {https://link.aps.org/doi/10.1103/PhysRevLett.119.158301},\n\tdoi = {10.1103/PhysRevLett.119.158301},\n\tabstract = {Environment plays a fundamental role in the competition for resources, and hence in the evolution of populations. Here, we study a well-mixed, finite population consisting of two strains competing for the limited resources provided by an environment that randomly switches between states of abundance and scarcity. Assuming that one strain grows slightly faster than the other, we consider two scenarios—one of pure resource competition, and one in which one strain provides a public good—and investigate how environmental randomness (external noise) coupled to demographic (internal) noise determines the population’s fixation properties and size distribution. By analytical means and simulations, we show that these coupled sources of noise can significantly enhance the fixation probability of the slower-growing species. We also show that the population size distribution can be unimodal, bimodal, or multimodal and undergoes noise-induced transitions between these regimes when the rate of switching matches the population’s growth rate.},\n\tnumber = {15},\n\turldate = {2023-02-23},\n\tjournal = {Physical Review Letters},\n\tauthor = {Wienand, Karl and Frey, Erwin and Mobilia, Mauro},\n\tmonth = oct,\n\tyear = {2017},\n\tnote = {Publisher: American Physical Society},\n\tkeywords = {read, on website, ⛔ No INSPIRE recid found},\n\tpages = {158301},\n\tfile = {APS Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\RUV52LW2\\\\PhysRevLett.119.html:text/html;Full Text:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\ZRDRPDB7\\\\Wienand et al. - 2017 - Evolution of a Fluctuating Population in a Randoml.pdf:application/pdf},\n}\n\n\n\n Environment plays a fundamental role in the competition for resources, and hence in the evolution of populations. Here, we study a well-mixed, finite population consisting of two strains competing for the limited resources provided by an environment that randomly switches between states of abundance and scarcity. Assuming that one strain grows slightly faster than the other, we consider two scenarios—one of pure resource competition, and one in which one strain provides a public good—and investigate how environmental randomness (external noise) coupled to demographic (internal) noise determines the population’s fixation properties and size distribution. By analytical means and simulations, we show that these coupled sources of noise can significantly enhance the fixation probability of the slower-growing species. We also show that the population size distribution can be unimodal, bimodal, or multimodal and undergoes noise-induced transitions between these regimes when the rate of switching matches the population’s growth rate.\n
\n\n\n\n \n\n \n \n \n \n \n Bet hedging against demographic fluctuations.\n \n \n \n\n\n \n Xue, B. K.; and Leibler, S.\n\n\n \n\n\n\n , 119: 108103. 2017.\n \n\n\n\n
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\n\n\n\n@article{Xue17,\n\ttitle = {Bet hedging against demographic fluctuations},\n\tvolume = {119},\n\tauthor = {Xue, B. K. and Leibler, S.},\n\tyear = {2017},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {108103},\n\tfile = {Xue and Leibler - 2017 - Bet hedging against demographic fluctuations.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\33CMR9P8\\\\Xue and Leibler - 2017 - Bet hedging against demographic fluctuations.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Persistence and reversal of plasmid-mediated antibiotic resistance.\n \n \n \n\n\n \n Lopatkin, A.; Meredith, H.; Srimani, J.; Pfeiffer, C.; Durrett, R.; and You, L.\n\n\n \n\n\n\n Nature Communications, 8: 1689. 2017.\n \n\n\n\n
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\n\n\n\n@article{Lopatkin17,\n\ttitle = {Persistence and reversal of plasmid-mediated antibiotic resistance},\n\tvolume = {8},\n\tjournal = {Nature Communications},\n\tauthor = {Lopatkin, A.J. and Meredith, H.R. and Srimani, J.K. and Pfeiffer, C. and Durrett, R. and You, L.},\n\tyear = {2017},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {1689},\n\tfile = {Lopatkin et al. - 2017 - Persistence and reversal of plasmid-mediated antib.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\XWYVP3ZW\\\\Lopatkin et al. - 2017 - Persistence and reversal of plasmid-mediated antib.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n WKB theory of large deviations in stochastic populations.\n \n \n \n\n\n \n Assaf, M.; and Meerson, B.\n\n\n \n\n\n\n Journal of Physics A: Mathematical and Theoretical, 50: 263001. 2017.\n \n\n\n\n
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\n\n\n\n@article{assaf2017,\n\ttitle = {{WKB} theory of large deviations in stochastic populations},\n\tvolume = {50},\n\tjournal = {Journal of Physics A: Mathematical and Theoretical},\n\tauthor = {Assaf, M. and Meerson, B.},\n\tyear = {2017},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {263001},\n\tfile = {Assaf and Meerson - 2017 - WKB theory of large deviations in stochastic popul.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\Y85AWGNX\\\\Assaf and Meerson - 2017 - WKB theory of large deviations in stochastic popul.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Resonant activation of population extinctions.\n \n \n \n\n\n \n Spalding, C.; Doering, C.; and Flierl, G.\n\n\n \n\n\n\n Physical Review E: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 96: 042411. 2017.\n Publisher: APS\n\n\n\n
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\n\n\n\n@article{Spalding17,\n\ttitle = {Resonant activation of population extinctions},\n\tvolume = {96},\n\tjournal = {Physical Review E: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics},\n\tauthor = {Spalding, C. and Doering, C.R. and Flierl, G.R.},\n\tyear = {2017},\n\tnote = {Publisher: APS},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {042411},\n\tfile = {Spalding et al. - 2017 - Resonant activation of population extinctions.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\22PBQVEK\\\\Spalding et al. - 2017 - Resonant activation of population extinctions.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Fitness costs of plasmids: a limit to plasmid transmission.\n \n \n \n\n\n \n San Millan, A.; and Maclean, R C.\n\n\n \n\n\n\n Microbiol. Spectrum, 5(5): 5–5. 2017.\n \n\n\n\n
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\n\n\n\n@article{sanmillan2017fitness,\n\ttitle = {Fitness costs of plasmids: a limit to plasmid transmission},\n\tvolume = {5},\n\tdoi = {10.1128/microbiolspec.MTBP-0016-2017},\n\tnumber = {5},\n\tjournal = {Microbiol. Spectrum},\n\tauthor = {San Millan, Alvaro and Maclean, R Craig},\n\tyear = {2017},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {5--5},\n\tfile = {San Millan and Maclean - 2017 - Fitness costs of plasmids a limit to plasmid tran.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\L7UPJQBP\\\\San Millan and Maclean - 2017 - Fitness costs of plasmids a limit to plasmid tran.pdf:application/pdf},\n}\n\n\n\n
\n\n \n \n 2016\n \n \n (8)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Intrinsic noise in systems with switching environments.\n \n \n \n \n\n\n \n Hufton, P. G.; Lin, Y. T.; Galla, T.; and McKane, A. J.\n\n\n \n\n\n\n Physical Review E, 93(5): 052119. May 2016.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n\n@article{hufton_intrinsic_2016,\n\ttitle = {Intrinsic noise in systems with switching environments},\n\tvolume = {93},\n\tissn = {2470-0045, 2470-0053},\n\turl = {https://link.aps.org/doi/10.1103/PhysRevE.93.052119},\n\tdoi = {10.1103/PhysRevE.93.052119},\n\tlanguage = {en},\n\tnumber = {5},\n\turldate = {2022-02-08},\n\tjournal = {Physical Review E},\n\tauthor = {Hufton, Peter G. and Lin, Yen Ting and Galla, Tobias and McKane, Alan J.},\n\tmonth = may,\n\tyear = {2016},\n\tkeywords = {read, on website, ⛔ No INSPIRE recid found},\n\tpages = {052119},\n\tfile = {Hufton et al. - 2016 - Intrinsic noise in systems with switching environm.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\8EC75M2Y\\\\Hufton et al. - 2016 - Intrinsic noise in systems with switching environm.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n \n Tackling drug-resistant infections globally: final report and recommendations.\n \n \n \n \n\n\n \n O'Neill, J.\n\n\n \n\n\n\n Technical Report Government of the United Kingdom, May 2016.\n \n\n\n\n
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\n\n\n@techreport{oneill_tackling_2016,\n\ttype = {Report},\n\ttitle = {Tackling drug-resistant infections globally: final report and recommendations},\n\tshorttitle = {Tackling drug-resistant infections globally},\n\turl = {https://apo.org.au/node/63983},\n\tabstract = {Concerned about the rising levels of drug resistance whereby microbes evolve to become immune to a known drugs, the UK Prime Minister asked economist Jim O’Neill to analyse this global problem of antimicrobial resistance (AMR) and propose concrete actions to tackle it internationally. In July 2014, the UK Government commissioned the Review on Antimicrobial Resistance in collaboration with the Wellcome Trust.},\n\tlanguage = {en},\n\turldate = {2022-07-04},\n\tinstitution = {Government of the United Kingdom},\n\tauthor = {O'Neill, Jim},\n\tmonth = may,\n\tyear = {2016},\n\tkeywords = {unread, ⛔ No INSPIRE recid found},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\89AW2GQX\\\\O'Neill - 2016 - Tackling drug-resistant infections globally final.pdf:application/pdf;Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\G92CJG4J\\\\63983.html:text/html},\n}\n\n\n\n Concerned about the rising levels of drug resistance whereby microbes evolve to become immune to a known drugs, the UK Prime Minister asked economist Jim O’Neill to analyse this global problem of antimicrobial resistance (AMR) and propose concrete actions to tackle it internationally. In July 2014, the UK Government commissioned the Review on Antimicrobial Resistance in collaboration with the Wellcome Trust.\n
\n\n\n\n \n\n \n \n \n \n \n \n Statistical Mechanics of Ecological Systems: Neutral Theory and Beyond.\n \n \n \n \n\n\n \n Azaele, S.; Suweis, S.; Grilli, J.; Volkov, I.; Banavar, J. R.; and Maritan, A.\n\n\n \n\n\n\n Reviews of Modern Physics, 88(3): 035003. July 2016.\n arXiv:1506.01721 [cond-mat, physics:physics, q-bio]\n\n\n\n
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Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n
\n\n\n@article{azaele_statistical_2016,\n\ttitle = {Statistical {Mechanics} of {Ecological} {Systems}: {Neutral} {Theory} and {Beyond}},\n\tvolume = {88},\n\tissn = {0034-6861, 1539-0756},\n\tshorttitle = {Statistical {Mechanics} of {Ecological} {Systems}},\n\turl = {http://arxiv.org/abs/1506.01721},\n\tdoi = {10.1103/RevModPhys.88.035003},\n\tabstract = {The simplest theories often have much merit and many limitations, and in this vein, the value of Neutral Theory (NT) has been the subject of much debate over the past 15 years. NT was proposed at the turn of the century by Stephen Hubbell to explain pervasive patterns observed in the organization of ecosystems. Its originally tepid reception among ecologists contrasted starkly with the excitement it caused among physicists and mathematicians. Indeed, NT spawned several theoretical studies that attempted to explain empirical data and predicted trends of quantities that had not yet been studied. While there are a few reviews of NT oriented towards ecologists, our goal here is to review the quantitative results of NT and its extensions for physicists who are interested in learning what NT is, what its successes are and what important problems remain unresolved. Furthermore, we hope that this review could also be of interest to theoretical ecologists because many potentially interesting results are buried in the vast NT literature. We propose to make these more accessible by extracting them and presenting them in a logical fashion. We conclude the review by discussing how one might introduce realistic non-neutral elements into the current models.},\n\tnumber = {3},\n\turldate = {2023-03-14},\n\tjournal = {Reviews of Modern Physics},\n\tauthor = {Azaele, Sandro and Suweis, Samir and Grilli, Jacopo and Volkov, Igor and Banavar, Jayanth R. and Maritan, Amos},\n\tmonth = jul,\n\tyear = {2016},\n\tnote = {arXiv:1506.01721 [cond-mat, physics:physics, q-bio]},\n\tkeywords = {Quantitative Biology - Populations and Evolution, Condensed Matter - Statistical Mechanics, Physics - Biological Physics, ⛔ No INSPIRE recid found},\n\tpages = {035003},\n\tfile = {arXiv Fulltext PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\U7I52CWJ\\\\Azaele et al. - 2016 - Statistical Mechanics of Ecological Systems Neutr.pdf:application/pdf;arXiv.org Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\4HMACQ98\\\\1506.html:text/html},\n}\n\n\n\n The simplest theories often have much merit and many limitations, and in this vein, the value of Neutral Theory (NT) has been the subject of much debate over the past 15 years. NT was proposed at the turn of the century by Stephen Hubbell to explain pervasive patterns observed in the organization of ecosystems. Its originally tepid reception among ecologists contrasted starkly with the excitement it caused among physicists and mathematicians. Indeed, NT spawned several theoretical studies that attempted to explain empirical data and predicted trends of quantities that had not yet been studied. While there are a few reviews of NT oriented towards ecologists, our goal here is to review the quantitative results of NT and its extensions for physicists who are interested in learning what NT is, what its successes are and what important problems remain unresolved. Furthermore, we hope that this review could also be of interest to theoretical ecologists because many potentially interesting results are buried in the vast NT literature. We propose to make these more accessible by extracting them and presenting them in a logical fashion. We conclude the review by discussing how one might introduce realistic non-neutral elements into the current models.\n
\n\n\n\n \n\n \n \n \n \n \n The effect of environmental stochasticity on species richness in neutral communities.\n \n \n \n\n\n \n Danino, M.; Shnerb, N. M.; Azaele, S.; Kunin, W. E.; and Kessler, D. A.\n\n\n \n\n\n\n Journal of Theoretical Biology, 409: 155–164. November 2016.\n \n\n\n\n
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\n\n\n@article{danino_effect_2016,\n\ttitle = {The effect of environmental stochasticity on species richness in neutral communities},\n\tvolume = {409},\n\tissn = {1095-8541},\n\tdoi = {10.1016/j.jtbi.2016.08.029},\n\tabstract = {Environmental stochasticity is known to be a destabilizing factor, increasing abundance fluctuations and extinction rates of populations. However, the stability of a community may benefit from the differential response of species to environmental variations due to the storage effect. This paper provides a systematic and comprehensive discussion of these two contradicting tendencies, using the metacommunity version of the recently proposed time-average neutral model of biodiversity which incorporates environmental stochasticity and demographic noise and allows for extinction and speciation. We show that the incorporation of demographic noise into the model is essential to its applicability, yielding realistic behavior of the system when fitness variations are relatively weak. The dependence of species richness on the strength of environmental stochasticity changes sign when the correlation time of the environmental variations increases. This transition marks the point at which the storage effect no longer succeeds in stabilizing the community.},\n\tlanguage = {eng},\n\tjournal = {Journal of Theoretical Biology},\n\tauthor = {Danino, Matan and Shnerb, Nadav M. and Azaele, Sandro and Kunin, William E. and Kessler, David A.},\n\tmonth = nov,\n\tyear = {2016},\n\tpmid = {27565247},\n\tkeywords = {Biodiversity, Community dynamics, Environmental stochasticity, Models, Biological, Neutral theory, Storage effect, ⛔ No INSPIRE recid found},\n\tpages = {155--164},\n\tfile = {Accepted Version:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\GH3ITXSR\\\\Danino et al. - 2016 - The effect of environmental stochasticity on speci.pdf:application/pdf},\n}\n\n\n\n Environmental stochasticity is known to be a destabilizing factor, increasing abundance fluctuations and extinction rates of populations. However, the stability of a community may benefit from the differential response of species to environmental variations due to the storage effect. This paper provides a systematic and comprehensive discussion of these two contradicting tendencies, using the metacommunity version of the recently proposed time-average neutral model of biodiversity which incorporates environmental stochasticity and demographic noise and allows for extinction and speciation. We show that the incorporation of demographic noise into the model is essential to its applicability, yielding realistic behavior of the system when fitness variations are relatively weak. The dependence of species richness on the strength of environmental stochasticity changes sign when the correlation time of the environmental variations increases. This transition marks the point at which the storage effect no longer succeeds in stabilizing the community.\n
\n\n\n\n \n\n \n \n \n \n \n Complex interplay of physiology and selection in the emergence of antibiotic resistance.\n \n \n \n\n\n \n Lin, W.; and Kussell, E.\n\n\n \n\n\n\n Current Biology, 26: 1486. 2016.\n \n\n\n\n
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\n\n\n\n@article{Kussell16,\n\ttitle = {Complex interplay of physiology and selection in the emergence of antibiotic resistance},\n\tvolume = {26},\n\tjournal = {Current Biology},\n\tauthor = {Lin, W.-H. and Kussell, E.},\n\tyear = {2016},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {1486},\n\tfile = {Lin and Kussell - 2016 - Complex interplay of physiology and selection in t.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\ZSWDWNHC\\\\Lin and Kussell - 2016 - Complex interplay of physiology and selection in t.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n The ecology and evolution of microbial competition.\n \n \n \n\n\n \n Ghoul, M.; and Mitri, S.\n\n\n \n\n\n\n Trends in Microbiology, 24(10): 833–845. 2016.\n \n\n\n\n
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\n\n\n\n@article{Mitri16,\n\ttitle = {The ecology and evolution of microbial competition},\n\tvolume = {24},\n\tnumber = {10},\n\tjournal = {Trends in Microbiology},\n\tauthor = {Ghoul, M. and Mitri, S.},\n\tyear = {2016},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {833--845},\n\tfile = {Ghoul and Mitri - 2016 - The ecology and evolution of microbial competition.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\7AJHY25Y\\\\Ghoul and Mitri - 2016 - The ecology and evolution of microbial competition.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Eco-evolutionary dynamics of social dilemmas.\n \n \n \n\n\n \n Gokhale, C. S.; and Hauert, C\n\n\n \n\n\n\n Theoretical Population Biology, 111: 28. 2016.\n \n\n\n\n
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\n\n\n\n@article{Gokhale16,\n\ttitle = {Eco-evolutionary dynamics of social dilemmas},\n\tvolume = {111},\n\tjournal = {Theoretical Population Biology},\n\tauthor = {Gokhale, C. S. and Hauert, C},\n\tyear = {2016},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {28},\n\tfile = {Gokhale and Hauert - 2016 - Eco-evolutionary dynamics of social dilemmas.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\ANNCPPDW\\\\Gokhale and Hauert - 2016 - Eco-evolutionary dynamics of social dilemmas.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n The initial state of the human gut microbiome determines its reshaping by antibiotics.\n \n \n \n\n\n \n Raymond, F.; and et al.\n\n\n \n\n\n\n ISME Journal, 10: 707. 2016.\n \n\n\n\n
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\n\n\n\n@article{Raymond16,\n\ttitle = {The initial state of the human gut microbiome determines its reshaping by antibiotics},\n\tvolume = {10},\n\tjournal = {ISME Journal},\n\tauthor = {Raymond, F. and {\\textit{et al.}}},\n\tyear = {2016},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {707},\n\tfile = {Raymond and et al. - 2016 - The initial state of the human gut microbiome dete.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\DMLLCH29\\\\Raymond and et al. - 2016 - The initial state of the human gut microbiome dete.pdf:application/pdf},\n}\n\n\n\n
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\n \n \n\n \n \n \n \n \n \n The emergence of cooperation from a single mutant during microbial life cycles.\n \n \n \n \n\n\n \n Melbinger, A.; Cremer, J.; and Frey, E.\n\n\n \n\n\n\n Journal of The Royal Society Interface, 12(108): 20150171. July 2015.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{melbinger_emergence_2015,\n\ttitle = {The emergence of cooperation from a single mutant during microbial life cycles},\n\tvolume = {12},\n\tissn = {1742-5689, 1742-5662},\n\turl = {https://royalsocietypublishing.org/doi/10.1098/rsif.2015.0171},\n\tdoi = {10.1098/rsif.2015.0171},\n\tabstract = {Cooperative behaviour is widespread in nature, even though cooperating individuals always run the risk of being exploited by free-riders. Population structure effectively promotes cooperation given that a threshold in the level of cooperation was already reached. However, the question how cooperation can emerge from a single mutant, which cannot rely on a benefit provided by other cooperators, is still puzzling. Here, we investigate this question for a well-defined but generic situation based on typical life cycles of microbial populations where individuals regularly form new colonies followed by growth phases. We analyse two evolutionary mechanisms favouring cooperative behaviour and study their strength depending on the inoculation size and the length of a life cycle. In particular, we find that population bottlenecks followed by exponential growth phases strongly increase the survival and fixation probabilities of a single cooperator in a free-riding population.},\n\tlanguage = {en},\n\tnumber = {108},\n\turldate = {2022-02-03},\n\tjournal = {Journal of The Royal Society Interface},\n\tauthor = {Melbinger, Anna and Cremer, Jonas and Frey, Erwin},\n\tmonth = jul,\n\tyear = {2015},\n\tkeywords = {read, fixation probability, coexistence, metapopulation model, on website, ⛔ No INSPIRE recid found},\n\tpages = {20150171},\n\tfile = {Melbinger et al. - 2015 - The emergence of cooperation from a single mutant .pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\UIJLDMY9\\\\Melbinger et al. - 2015 - The emergence of cooperation from a single mutant .pdf:application/pdf},\n}\n\n\n\n Cooperative behaviour is widespread in nature, even though cooperating individuals always run the risk of being exploited by free-riders. Population structure effectively promotes cooperation given that a threshold in the level of cooperation was already reached. However, the question how cooperation can emerge from a single mutant, which cannot rely on a benefit provided by other cooperators, is still puzzling. Here, we investigate this question for a well-defined but generic situation based on typical life cycles of microbial populations where individuals regularly form new colonies followed by growth phases. We analyse two evolutionary mechanisms favouring cooperative behaviour and study their strength depending on the inoculation size and the length of a life cycle. In particular, we find that population bottlenecks followed by exponential growth phases strongly increase the survival and fixation probabilities of a single cooperator in a free-riding population.\n
\n\n\n\n \n\n \n \n \n \n \n \n A neutral theory with environmental stochasticity explains static and dynamic properties of ecological communities.\n \n \n \n \n\n\n \n Kalyuzhny, M.; Kadmon, R.; and Shnerb, N. M.\n\n\n \n\n\n\n Ecology Letters, 18(6): 572–580. 2015.\n _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.12439\n\n\n\n
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\n\n\n@article{kalyuzhny_neutral_2015,\n\ttitle = {A neutral theory with environmental stochasticity explains static and dynamic properties of ecological communities},\n\tvolume = {18},\n\tissn = {1461-0248},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ele.12439},\n\tdoi = {10.1111/ele.12439},\n\tabstract = {Understanding the forces shaping ecological communities is crucial to basic science and conservation. Neutral theory has made considerable progress in explaining static properties of communities, like species abundance distributions (SADs), with a simple and generic model, but was criticised for making unrealistic predictions of fundamental dynamic patterns and for being sensitive to interspecific differences in fitness. Here, we show that a generalised neutral theory incorporating environmental stochasticity may resolve these limitations. We apply the theory to real data (the tropical forest of Barro Colorado Island) and demonstrate that it much better explains the properties of short-term population fluctuations and the decay of compositional similarity with time, while retaining the ability to explain SADs. Furthermore, the predictions are considerably more robust to interspecific fitness differences. Our results suggest that this integration of niches and stochasticity may serve as a minimalistic framework explaining fundamental static and dynamic characteristics of ecological communities.},\n\tlanguage = {en},\n\tnumber = {6},\n\turldate = {2022-07-02},\n\tjournal = {Ecology Letters},\n\tauthor = {Kalyuzhny, Michael and Kadmon, Ronen and Shnerb, Nadav M.},\n\tyear = {2015},\n\tnote = {\\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.12439},\n\tkeywords = {unread, BCI, community dynamics, community similarity, demographic stochasticity, environmental stochasticity, fluctuation scaling, neutral theory, population fluctuations, species abundance distributions, ⛔ No INSPIRE recid found},\n\tpages = {572--580},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\JBKWSXS2\\\\Kalyuzhny et al. - 2015 - A neutral theory with environmental stochasticity .pdf:application/pdf;Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\IITU5NMH\\\\Kalyuzhny et al. - 2015 - A neutral theory with environmental stochasticity .pdf:application/pdf;Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\GMJPRIDZ\\\\ele.html:text/html},\n}\n\n\n\n Understanding the forces shaping ecological communities is crucial to basic science and conservation. Neutral theory has made considerable progress in explaining static properties of communities, like species abundance distributions (SADs), with a simple and generic model, but was criticised for making unrealistic predictions of fundamental dynamic patterns and for being sensitive to interspecific differences in fitness. Here, we show that a generalised neutral theory incorporating environmental stochasticity may resolve these limitations. We apply the theory to real data (the tropical forest of Barro Colorado Island) and demonstrate that it much better explains the properties of short-term population fluctuations and the decay of compositional similarity with time, while retaining the ability to explain SADs. Furthermore, the predictions are considerably more robust to interspecific fitness differences. Our results suggest that this integration of niches and stochasticity may serve as a minimalistic framework explaining fundamental static and dynamic characteristics of ecological communities.\n
\n\n\n\n \n\n \n \n \n \n \n \n Evolutionary consequences of drug resistance: shared principles across diverse targets and organisms.\n \n \n \n \n\n\n \n Hughes, D.; and Andersson, D. I.\n\n\n \n\n\n\n Nature Reviews Genetics, 16(8): 459–471. August 2015.\n Number: 8 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n
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Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n\n
\n\n\n@article{hughes_evolutionary_2015,\n\ttitle = {Evolutionary consequences of drug resistance: shared principles across diverse targets and organisms},\n\tvolume = {16},\n\tcopyright = {2015 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},\n\tissn = {1471-0064},\n\tshorttitle = {Evolutionary consequences of drug resistance},\n\turl = {https://www.nature.com/articles/nrg3922},\n\tdoi = {10.1038/nrg3922},\n\tabstract = {Across the diverse biological systems discussed in this Review, the underlying principles concerning the mechanisms and dynamics of resistance development are similar.Drug resistance has emerged in all biological systems in which drugs are used as a standard therapeutic strategy to control infections or cancer. There is an urgent need not only to develop new drugs to support effective therapy but also to develop a better understanding of the underlying mechanisms and forces that drive resistance development.Large population sizes and/or high mutation rates ensure that the emergence of drug resistance is not limited by mutation supply in HIV, in many bacterial infections or in human cancers. Mutation supply may be a limiting factor for fungal and parasitic infections.Horizontal gene transfer (HGT) from a very broad gene pool substantially contributes to the emergence of drug resistance in bacteria but is absent as a source of genetic variation in the other systems discussed. We currently know very little about the dynamics and trajectories of HGT events and have a very poor ability to make predictions.The study and understanding of the dynamics of growth and competition within complex populations subjected to drug therapy are being advanced by the increasing application of next-generation sequencing technologies.In biological systems in which resistance emergence has long been acknowledged to be a problem (particularly HIV infection and human cancer), therapy with combinations of drugs is standard of care. The systematic use of drug combinations in the treatment of bacterial, fungal and parasitic infections might be the most effective short-term means to slow resistance emergence.},\n\tlanguage = {en},\n\tnumber = {8},\n\turldate = {2022-07-02},\n\tjournal = {Nature Reviews Genetics},\n\tauthor = {Hughes, Diarmaid and Andersson, Dan I.},\n\tmonth = aug,\n\tyear = {2015},\n\tnote = {Number: 8\nPublisher: Nature Publishing Group},\n\tkeywords = {unread, ⛔ No INSPIRE recid found},\n\tpages = {459--471},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\UVSLQC6Z\\\\Hughes and Andersson - 2015 - Evolutionary consequences of drug resistance shar.pdf:application/pdf;Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\VA86K2W5\\\\nrg3922.html:text/html},\n}\n\n\n\n Across the diverse biological systems discussed in this Review, the underlying principles concerning the mechanisms and dynamics of resistance development are similar.Drug resistance has emerged in all biological systems in which drugs are used as a standard therapeutic strategy to control infections or cancer. There is an urgent need not only to develop new drugs to support effective therapy but also to develop a better understanding of the underlying mechanisms and forces that drive resistance development.Large population sizes and/or high mutation rates ensure that the emergence of drug resistance is not limited by mutation supply in HIV, in many bacterial infections or in human cancers. Mutation supply may be a limiting factor for fungal and parasitic infections.Horizontal gene transfer (HGT) from a very broad gene pool substantially contributes to the emergence of drug resistance in bacteria but is absent as a source of genetic variation in the other systems discussed. We currently know very little about the dynamics and trajectories of HGT events and have a very poor ability to make predictions.The study and understanding of the dynamics of growth and competition within complex populations subjected to drug therapy are being advanced by the increasing application of next-generation sequencing technologies.In biological systems in which resistance emergence has long been acknowledged to be a problem (particularly HIV infection and human cancer), therapy with combinations of drugs is standard of care. The systematic use of drug combinations in the treatment of bacterial, fungal and parasitic infections might be the most effective short-term means to slow resistance emergence.\n
\n\n\n\n \n\n \n \n \n \n \n Stochastic game dynamics under demographic fluctuations.\n \n \n \n\n\n \n Huang, W.; Hauert, C.; and Traulsen, A.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 112(29): 9064–9069. July 2015.\n MAG ID: 1821620939\n\n\n\n
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\n\n\n@article{huang_stochastic_2015,\n\ttitle = {Stochastic game dynamics under demographic fluctuations},\n\tvolume = {112},\n\tdoi = {10.1073/pnas.1418745112},\n\tabstract = {Frequency-dependent selection and demographic fluctuations play important roles in evolutionary and ecological processes. Under frequency-dependent selection, the average fitness of the population may increase or decrease based on interactions between individuals within the population. This should be reflected in fluctuations of the population size even in constant environments. Here, we propose a stochastic model that naturally combines these two evolutionary ingredients by assuming frequency-dependent competition between different types in an individual-based model. In contrast to previous game theoretic models, the carrying capacity of the population, and thus the population size, is determined by pairwise competition of individuals mediated by evolutionary games and demographic stochasticity. In the limit of infinite population size, the averaged stochastic dynamics is captured by deterministic competitive Lotka–Volterra equations. In small populations, demographic stochasticity may instead lead to the extinction of the entire population. Because the population size is driven by fitness in evolutionary games, a population of cooperators is less prone to go extinct than a population of defectors, whereas in the usual systems of fixed size the population would thrive regardless of its average payoff.},\n\tnumber = {29},\n\tjournal = {Proceedings of the National Academy of Sciences of the United States of America},\n\tauthor = {Huang, Weini and Hauert, Christoph and Traulsen, Arne},\n\tmonth = jul,\n\tyear = {2015},\n\tdoi = {10.1073/pnas.1418745112},\n\tpmcid = {4517200},\n\tpmid = {26150518},\n\tnote = {MAG ID: 1821620939},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {9064--9069},\n\tfile = {Full Text:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\53VLYFX9\\\\Huang et al. - 2015 - Stochastic game dynamics under demographic fluctua.pdf:application/pdf},\n}\n\n\n\n Frequency-dependent selection and demographic fluctuations play important roles in evolutionary and ecological processes. Under frequency-dependent selection, the average fitness of the population may increase or decrease based on interactions between individuals within the population. This should be reflected in fluctuations of the population size even in constant environments. Here, we propose a stochastic model that naturally combines these two evolutionary ingredients by assuming frequency-dependent competition between different types in an individual-based model. In contrast to previous game theoretic models, the carrying capacity of the population, and thus the population size, is determined by pairwise competition of individuals mediated by evolutionary games and demographic stochasticity. In the limit of infinite population size, the averaged stochastic dynamics is captured by deterministic competitive Lotka–Volterra equations. In small populations, demographic stochasticity may instead lead to the extinction of the entire population. Because the population size is driven by fitness in evolutionary games, a population of cooperators is less prone to go extinct than a population of defectors, whereas in the usual systems of fixed size the population would thrive regardless of its average payoff.\n
\n\n\n\n \n\n \n \n \n \n \n The Impact of Environmental Fluctuations on Evolutionary Fitness Functions.\n \n \n \n\n\n \n Melbinger, A.; and Vergassola, M.\n\n\n \n\n\n\n Scientific Reports. October 2015.\n MAG ID: 2170960409\n\n\n\n
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\n\n\n@article{melbinger_impact_2015,\n\ttitle = {The {Impact} of {Environmental} {Fluctuations} on {Evolutionary} {Fitness} {Functions}},\n\tdoi = {10.1038/srep15211},\n\tabstract = {The concept of fitness as a measure for a species’ success in natural selection is central to the theory of evolution. We here investigate how reproduction rates which are not constant but vary in response to environmental fluctuations, influence a species’ prosperity and thereby its fitness. Interestingly, we find that not only larger growth rates but also reduced sensitivities to environmental changes substantially increase the fitness. Thereby, depending on the noise level of the environment, it might be an evolutionary successful strategy to minimize this sensitivity rather than to optimize the reproduction speed. Also for neutral evolution, where species with exactly the same properties compete, variability in the growth rates plays a crucial role. The time for one species to fixate is strongly reduced in the presence of environmental noise. Hence, environmental fluctuations constitute a possible explanation for effective population sizes inferred from genetic data that often are much smaller than the census population size.},\n\tjournal = {Scientific Reports},\n\tauthor = {Melbinger, Anna and Vergassola, Massimo},\n\tmonth = oct,\n\tyear = {2015},\n\tdoi = {10.1038/srep15211},\n\tpmcid = {4609966},\n\tpmid = {26477392},\n\tnote = {MAG ID: 2170960409},\n\tkeywords = {Evolutionary ecology, Evolutionary theory, ⛔ No INSPIRE recid found},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\58E2K33S\\\\Melbinger and Vergassola - 2015 - The Impact of Environmental Fluctuations on Evolut.pdf:application/pdf;Melbinger and Vergassola - 2015 - The Impact of Environmental Fluctuations on Evolut.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\CJEZH8MF\\\\Melbinger and Vergassola - 2015 - The Impact of Environmental Fluctuations on Evolut.pdf:application/pdf},\n}\n\n\n\n The concept of fitness as a measure for a species’ success in natural selection is central to the theory of evolution. We here investigate how reproduction rates which are not constant but vary in response to environmental fluctuations, influence a species’ prosperity and thereby its fitness. Interestingly, we find that not only larger growth rates but also reduced sensitivities to environmental changes substantially increase the fitness. Thereby, depending on the noise level of the environment, it might be an evolutionary successful strategy to minimize this sensitivity rather than to optimize the reproduction speed. Also for neutral evolution, where species with exactly the same properties compete, variability in the growth rates plays a crucial role. The time for one species to fixate is strongly reduced in the presence of environmental noise. Hence, environmental fluctuations constitute a possible explanation for effective population sizes inferred from genetic data that often are much smaller than the census population size.\n
\n\n\n\n \n\n \n \n \n \n \n \n Bacteriostatic versus bactericidal antibiotics for patients with serious bacterial infections: systematic review and meta-analysis.\n \n \n \n \n\n\n \n Nemeth, J.; Oesch, G.; and Kuster, S. P.\n\n\n \n\n\n\n Journal of Antimicrobial Chemotherapy, 70(2): 382–395. February 2015.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n\n
\n\n\n@article{nemeth_bacteriostatic_2015,\n\ttitle = {Bacteriostatic versus bactericidal antibiotics for patients with serious bacterial infections: systematic review and meta-analysis},\n\tvolume = {70},\n\tissn = {0305-7453},\n\tshorttitle = {Bacteriostatic versus bactericidal antibiotics for patients with serious bacterial infections},\n\turl = {https://doi.org/10.1093/jac/dku379},\n\tdoi = {10.1093/jac/dku379},\n\tabstract = {Antibiotics are commonly classified into bactericidal and bacteriostatic agents based on their antimicrobial action. We aimed to assess whether this distinction is clinically relevant.OVID MEDLINE, EMBASE, The Cochrane Central Register of Controlled Trials (CENTRAL) and relevant references and conference proceedings using the Web of Science and Scopus databases were searched for randomized controlled trials comparing bactericidal with bacteriostatic antibiotics for treatment of severe infections. Main outcome measures were clinical cure rates and overall mortality. Abstracts of studies selected in the database search were screened by one reviewer; full-text screening and data extraction were performed by three independent reviewers.Thirty-three studies were included. Approximately half of patients were treated with bacteriostatic monotherapy. Infections covered were pneumonia (n = 13), skin and soft tissue infections (n = 8), intra-abdominal infections (n = 4) and others (n = 8). Neither clinical cure rates [risk ratio (RR), 0.99; 95\\% CI, 0.97–1.01; P = 0.11] nor mortality rates (RR, 0.91; 95\\% CI, 0.76–1.08; P = 0.28) were different between patients treated with bactericidal drugs and those treated with bacteriostatic drugs. Subgroup analyses showed a benefit for clinical cure rates associated with linezolid and increased mortality associated with tigecycline. In meta-regression, clinical cure rates remained higher in patients treated with linezolid (P = 0.01); tigecycline displayed a close to significant association with increased mortality (P = 0.05) if compared with other bacteriostatic agents.The categorization of antibiotics into bacteriostatic and bactericidal is unlikely to be relevant in clinical practice if used for abdominal infections, skin and soft tissue infections and pneumonia. Because we were not able to include studies on meningitis, endocarditis or neutropenia, no conclusion regarding these diseases can be drawn.},\n\tnumber = {2},\n\turldate = {2023-03-31},\n\tjournal = {Journal of Antimicrobial Chemotherapy},\n\tauthor = {Nemeth, Johannes and Oesch, Gabriela and Kuster, Stefan P.},\n\tmonth = feb,\n\tyear = {2015},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {382--395},\n\tfile = {Full Text:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\NQJF8TXG\\\\Nemeth et al. - 2015 - Bacteriostatic versus bactericidal antibiotics for.pdf:application/pdf;Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\AEDCMR27\\\\Nemeth et al. - 2015 - Bacteriostatic versus bactericidal antibiotics for.pdf:application/pdf},\n}\n\n\n\n Antibiotics are commonly classified into bactericidal and bacteriostatic agents based on their antimicrobial action. We aimed to assess whether this distinction is clinically relevant.OVID MEDLINE, EMBASE, The Cochrane Central Register of Controlled Trials (CENTRAL) and relevant references and conference proceedings using the Web of Science and Scopus databases were searched for randomized controlled trials comparing bactericidal with bacteriostatic antibiotics for treatment of severe infections. Main outcome measures were clinical cure rates and overall mortality. Abstracts of studies selected in the database search were screened by one reviewer; full-text screening and data extraction were performed by three independent reviewers.Thirty-three studies were included. Approximately half of patients were treated with bacteriostatic monotherapy. Infections covered were pneumonia (n = 13), skin and soft tissue infections (n = 8), intra-abdominal infections (n = 4) and others (n = 8). Neither clinical cure rates [risk ratio (RR), 0.99; 95% CI, 0.97–1.01; P = 0.11] nor mortality rates (RR, 0.91; 95% CI, 0.76–1.08; P = 0.28) were different between patients treated with bactericidal drugs and those treated with bacteriostatic drugs. Subgroup analyses showed a benefit for clinical cure rates associated with linezolid and increased mortality associated with tigecycline. In meta-regression, clinical cure rates remained higher in patients treated with linezolid (P = 0.01); tigecycline displayed a close to significant association with increased mortality (P = 0.05) if compared with other bacteriostatic agents.The categorization of antibiotics into bacteriostatic and bactericidal is unlikely to be relevant in clinical practice if used for abdominal infections, skin and soft tissue infections and pneumonia. Because we were not able to include studies on meningitis, endocarditis or neutropenia, no conclusion regarding these diseases can be drawn.\n
\n\n\n\n \n\n \n \n \n \n \n \n Dynamics of simple gene-network motifs subject to extrinsic fluctuations.\n \n \n \n \n\n\n \n Roberts, E.; Be'er, S.; Bohrer, C.; Sharma, R.; and Assaf, M.\n\n\n \n\n\n\n Physical Review E, 92(6): 062717. December 2015.\n \n\n\n\n
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\n\n\n\n@article{roberts_dynamics_2015,\n\ttitle = {Dynamics of simple gene-network motifs subject to extrinsic fluctuations},\n\tvolume = {92},\n\tissn = {1539-3755, 1550-2376},\n\turl = {https://link.aps.org/doi/10.1103/PhysRevE.92.062717},\n\tdoi = {10.1103/PhysRevE.92.062717},\n\tlanguage = {en},\n\tnumber = {6},\n\turldate = {2023-05-03},\n\tjournal = {Physical Review E},\n\tauthor = {Roberts, Elijah and Be'er, Shay and Bohrer, Chris and Sharma, Rati and Assaf, Michael},\n\tmonth = dec,\n\tyear = {2015},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {062717},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\XU8V5LLU\\\\Roberts et al. - 2015 - Dynamics of simple gene-network motifs subject to .pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Quantifying selective pressures driving bacterial evolution using lineage analysis.\n \n \n \n\n\n \n Lambert, G.; and Kussell, E.\n\n\n \n\n\n\n Physical Review X, 5: 011016. 2015.\n \n\n\n\n
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\n\n\n\n@article{Lambert15,\n\ttitle = {Quantifying selective pressures driving bacterial evolution using lineage analysis},\n\tvolume = {5},\n\tjournal = {Physical Review X},\n\tauthor = {Lambert, G. and Kussell, E.},\n\tyear = {2015},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {011016},\n\tfile = {Lambert and Kussell - 2015 - Quantifying selective pressures driving bacterial .pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\I8R9GCL3\\\\Lambert and Kussell - 2015 - Quantifying selective pressures driving bacterial .pdf:application/pdf},\n}\n\n\n\n
\n\n \n \n 2014\n \n \n (2)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Fixation in finite populations evolving in fluctuating environments.\n \n \n \n \n\n\n \n Ashcroft, P.; Altrock, P. M.; and Galla, T.\n\n\n \n\n\n\n Journal of The Royal Society Interface, 11(100): 20140663. November 2014.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n
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Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n\n
\n\n\n@article{ashcroft_fixation_2014,\n\ttitle = {Fixation in finite populations evolving in fluctuating environments},\n\tvolume = {11},\n\tissn = {1742-5689, 1742-5662},\n\turl = {https://royalsocietypublishing.org/doi/10.1098/rsif.2014.0663},\n\tdoi = {10.1098/rsif.2014.0663},\n\tabstract = {The environment in which a population evolves can have a crucial impact on selection. We study evolutionary dynamics in finite populations of fixed size in a changing environment. The population dynamics are driven by birth and death events. The rates of these events may vary in time depending on the state of the environment, which follows an independent Markov process. We develop a general theory for the fixation probability of a mutant in a population of wild-types, and for mean unconditional and conditional fixation times. We apply our theory to evolutionary games for which the payoff structure varies in time. The mutant can exploit the environmental noise; a dynamic environment that switches between two states can lead to a probability of fixation that is higher than in any of the individual environmental states. We provide an intuitive interpretation of this surprising effect. We also investigate stationary distributions when mutations are present in the dynamics. In this regime, we find two approximations of the stationary measure. One works well for rapid switching, the other for slowly fluctuating environments.},\n\tlanguage = {en},\n\tnumber = {100},\n\turldate = {2022-05-17},\n\tjournal = {Journal of The Royal Society Interface},\n\tauthor = {Ashcroft, Peter and Altrock, Philipp M. and Galla, Tobias},\n\tmonth = nov,\n\tyear = {2014},\n\tkeywords = {read, on website, ⛔ No INSPIRE recid found},\n\tpages = {20140663},\n\tfile = {Ashcroft et al. - 2014 - Fixation in finite populations evolving in fluctua.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\KVRQ4ABY\\\\Ashcroft et al. - 2014 - Fixation in finite populations evolving in fluctua.pdf:application/pdf},\n}\n\n\n\n The environment in which a population evolves can have a crucial impact on selection. We study evolutionary dynamics in finite populations of fixed size in a changing environment. The population dynamics are driven by birth and death events. The rates of these events may vary in time depending on the state of the environment, which follows an independent Markov process. We develop a general theory for the fixation probability of a mutant in a population of wild-types, and for mean unconditional and conditional fixation times. We apply our theory to evolutionary games for which the payoff structure varies in time. The mutant can exploit the environmental noise; a dynamic environment that switches between two states can lead to a probability of fixation that is higher than in any of the individual environmental states. We provide an intuitive interpretation of this surprising effect. We also investigate stationary distributions when mutations are present in the dynamics. In this regime, we find two approximations of the stationary measure. One works well for rapid switching, the other for slowly fluctuating environments.\n
\n\n\n\n \n\n \n \n \n \n \n Temporal variability of forest communities: empirical estimates of population change in 4000 tree species.\n \n \n \n\n\n \n Chisholm, R. A.; Condit, R.; and Rahman, K. A. <. a.\n\n\n \n\n\n\n Ecology Letters, 17: 855. 2014.\n \n\n\n\n
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\n\n\n\n@article{Chisholm14,\n\ttitle = {Temporal variability of forest communities: empirical estimates of population change in 4000 tree species},\n\tvolume = {17},\n\tjournal = {Ecology Letters},\n\tauthor = {Chisholm, R. A. and Condit, R. and Rahman, K. A. \\textit{et al.}},\n\tyear = {2014},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {855},\n\tfile = {Chisholm et al. - 2014 - Temporal variability of forest communities empiri.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\GTWTGCPP\\\\Chisholm et al. - 2014 - Temporal variability of forest communities empiri.pdf:application/pdf},\n}\n\n\n\n
\n\n \n \n 2013\n \n \n (9)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Feedback between Population and Evolutionary Dynamics Determines the Fate of Social Microbial Populations.\n \n \n \n \n\n\n \n Sanchez, A.; and Gore, J.\n\n\n \n\n\n\n PLoS Biology, 11(4): e1001547. April 2013.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{sanchez_feedback_2013,\n\ttitle = {Feedback between {Population} and {Evolutionary} {Dynamics} {Determines} the {Fate} of {Social} {Microbial} {Populations}},\n\tvolume = {11},\n\tissn = {1545-7885},\n\turl = {https://dx.plos.org/10.1371/journal.pbio.1001547},\n\tdoi = {10.1371/journal.pbio.1001547},\n\tabstract = {The evolutionary spread of cheater strategies can destabilize populations engaging in social cooperative behaviors, thus demonstrating that evolutionary changes can have profound implications for population dynamics. At the same time, the relative fitness of cooperative traits often depends upon population density, thus leading to the potential for bi-directional coupling between population density and the evolution of a cooperative trait. Despite the potential importance of these eco-evolutionary feedback loops in social species, they have not yet been demonstrated experimentally and their ecological implications are poorly understood. Here, we demonstrate the presence of a strong feedback loop between population dynamics and the evolutionary dynamics of a social microbial gene, SUC2, in laboratory yeast populations whose cooperative growth is mediated by the SUC2 gene. We directly visualize eco-evolutionary trajectories of hundreds of populations over 50–100 generations, allowing us to characterize the phase space describing the interplay of evolution and ecology in this system. Small populations collapse despite continual evolution towards increased cooperative allele frequencies; large populations with a sufficient number of cooperators ‘‘spiral’’ to a stable state of coexistence between cooperator and cheater strategies. The presence of cheaters does not significantly affect the equilibrium population density, but it does reduce the resilience of the population as well as its ability to adapt to a rapidly deteriorating environment. Our results demonstrate the potential ecological importance of coupling between evolutionary dynamics and the population dynamics of cooperatively growing organisms, particularly in microbes. Our study suggests that this interaction may need to be considered in order to explain intraspecific variability in cooperative behaviors, and also that this feedback between evolution and ecology can critically affect the demographic fate of those species that rely on cooperation for their survival.},\n\tlanguage = {en},\n\tnumber = {4},\n\turldate = {2022-06-07},\n\tjournal = {PLoS Biology},\n\tauthor = {Sanchez, Alvaro and Gore, Jeff},\n\teditor = {Ellner, Stephen P.},\n\tmonth = apr,\n\tyear = {2013},\n\tkeywords = {read, public good, coexistence, batch, experimental, on website, ⛔ No INSPIRE recid found},\n\tpages = {e1001547},\n\tfile = {Sanchez and Gore - 2013 - Feedback between Population and Evolutionary Dynam.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\5BS68SB9\\\\Sanchez and Gore - 2013 - Feedback between Population and Evolutionary Dynam.pdf:application/pdf;Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\BHPWUMSI\\\\article.html:text/html},\n}\n\n\n\n The evolutionary spread of cheater strategies can destabilize populations engaging in social cooperative behaviors, thus demonstrating that evolutionary changes can have profound implications for population dynamics. At the same time, the relative fitness of cooperative traits often depends upon population density, thus leading to the potential for bi-directional coupling between population density and the evolution of a cooperative trait. Despite the potential importance of these eco-evolutionary feedback loops in social species, they have not yet been demonstrated experimentally and their ecological implications are poorly understood. Here, we demonstrate the presence of a strong feedback loop between population dynamics and the evolutionary dynamics of a social microbial gene, SUC2, in laboratory yeast populations whose cooperative growth is mediated by the SUC2 gene. We directly visualize eco-evolutionary trajectories of hundreds of populations over 50–100 generations, allowing us to characterize the phase space describing the interplay of evolution and ecology in this system. Small populations collapse despite continual evolution towards increased cooperative allele frequencies; large populations with a sufficient number of cooperators ‘‘spiral’’ to a stable state of coexistence between cooperator and cheater strategies. The presence of cheaters does not significantly affect the equilibrium population density, but it does reduce the resilience of the population as well as its ability to adapt to a rapidly deteriorating environment. Our results demonstrate the potential ecological importance of coupling between evolutionary dynamics and the population dynamics of cooperatively growing organisms, particularly in microbes. Our study suggests that this interaction may need to be considered in order to explain intraspecific variability in cooperative behaviors, and also that this feedback between evolution and ecology can critically affect the demographic fate of those species that rely on cooperation for their survival.\n
\n\n\n\n \n\n \n \n \n \n \n \n Cooperation dilemma in finite populations under fluctuating environments.\n \n \n \n \n\n\n \n Assaf, M.; Mobilia, M.; and Roberts, E.\n\n\n \n\n\n\n Physical Review Letters, 111(23): 238101. December 2013.\n arXiv:1305.6580 [cond-mat, q-bio]\n\n\n\n
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\n\n\n@article{assaf_cooperation_2013,\n\ttitle = {Cooperation dilemma in finite populations under fluctuating environments},\n\tvolume = {111},\n\tissn = {0031-9007, 1079-7114},\n\turl = {http://arxiv.org/abs/1305.6580},\n\tdoi = {10.1103/PhysRevLett.111.238101},\n\tabstract = {We present a novel approach allowing the study of rare events like fixation under fluctuating environments, modeled as extrinsic noise, in evolutionary processes characterized by the dominance of one species. Our treatment consists of mapping the system onto an auxiliary model, exhibiting metastable species coexistence, that can be analyzed semiclassically. This approach enables us to study the interplay between extrinsic and demographic noise on the statistics of interest. We illustrate our theory by considering the paradigmatic prisoner's dilemma game whose evolution is described by the probability that cooperators fixate the population and replace all defectors. We analytically and numerically demonstrate that extrinsic noise may drastically enhance the cooperation fixation probability and even change its functional dependence on the population size. These results, which generalize earlier works in population genetics, indicate that extrinsic noise may help sustain and promote a much higher level of cooperation than static settings.},\n\tnumber = {23},\n\turldate = {2022-07-02},\n\tjournal = {Physical Review Letters},\n\tauthor = {Assaf, Michael and Mobilia, Mauro and Roberts, Elijah},\n\tmonth = dec,\n\tyear = {2013},\n\tnote = {arXiv:1305.6580 [cond-mat, q-bio]},\n\tkeywords = {read, ⛔ No INSPIRE recid found},\n\tpages = {238101},\n\tfile = {arXiv Fulltext PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\DE5GRHWC\\\\Assaf et al. - 2013 - Cooperation dilemma in finite populations under fl.pdf:application/pdf;arXiv.org Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\CPVKDF6Y\\\\1305.html:text/html;Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\HCU7N4HQ\\\\Assaf et al. - 2013 - Cooperation Dilemma in Finite Populations under Fl.pdf:application/pdf},\n}\n\n\n\n We present a novel approach allowing the study of rare events like fixation under fluctuating environments, modeled as extrinsic noise, in evolutionary processes characterized by the dominance of one species. Our treatment consists of mapping the system onto an auxiliary model, exhibiting metastable species coexistence, that can be analyzed semiclassically. This approach enables us to study the interplay between extrinsic and demographic noise on the statistics of interest. We illustrate our theory by considering the paradigmatic prisoner's dilemma game whose evolution is described by the probability that cooperators fixate the population and replace all defectors. We analytically and numerically demonstrate that extrinsic noise may drastically enhance the cooperation fixation probability and even change its functional dependence on the population size. These results, which generalize earlier works in population genetics, indicate that extrinsic noise may help sustain and promote a much higher level of cooperation than static settings.\n
\n\n\n\n \n\n \n \n \n \n \n \n The intermediate disturbance hypothesis should be abandoned.\n \n \n \n \n\n\n \n Fox, J. W.\n\n\n \n\n\n\n Trends in Ecology & Evolution, 28(2): 86–92. February 2013.\n \n\n\n\n
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\n\n\n@article{fox_intermediate_2013,\n\ttitle = {The intermediate disturbance hypothesis should be abandoned},\n\tvolume = {28},\n\tissn = {0169-5347},\n\turl = {https://www.sciencedirect.com/science/article/pii/S0169534712002091},\n\tdoi = {10.1016/j.tree.2012.08.014},\n\tabstract = {A leading idea about how disturbances and other environmental fluctuations affect species diversity is the intermediate disturbance hypothesis (IDH). The IDH states that diversity of competing species is, or should be expected to be, maximized at intermediate frequencies and/or intensities of disturbance or environmental change. I argue that the IDH has been refuted on both empirical and theoretical grounds, and so should be abandoned. Empirical studies only rarely find the predicted humped diversity–disturbance relationship. Theoretically, the three major mechanisms thought to produce humped diversity–disturbance relationships are logically invalid and do not actually predict what they are thought to predict. Disturbances and other environmental fluctuations can affect diversity, but for different reasons than are commonly recognized.},\n\tlanguage = {en},\n\tnumber = {2},\n\turldate = {2023-03-10},\n\tjournal = {Trends in Ecology \\& Evolution},\n\tauthor = {Fox, Jeremy W.},\n\tmonth = feb,\n\tyear = {2013},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {86--92},\n\tfile = {ScienceDirect Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\PSQV3VXL\\\\Fox - 2013 - The intermediate disturbance hypothesis should be .pdf:application/pdf;ScienceDirect Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\XPQKJT2N\\\\S0169534712002091.html:text/html},\n}\n\n\n\n A leading idea about how disturbances and other environmental fluctuations affect species diversity is the intermediate disturbance hypothesis (IDH). The IDH states that diversity of competing species is, or should be expected to be, maximized at intermediate frequencies and/or intensities of disturbance or environmental change. I argue that the IDH has been refuted on both empirical and theoretical grounds, and so should be abandoned. Empirical studies only rarely find the predicted humped diversity–disturbance relationship. Theoretically, the three major mechanisms thought to produce humped diversity–disturbance relationships are logically invalid and do not actually predict what they are thought to predict. Disturbances and other environmental fluctuations can affect diversity, but for different reasons than are commonly recognized.\n
\n\n\n\n \n\n \n \n \n \n \n \n Following the Mechanisms of Bacteriostatic versus Bactericidal Action Using Raman Spectroscopy.\n \n \n \n \n\n\n \n Bernatová, S.; Samek, O.; Pilát, Z.; Šerý, M.; Ježek, J.; Jákl, P.; Šiler, M.; Krzyžánek, V.; Zemánek, P.; Holá, V.; Dvořáčková, M.; and Růžička, F.\n\n\n \n\n\n\n Molecules, 18(11): 13188–13199. October 2013.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n\n
\n\n\n@article{bernatova_following_2013,\n\ttitle = {Following the {Mechanisms} of {Bacteriostatic} versus {Bactericidal} {Action} {Using} {Raman} {Spectroscopy}},\n\tvolume = {18},\n\tissn = {1420-3049},\n\turl = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6270526/},\n\tdoi = {10.3390/molecules181113188},\n\tabstract = {Antibiotics cure infections by influencing bacterial growth or viability. Antibiotics can be divided to two groups on the basis of their effect on microbial cells through two main mechanisms, which are either bactericidal or bacteriostatic. Bactericidal antibiotics kill the bacteria and bacteriostatic antibiotics suppress the growth of bacteria (keep them in the stationary phase of growth). One of many factors to predict a favorable clinical outcome of the potential action of antimicrobial chemicals may be provided using in vitro bactericidal/bacteriostatic data (e.g., minimum inhibitory concentrations—MICs). Consequently, MICs are used in clinical situations mainly to confirm resistance, and to determine the in vitro activities of new antimicrobials. We report on the combination of data obtained from MICs with information on microorganisms’ “fingerprint” (e.g., DNA/RNA, and proteins) provided by Raman spectroscopy. Thus, we could follow mechanisms of the bacteriostatic versus bactericidal action simply by detecting the Raman bands corresponding to DNA. The Raman spectra of Staphylococcus epidermidis treated with clindamycin (a bacteriostatic agent) indeed show little effect on DNA which is in contrast with the action of ciprofloxacin (a bactericidal agent), where the Raman spectra show a decrease in strength of the signal assigned to DNA, suggesting DNA fragmentation.},\n\tnumber = {11},\n\turldate = {2023-03-31},\n\tjournal = {Molecules},\n\tauthor = {Bernatová, Silvie and Samek, Ota and Pilát, Zdeněk and Šerý, Mojmír and Ježek, Jan and Jákl, Petr and Šiler, Martin and Krzyžánek, Vladislav and Zemánek, Pavel and Holá, Veronika and Dvořáčková, Milada and Růžička, Filip},\n\tmonth = oct,\n\tyear = {2013},\n\tpmid = {24284484},\n\tpmcid = {PMC6270526},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {13188--13199},\n\tfile = {PubMed Central Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\WIT52622\\\\Bernatová et al. - 2013 - Following the Mechanisms of Bacteriostatic versus .pdf:application/pdf},\n}\n\n\n\n Antibiotics cure infections by influencing bacterial growth or viability. Antibiotics can be divided to two groups on the basis of their effect on microbial cells through two main mechanisms, which are either bactericidal or bacteriostatic. Bactericidal antibiotics kill the bacteria and bacteriostatic antibiotics suppress the growth of bacteria (keep them in the stationary phase of growth). One of many factors to predict a favorable clinical outcome of the potential action of antimicrobial chemicals may be provided using in vitro bactericidal/bacteriostatic data (e.g., minimum inhibitory concentrations—MICs). Consequently, MICs are used in clinical situations mainly to confirm resistance, and to determine the in vitro activities of new antimicrobials. We report on the combination of data obtained from MICs with information on microorganisms’ “fingerprint” (e.g., DNA/RNA, and proteins) provided by Raman spectroscopy. Thus, we could follow mechanisms of the bacteriostatic versus bactericidal action simply by detecting the Raman bands corresponding to DNA. The Raman spectra of Staphylococcus epidermidis treated with clindamycin (a bacteriostatic agent) indeed show little effect on DNA which is in contrast with the action of ciprofloxacin (a bactericidal agent), where the Raman spectra show a decrease in strength of the signal assigned to DNA, suggesting DNA fragmentation.\n
\n\n\n\n \n\n \n \n \n \n \n \n Environmental Versus Demographic Variability in Two-Species Predator-Prey Models.\n \n \n \n \n\n\n \n Dobramysl, U.; and Täuber, U. C.\n\n\n \n\n\n\n Physical Review Letters, 110(4): 048105. January 2013.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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\n\n\n\n@article{dobramysl_environmental_2013,\n\ttitle = {Environmental {Versus} {Demographic} {Variability} in {Two}-{Species} {Predator}-{Prey} {Models}},\n\tvolume = {110},\n\tissn = {0031-9007, 1079-7114},\n\turl = {https://link.aps.org/doi/10.1103/PhysRevLett.110.048105},\n\tdoi = {10.1103/PhysRevLett.110.048105},\n\tlanguage = {en},\n\tnumber = {4},\n\turldate = {2023-05-03},\n\tjournal = {Physical Review Letters},\n\tauthor = {Dobramysl, Ulrich and Täuber, Uwe C.},\n\tmonth = jan,\n\tyear = {2013},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {048105},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\9CNT8RG9\\\\Dobramysl and Täuber - 2013 - Environmental Versus Demographic Variability in Tw.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Evolutionary rescue from extinction is contingent on a lower rate of environmental change.\n \n \n \n\n\n \n Lindsey, H. A.; Gallie, J.; Taylor, S.; and B., K.\n\n\n \n\n\n\n Nature, 494: 463. 2013.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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\n\n\n\n@article{Kerr13,\n\ttitle = {Evolutionary rescue from extinction is contingent on a lower rate of environmental change},\n\tvolume = {494},\n\tjournal = {Nature},\n\tauthor = {Lindsey, H. A. and Gallie, J. and Taylor, S. and B., Kerr},\n\tyear = {2013},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {463},\n\tfile = {Lindsey et al. - 2013 - Evolutionary rescue from extinction is contingent .pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\98AHNRJM\\\\Lindsey et al. - 2013 - Evolutionary rescue from extinction is contingent .pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Bacterial cheating drives the population dynamics of cooperative antibiotic resistance plasmids.\n \n \n \n\n\n \n Yurtsev, E. A.; Chao1, H. X.; Datta, M. S; and Artemova, T J. G.\n\n\n \n\n\n\n Molecular Systems Biology, 9: 683. 2013.\n \n\n\n\n
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\n\n\n\n@article{Yurtsev13,\n\ttitle = {Bacterial cheating drives the population dynamics of cooperative antibiotic resistance plasmids},\n\tvolume = {9},\n\tjournal = {Molecular Systems Biology},\n\tauthor = {Yurtsev, E. A. and Chao1, H. X. and Datta, M. S and Artemova, T Jeff Gore, J.},\n\tyear = {2013},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {683},\n\tfile = {Yurtsev et al. - 2013 - Bacterial cheating drives the population dynamics .pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\H66L2QSF\\\\Yurtsev et al. - 2013 - Bacterial cheating drives the population dynamics .pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n The unified neutral theory of biodiversity and biogeography.\n \n \n \n\n\n \n Hubbell, S. P.\n\n\n \n\n\n\n Princeton University Press, Princeton, 2013.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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\n\n\n\n@book{hubbell_2013,\n\taddress = {Princeton},\n\ttitle = {The unified neutral theory of biodiversity and biogeography},\n\tpublisher = {Princeton University Press},\n\tauthor = {Hubbell, Stephen P.},\n\tyear = {2013},\n\tkeywords = {⛔ No INSPIRE recid found},\n}\n\n\n\n \n\n \n \n \n \n \n Extrinsic noise driven phenotype switching in a self-regulating gene.\n \n \n \n\n\n \n Assaf, M.; Roberts, E.; Luthey-Schulten, Z.; and Goldenfeld, N.\n\n\n \n\n\n\n Physical Review Letters, 111: 058102. 2013.\n \n\n\n\n
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\n\n\n\n@article{Assaf13a,\n\ttitle = {Extrinsic noise driven phenotype switching in a self-regulating gene},\n\tvolume = {111},\n\tdoi = {10.1103/PhysRevLett.111.058102},\n\tjournal = {Physical Review Letters},\n\tauthor = {Assaf, M. and Roberts, E. and Luthey-Schulten, Z. and Goldenfeld, N.},\n\tyear = {2013},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {058102},\n\tfile = {Assaf et al. - 2013 - Extrinsic noise driven phenotype switching in a se.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\Z5IIPABX\\\\Assaf et al. - 2013 - Extrinsic noise driven phenotype switching in a se.pdf:application/pdf},\n}\n\n\n\n
\n\n \n \n 2012\n \n \n (1)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Growth dynamics and the evolution of cooperation in microbial populations.\n \n \n \n \n\n\n \n Cremer, J.; Melbinger, A.; and Frey, E.\n\n\n \n\n\n\n Scientific Reports, 2(1): 281. December 2012.\n \n\n\n\n
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\n\n\n\n@article{cremer_growth_2012,\n\ttitle = {Growth dynamics and the evolution of cooperation in microbial populations},\n\tvolume = {2},\n\tissn = {2045-2322},\n\turl = {http://www.nature.com/articles/srep00281},\n\tdoi = {10.1038/srep00281},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2022-02-03},\n\tjournal = {Scientific Reports},\n\tauthor = {Cremer, Jonas and Melbinger, Anna and Frey, Erwin},\n\tmonth = dec,\n\tyear = {2012},\n\tkeywords = {read, public good, coexistence, metapopulation model, on website, ⛔ No INSPIRE recid found},\n\tpages = {281},\n\tfile = {Cremer et al. - 2012 - Growth dynamics and the evolution of cooperation i.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\7GX3EH2V\\\\Cremer et al. - 2012 - Growth dynamics and the evolution of cooperation i.pdf:application/pdf},\n}\n\n\n\n
\n\n \n \n 2011\n \n \n (6)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Social interaction in synthetic and natural microbial communities.\n \n \n \n \n\n\n \n Xavier, J. B\n\n\n \n\n\n\n Molecular Systems Biology, 7(1): 483. January 2011.\n Publisher: John Wiley & Sons, Ltd\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{xavier_social_2011,\n\ttitle = {Social interaction in synthetic and natural microbial communities},\n\tvolume = {7},\n\tissn = {1744-4292},\n\turl = {https://www.embopress.org/doi/full/10.1038/msb.2011.16},\n\tdoi = {10.1038/msb.2011.16},\n\tabstract = {Social interaction among cells is essential for multicellular complexity. But how do molecular networks within individual cells confer the ability to interact? And how do those same networks evolve from the evolutionary conflict between individual- and population-level interests? Recent studies have dissected social interaction at the molecular level by analyzing both synthetic and natural microbial populations. These studies shed new light on the role of population structure for the evolution of cooperative interactions and revealed novel molecular mechanisms that stabilize cooperation among cells. New understanding of populations is changing our view of microbial processes, such as pathogenesis and antibiotic resistance, and suggests new ways to fight infection by exploiting social interaction. The study of social interaction is also challenging established paradigms in cancer evolution and immune system dynamics. Finding similar patterns in such diverse systems suggests that the same ?social interaction motifs? may be general to many cell populations.},\n\tnumber = {1},\n\turldate = {2022-09-27},\n\tjournal = {Molecular Systems Biology},\n\tauthor = {Xavier, Joao B},\n\tmonth = jan,\n\tyear = {2011},\n\tnote = {Publisher: John Wiley \\& Sons, Ltd},\n\tkeywords = {unread, ⛔ No INSPIRE recid found},\n\tpages = {483},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\Q3E8ZJ6R\\\\Xavier - 2011 - Social interaction in synthetic and natural microb.pdf:application/pdf},\n}\n\n\n\n Social interaction among cells is essential for multicellular complexity. But how do molecular networks within individual cells confer the ability to interact? And how do those same networks evolve from the evolutionary conflict between individual- and population-level interests? Recent studies have dissected social interaction at the molecular level by analyzing both synthetic and natural microbial populations. These studies shed new light on the role of population structure for the evolution of cooperative interactions and revealed novel molecular mechanisms that stabilize cooperation among cells. New understanding of populations is changing our view of microbial processes, such as pathogenesis and antibiotic resistance, and suggests new ways to fight infection by exploiting social interaction. The study of social interaction is also challenging established paradigms in cancer evolution and immune system dynamics. Finding similar patterns in such diverse systems suggests that the same ?social interaction motifs? may be general to many cell populations.\n
\n\n\n\n \n\n \n \n \n \n \n \n How frequency and intensity shape diversity–disturbance relationships.\n \n \n \n \n\n\n \n Miller, A. D.; Roxburgh, S. H.; and Shea, K.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences, 108(14): 5643–5648. April 2011.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{miller_how_2011,\n\ttitle = {How frequency and intensity shape diversity–disturbance relationships},\n\tvolume = {108},\n\tissn = {0027-8424, 1091-6490},\n\turl = {https://pnas.org/doi/full/10.1073/pnas.1018594108},\n\tdoi = {10.1073/pnas.1018594108},\n\tabstract = {Understanding the relationship between disturbance regimes and species diversity has been of central interest to ecologists for decades. For example, the intermediate disturbance hypothesis proposes that diversity will be highest at intermediate levels of disturbance. Although peaked (hump-shaped) diversity–disturbance relationships (DDRs) have been documented in nature, many other DDRs have been reported as well. Here, we begin to theoretically unify these diverse empirical findings by showing how a single simple model can generate several different DDRs, depending on the aspect of disturbance that is considered. Additionally, we elucidate the competition-mediated mechanism underlying our results. Our findings have the potential to reconcile apparently conflicting empirical results on the effects of disturbance on diversity.},\n\tlanguage = {en},\n\tnumber = {14},\n\turldate = {2023-03-07},\n\tjournal = {Proceedings of the National Academy of Sciences},\n\tauthor = {Miller, Adam D. and Roxburgh, Stephen H. and Shea, Katriona},\n\tmonth = apr,\n\tyear = {2011},\n\tkeywords = {unread, ⛔ No INSPIRE recid found},\n\tpages = {5643--5648},\n\tfile = {Full Text:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\5WYSKAAM\\\\Miller et al. - 2011 - How frequency and intensity shape diversity–distur.pdf:application/pdf},\n}\n\n\n\n Understanding the relationship between disturbance regimes and species diversity has been of central interest to ecologists for decades. For example, the intermediate disturbance hypothesis proposes that diversity will be highest at intermediate levels of disturbance. Although peaked (hump-shaped) diversity–disturbance relationships (DDRs) have been documented in nature, many other DDRs have been reported as well. Here, we begin to theoretically unify these diverse empirical findings by showing how a single simple model can generate several different DDRs, depending on the aspect of disturbance that is considered. Additionally, we elucidate the competition-mediated mechanism underlying our results. Our findings have the potential to reconcile apparently conflicting empirical results on the effects of disturbance on diversity.\n
\n\n\n\n \n\n \n \n \n \n \n \n Moving pictures of the human microbiome.\n \n \n \n \n\n\n \n Caporaso, J. G.; Lauber, C. L.; Costello, E. K.; Berg-Lyons, D.; Gonzalez, A.; Stombaugh, J.; Knights, D.; Gajer, P.; Ravel, J.; Fierer, N.; Gordon, J. I.; and Knight, R.\n\n\n \n\n\n\n Genome Biology, 12(5): R50. May 2011.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{caporaso_moving_2011,\n\ttitle = {Moving pictures of the human microbiome},\n\tvolume = {12},\n\tissn = {1474-760X},\n\turl = {https://doi.org/10.1186/gb-2011-12-5-r50},\n\tdoi = {10.1186/gb-2011-12-5-r50},\n\tabstract = {Understanding the normal temporal variation in the human microbiome is critical to developing treatments for putative microbiome-related afflictions such as obesity, Crohn's disease, inflammatory bowel disease and malnutrition. Sequencing and computational technologies, however, have been a limiting factor in performing dense time series analysis of the human microbiome. Here, we present the largest human microbiota time series analysis to date, covering two individuals at four body sites over 396 timepoints.},\n\tnumber = {5},\n\turldate = {2023-04-04},\n\tjournal = {Genome Biology},\n\tauthor = {Caporaso, J. Gregory and Lauber, Christian L. and Costello, Elizabeth K. and Berg-Lyons, Donna and Gonzalez, Antonio and Stombaugh, Jesse and Knights, Dan and Gajer, Pawel and Ravel, Jacques and Fierer, Noah and Gordon, Jeffrey I. and Knight, Rob},\n\tmonth = may,\n\tyear = {2011},\n\tkeywords = {Body Site, Human Microbiome, Microbial Community Dynamic, UniFrac Distance, Virtual Cluster, ⛔ No INSPIRE recid found},\n\tpages = {R50},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\MF6Q75TI\\\\Caporaso et al. - 2011 - Moving pictures of the human microbiome.pdf:application/pdf;Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\E8AS4FX9\\\\gb-2011-12-5-r50.html:text/html},\n}\n\n\n\n Understanding the normal temporal variation in the human microbiome is critical to developing treatments for putative microbiome-related afflictions such as obesity, Crohn's disease, inflammatory bowel disease and malnutrition. Sequencing and computational technologies, however, have been a limiting factor in performing dense time series analysis of the human microbiome. Here, we present the largest human microbiota time series analysis to date, covering two individuals at four body sites over 396 timepoints.\n
\n\n\n\n \n\n \n \n \n \n \n Noise-induced phenomena in the environmental sciences.\n \n \n \n\n\n \n Ridolfi, L.; D'Odorico, P.; and Laio, F.\n\n\n \n\n\n\n Cambridge University Press, Cambridge, U.K., 2011.\n \n\n\n\n
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\n\n\n\n@book{Ridolfi2011,\n\ttitle = {Noise-induced phenomena in the environmental sciences},\n\tpublisher = {Cambridge University Press, Cambridge, U.K.},\n\tauthor = {Ridolfi, L. and D'Odorico, P. and Laio, F.},\n\tyear = {2011},\n\tkeywords = {⛔ No INSPIRE recid found},\n}\n\n\n\n \n\n \n \n \n \n \n Coexistence in the two-dimensional May-Leonard model with random rates.\n \n \n \n\n\n \n He, Q.; Mobilia, M.; and Täuber, U. C.\n\n\n \n\n\n\n , 82: 97. 2011.\n Publisher: Springer\n\n\n\n
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\n\n\n\n@article{he2011,\n\ttitle = {Coexistence in the two-dimensional {May}-{Leonard} model with random rates},\n\tvolume = {82},\n\tauthor = {He, Q. and Mobilia, M. and Täuber, U. C.},\n\tyear = {2011},\n\tnote = {Publisher: Springer},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {97},\n\tfile = {He et al. - 2011 - Coexistence in the two-dimensional May-Leonard mod.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\2C3A82KM\\\\He et al. - 2011 - Coexistence in the two-dimensional May-Leonard mod.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Markov chains in genetics.\n \n \n \n\n\n \n Pinsky, M. A; and Karlin, S.\n\n\n \n\n\n\n In An introduction to stochastic modeling, pages 90–92. Elsevier, 2011.\n \n\n\n\n
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\n\n\n\n@incollection{Pinsky2011-px,\n\ttitle = {Markov chains in genetics},\n\tbooktitle = {An introduction to stochastic modeling},\n\tpublisher = {Elsevier},\n\tauthor = {Pinsky, Mark A and Karlin, Samuel},\n\tyear = {2011},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {90--92},\n}\n\n\n\n
\n\n \n \n 2010\n \n \n (9)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Large fluctuations and fixation in evolutionary games.\n \n \n \n \n\n\n \n Assaf, M.; and Mobilia, M.\n\n\n \n\n\n\n Journal of Statistical Mechanics: Theory and Experiment, 2010(09): P09009. September 2010.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{assaf_large_2010,\n\ttitle = {Large fluctuations and fixation in evolutionary games},\n\tvolume = {2010},\n\tissn = {1742-5468},\n\turl = {https://iopscience.iop.org/article/10.1088/1742-5468/2010/09/P09009},\n\tdoi = {10.1088/1742-5468/2010/09/P09009},\n\tabstract = {We study large fluctuations in evolutionary games belonging to the coordination and anti-coordination classes. The dynamics of these games, modeling cooperation dilemmas, is characterized by a coexistence fixed point separating two absorbing states. We are particularly interested in the problem of fixation that refers to the possibility that a few mutants take over the entire population. Here, the fixation phenomenon is induced by large fluctuations and is investigated by a semiclassical WKB (Wentzel–Kramers–Brillouin) theory generalized to treat stochastic systems possessing multiple absorbing states. Importantly, this method allows us to analyze the combined influence of selection and random fluctuations on the evolutionary dynamics beyond the weak selection limit often considered in previous works. We accurately compute, including pre-exponential factors, the probability distribution function in the long-lived coexistence state and the mean fixation time necessary for a few mutants to take over the entire population in anti-coordination games, and also the fixation probability in the coordination class. Our analytical results compare excellently with extensive numerical simulations. Furthermore, we demonstrate that our treatment is superior to the Fokker–Planck approximation when the selection intensity is finite.},\n\tlanguage = {en},\n\tnumber = {09},\n\turldate = {2022-05-27},\n\tjournal = {Journal of Statistical Mechanics: Theory and Experiment},\n\tauthor = {Assaf, Michael and Mobilia, Mauro},\n\tmonth = sep,\n\tyear = {2010},\n\tkeywords = {unread, ⛔ No INSPIRE recid found},\n\tpages = {P09009},\n\tfile = {Assaf and Mobilia - 2010 - Large fluctuations and fixation in evolutionary ga.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\4FNHVENK\\\\Assaf and Mobilia - 2010 - Large fluctuations and fixation in evolutionary ga.pdf:application/pdf},\n}\n\n\n\n We study large fluctuations in evolutionary games belonging to the coordination and anti-coordination classes. The dynamics of these games, modeling cooperation dilemmas, is characterized by a coexistence fixed point separating two absorbing states. We are particularly interested in the problem of fixation that refers to the possibility that a few mutants take over the entire population. Here, the fixation phenomenon is induced by large fluctuations and is investigated by a semiclassical WKB (Wentzel–Kramers–Brillouin) theory generalized to treat stochastic systems possessing multiple absorbing states. Importantly, this method allows us to analyze the combined influence of selection and random fluctuations on the evolutionary dynamics beyond the weak selection limit often considered in previous works. We accurately compute, including pre-exponential factors, the probability distribution function in the long-lived coexistence state and the mean fixation time necessary for a few mutants to take over the entire population in anti-coordination games, and also the fixation probability in the coordination class. Our analytical results compare excellently with extensive numerical simulations. Furthermore, we demonstrate that our treatment is superior to the Fokker–Planck approximation when the selection intensity is finite.\n
\n\n\n\n \n\n \n \n \n \n \n \n Evolutionary dynamics in structured populations.\n \n \n \n \n\n\n \n Nowak, M. A.; Tarnita, C. E.; and Antal, T.\n\n\n \n\n\n\n Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1537): 19–30. January 2010.\n \n\n\n\n
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\n\n\n@article{nowak_evolutionary_2010,\n\ttitle = {Evolutionary dynamics in structured populations},\n\tvolume = {365},\n\tissn = {0962-8436},\n\turl = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842709/},\n\tdoi = {10.1098/rstb.2009.0215},\n\tabstract = {Evolutionary dynamics shape the living world around us. At the centre of every evolutionary process is a population of reproducing individuals. The structure of that population affects evolutionary dynamics. The individuals can be molecules, cells, viruses, multicellular organisms or humans. Whenever the fitness of individuals depends on the relative abundance of phenotypes in the population, we are in the realm of evolutionary game theory. Evolutionary game theory is a general approach that can describe the competition of species in an ecosystem, the interaction between hosts and parasites, between viruses and cells, and also the spread of ideas and behaviours in the human population. In this perspective, we review the recent advances in evolutionary game dynamics with a particular emphasis on stochastic approaches in finite sized and structured populations. We give simple, fundamental laws that determine how natural selection chooses between competing strategies. We study the well-mixed population, evolutionary graph theory, games in phenotype space and evolutionary set theory. We apply these results to the evolution of cooperation. The mechanism that leads to the evolution of cooperation in these settings could be called ‘spatial selection’: cooperators prevail against defectors by clustering in physical or other spaces.},\n\tnumber = {1537},\n\turldate = {2022-06-28},\n\tjournal = {Philosophical Transactions of the Royal Society B: Biological Sciences},\n\tauthor = {Nowak, Martin A. and Tarnita, Corina E. and Antal, Tibor},\n\tmonth = jan,\n\tyear = {2010},\n\tpmid = {20008382},\n\tpmcid = {PMC2842709},\n\tkeywords = {unread, ⛔ No INSPIRE recid found},\n\tpages = {19--30},\n\tfile = {PubMed Central Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\H4QG4XLB\\\\Nowak et al. - 2010 - Evolutionary dynamics in structured populations.pdf:application/pdf},\n}\n\n\n\n Evolutionary dynamics shape the living world around us. At the centre of every evolutionary process is a population of reproducing individuals. The structure of that population affects evolutionary dynamics. The individuals can be molecules, cells, viruses, multicellular organisms or humans. Whenever the fitness of individuals depends on the relative abundance of phenotypes in the population, we are in the realm of evolutionary game theory. Evolutionary game theory is a general approach that can describe the competition of species in an ecosystem, the interaction between hosts and parasites, between viruses and cells, and also the spread of ideas and behaviours in the human population. In this perspective, we review the recent advances in evolutionary game dynamics with a particular emphasis on stochastic approaches in finite sized and structured populations. We give simple, fundamental laws that determine how natural selection chooses between competing strategies. We study the well-mixed population, evolutionary graph theory, games in phenotype space and evolutionary set theory. We apply these results to the evolution of cooperation. The mechanism that leads to the evolution of cooperation in these settings could be called ‘spatial selection’: cooperators prevail against defectors by clustering in physical or other spaces.\n
\n\n\n\n \n\n \n \n \n \n \n \n Cooperation and Hamilton's rule in a simple synthetic microbial system.\n \n \n \n \n\n\n \n Chuang, J. S; Rivoire, O.; and Leibler, S.\n\n\n \n\n\n\n Molecular Systems Biology, 6(1): 398. January 2010.\n Publisher: John Wiley & Sons, Ltd\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{chuang_cooperation_2010,\n\ttitle = {Cooperation and {Hamilton}'s rule in a simple synthetic microbial system},\n\tvolume = {6},\n\tissn = {1744-4292},\n\turl = {https://www.embopress.org/doi/full/10.1038/msb.2010.57},\n\tdoi = {10.1038/msb.2010.57},\n\tabstract = {A fundamental problem in biology is understanding the evolutionary emergence and maintenance of altruistic behaviors. A well-recognized conceptual insight is provided by a general mathematical relation, Hamilton's rule. This rule can in principle be invoked to explain natural examples of cooperation, but measuring the variables that it involves is a particularly challenging problem and controlling these variables experimentally an even more daunting task. Here, we overcome these difficulties by using a simple synthetic microbial system of producers and nonproducers of an extracellular growth-enhancing molecule, which acts as a ?common good.? For this system, we are able to manipulate the intrinsic growth difference between producers and nonproducers, as well as the impact of the common good on the growth rate of its recipients. Our synthetic system is thus uniquely suited for studying the relation between the parameters entering Hamilton's rule and the quantities governing the systems? behavior. The experimental results highlight a crucial effect of nonlinearities in the response to the common good, which in general tend to limit the predictive value of Hamilton's rule.},\n\tnumber = {1},\n\turldate = {2022-09-27},\n\tjournal = {Molecular Systems Biology},\n\tauthor = {Chuang, John S and Rivoire, Olivier and Leibler, Stanislas},\n\tmonth = jan,\n\tyear = {2010},\n\tnote = {Publisher: John Wiley \\& Sons, Ltd},\n\tkeywords = {unread, ⛔ No INSPIRE recid found},\n\tpages = {398},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\YKV9E87B\\\\Chuang et al. - 2010 - Cooperation and Hamilton's rule in a simple synthe.pdf:application/pdf},\n}\n\n\n\n A fundamental problem in biology is understanding the evolutionary emergence and maintenance of altruistic behaviors. A well-recognized conceptual insight is provided by a general mathematical relation, Hamilton's rule. This rule can in principle be invoked to explain natural examples of cooperation, but measuring the variables that it involves is a particularly challenging problem and controlling these variables experimentally an even more daunting task. Here, we overcome these difficulties by using a simple synthetic microbial system of producers and nonproducers of an extracellular growth-enhancing molecule, which acts as a ?common good.? For this system, we are able to manipulate the intrinsic growth difference between producers and nonproducers, as well as the impact of the common good on the growth rate of its recipients. Our synthetic system is thus uniquely suited for studying the relation between the parameters entering Hamilton's rule and the quantities governing the systems? behavior. The experimental results highlight a crucial effect of nonlinearities in the response to the common good, which in general tend to limit the predictive value of Hamilton's rule.\n
\n\n\n\n \n\n \n \n \n \n \n Evolutionary game theory in growing populations.\n \n \n \n\n\n \n Melbinger, A.; Cremer, J.; and Frey, E.\n\n\n \n\n\n\n Physical Review Letters, 105(17): 178101. October 2010.\n MAG ID: 2065673339\n\n\n\n
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\n\n\n@article{melbinger_evolutionary_2010,\n\ttitle = {Evolutionary game theory in growing populations.},\n\tvolume = {105},\n\tdoi = {10.1103/physrevlett.105.178101},\n\tabstract = {Existing theoretical models of evolution focus on the relative fitness advantages of different mutants in a population while the dynamic behavior of the population size is mostly left unconsidered. We present here a generic stochastic model which combines the growth dynamics of the population and its internal evolution. Our model thereby accounts for the fact that both evolutionary and growth dynamics are based on individual reproduction events and hence are highly coupled and stochastic in nature. We exemplify our approach by studying the dilemma of cooperation in growing populations and show that genuinely stochastic events can ease the dilemma by leading to a transient but robust increase in cooperation.},\n\tnumber = {17},\n\tjournal = {Physical Review Letters},\n\tauthor = {Melbinger, Anna and Cremer, Jonas and Frey, Erwin},\n\tmonth = oct,\n\tyear = {2010},\n\tdoi = {10.1103/physrevlett.105.178101},\n\tpmid = {21231082},\n\tnote = {MAG ID: 2065673339},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {178101},\n\tfile = {Accepted Version:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\8TF5CRUX\\\\Melbinger et al. - 2010 - Evolutionary game theory in growing populations..pdf:application/pdf},\n}\n\n\n\n Existing theoretical models of evolution focus on the relative fitness advantages of different mutants in a population while the dynamic behavior of the population size is mostly left unconsidered. We present here a generic stochastic model which combines the growth dynamics of the population and its internal evolution. Our model thereby accounts for the fact that both evolutionary and growth dynamics are based on individual reproduction events and hence are highly coupled and stochastic in nature. We exemplify our approach by studying the dilemma of cooperation in growing populations and show that genuinely stochastic events can ease the dilemma by leading to a transient but robust increase in cooperation.\n
\n\n\n\n \n\n \n \n \n \n \n \n Adaptation, Plasticity, and Extinction in a Changing Environment: Towards a Predictive Theory.\n \n \n \n \n\n\n \n Chevin, L.; Lande, R.; and Mace, G. M.\n\n\n \n\n\n\n PLOS Biology, 8(4): e1000357. April 2010.\n Publisher: Public Library of Science\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{chevin_adaptation_2010,\n\ttitle = {Adaptation, {Plasticity}, and {Extinction} in a {Changing} {Environment}: {Towards} a {Predictive} {Theory}},\n\tvolume = {8},\n\tissn = {1545-7885},\n\tshorttitle = {Adaptation, {Plasticity}, and {Extinction} in a {Changing} {Environment}},\n\turl = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000357},\n\tdoi = {10.1371/journal.pbio.1000357},\n\tabstract = {The authors analyze developmental, genetic, and demographic mechanisms by which populations tolerate changing environments and discuss empirical methods for determining the critical rate of sustained environmental change that causes population extinction.},\n\tlanguage = {en},\n\tnumber = {4},\n\turldate = {2023-03-14},\n\tjournal = {PLOS Biology},\n\tauthor = {Chevin, Luis-Miguel and Lande, Russell and Mace, Georgina M.},\n\tmonth = apr,\n\tyear = {2010},\n\tnote = {Publisher: Public Library of Science},\n\tkeywords = {Curve fitting, Ecological niches, Evolutionary genetics, Extinction risk, Natural selection, Phenotypes, Population genetics, Species extinction, ⛔ No INSPIRE recid found},\n\tpages = {e1000357},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\NBZIZNJM\\\\Chevin et al. - 2010 - Adaptation, Plasticity, and Extinction in a Changi.pdf:application/pdf},\n}\n\n\n\n The authors analyze developmental, genetic, and demographic mechanisms by which populations tolerate changing environments and discuss empirical methods for determining the critical rate of sustained environmental change that causes population extinction.\n
\n\n\n\n \n\n \n \n \n \n \n \n Spatial rock-paper-scissors models with inhomogeneous reaction rates.\n \n \n \n \n\n\n \n He, Q.; Mobilia, M.; and Täuber, U. C.\n\n\n \n\n\n\n Physical Review E, 82(5): 051909. November 2010.\n \n\n\n\n
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\n\n\n\n@article{he_spatial_2010,\n\ttitle = {Spatial rock-paper-scissors models with inhomogeneous reaction rates},\n\tvolume = {82},\n\tissn = {1539-3755, 1550-2376},\n\turl = {https://link.aps.org/doi/10.1103/PhysRevE.82.051909},\n\tdoi = {10.1103/PhysRevE.82.051909},\n\tlanguage = {en},\n\tnumber = {5},\n\turldate = {2023-05-03},\n\tjournal = {Physical Review E},\n\tauthor = {He, Qian and Mobilia, Mauro and Täuber, Uwe C.},\n\tmonth = nov,\n\tyear = {2010},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {051909},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\VE8DAE4V\\\\He et al. - 2010 - Spatial rock-paper-scissors models with inhomogene.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n \n Exact Results for the Evolution of Stochastic Switching in Variable Asymmetric Environments.\n \n \n \n \n\n\n \n Gaál, B.; Pitchford, J. W; and Wood, A J.\n\n\n \n\n\n\n Genetics, 184(4): 1113–1119. April 2010.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n\n
\n\n\n@article{gaal_exact_2010,\n\ttitle = {Exact {Results} for the {Evolution} of {Stochastic} {Switching} in {Variable} {Asymmetric} {Environments}},\n\tvolume = {184},\n\tissn = {1943-2631},\n\turl = {https://academic.oup.com/genetics/article/184/4/1113/6062984},\n\tdoi = {10.1534/genetics.109.113431},\n\tabstract = {The ability of bacteria to spontaneously switch their expressed phenotype from an identical underlying genotype is now widely acknowledged. Mechanisms behind these switches have been shown to be evolvable. Important questions thus arise: In a fluctuating environment, under what conditions can stochastic switching evolve and how is the evolutionarily optimal switching rate related to the environmental changes? Here we derive exact analytical results for the long-term exponential population growth rate in a two-state periodically changing environment, where the environmental states vary in both their duration and in their impact on the fitness of each phenotype. Using methods from statistical physics we derive conditions under which nonswitching is evolutionarily optimal, and we furthermore demonstrate that the transition between the nonswitching and switching regimes is discontinuous (a first-order phase transition). Our general analytical method allows the evolutionary effects of asymmetries in selection pressures and environmental growth rates to be quantified. The evolutionary implications of our findings are discussed in relation to their to real-world applications in the light of recent experimental evidence.},\n\tlanguage = {en},\n\tnumber = {4},\n\turldate = {2023-05-03},\n\tjournal = {Genetics},\n\tauthor = {Gaál, Bernadett and Pitchford, Jonathan W and Wood, A Jamie},\n\tmonth = apr,\n\tyear = {2010},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {1113--1119},\n\tfile = {Gaál et al. - 2010 - Exact Results for the Evolution of Stochastic Swit.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\JM4WLFCI\\\\Gaál et al. - 2010 - Exact Results for the Evolution of Stochastic Swit.pdf:application/pdf},\n}\n\n\n\n The ability of bacteria to spontaneously switch their expressed phenotype from an identical underlying genotype is now widely acknowledged. Mechanisms behind these switches have been shown to be evolvable. Important questions thus arise: In a fluctuating environment, under what conditions can stochastic switching evolve and how is the evolutionarily optimal switching rate related to the environmental changes? Here we derive exact analytical results for the long-term exponential population growth rate in a two-state periodically changing environment, where the environmental states vary in both their duration and in their impact on the fitness of each phenotype. Using methods from statistical physics we derive conditions under which nonswitching is evolutionarily optimal, and we furthermore demonstrate that the transition between the nonswitching and switching regimes is discontinuous (a first-order phase transition). Our general analytical method allows the evolutionary effects of asymmetries in selection pressures and environmental growth rates to be quantified. The evolutionary implications of our findings are discussed in relation to their to real-world applications in the light of recent experimental evidence.\n
\n\n\n\n \n\n \n \n \n \n \n Switching and growth for microbial populations in catastrophic responsive environments.\n \n \n \n\n\n \n Visco, P.; Allen, J.; Majumdar, S. N.; and Evans, M. R.\n\n\n \n\n\n\n Biophysical Journal, 98: 1099. 2010.\n \n\n\n\n
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\n\n\n\n@article{Visco10,\n\ttitle = {Switching and growth for microbial populations in catastrophic responsive environments},\n\tvolume = {98},\n\tjournal = {Biophysical Journal},\n\tauthor = {Visco, P. and Allen, J. and Majumdar, S. N. and Evans, M. R.},\n\tyear = {2010},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {1099},\n\tfile = {Visco et al. - 2010 - Switching and growth for microbial populations in .pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\3VB6GCGZ\\\\Visco et al. - 2010 - Switching and growth for microbial populations in .pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Fixation in evolutionary games under non-vanishing selection.\n \n \n \n\n\n \n Mobilia, M.; and Assaf, M.\n\n\n \n\n\n\n EPL, 91: 10002. 2010.\n Publisher: IoP\n\n\n\n
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\n\n\n\n@article{MA10,\n\ttitle = {Fixation in evolutionary games under non-vanishing selection},\n\tvolume = {91},\n\tjournal = {EPL},\n\tauthor = {Mobilia, M. and Assaf, M.},\n\tyear = {2010},\n\tnote = {Publisher: IoP},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {10002},\n\tfile = {Mobilia and Assaf - 2010 - Fixation in evolutionary games under non-vanishing.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\7FXDZFHB\\\\Mobilia and Assaf - 2010 - Fixation in evolutionary games under non-vanishing.pdf:application/pdf},\n}\n\n\n\n
\n\n \n \n 2009\n \n \n (5)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Simpson's Paradox in a Synthetic Microbial System.\n \n \n \n \n\n\n \n Chuang, J. S.; Rivoire, O.; and Leibler, S.\n\n\n \n\n\n\n Science, 323(5911): 272–275. January 2009.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{chuang_simpsons_2009,\n\ttitle = {Simpson's {Paradox} in a {Synthetic} {Microbial} {System}},\n\tvolume = {323},\n\tissn = {0036-8075, 1095-9203},\n\turl = {https://www.science.org/doi/10.1126/science.1166739},\n\tdoi = {10.1126/science.1166739},\n\tabstract = {The maintenance of “public” or “common good” producers is a major question in the evolution of cooperation. Because nonproducers benefit from the shared resource without bearing its cost of production, they may proliferate faster than producers. We established a synthetic microbial system consisting of two\n Escherichia coli\n strains of common-good producers and nonproducers. Depending on the population structure, which was varied by forming groups with different initial compositions, an apparently paradoxical situation could be attained in which nonproducers grew faster within each group, yet producers increased overall. We show that a simple way to generate the variance required for this effect is through stochastic fluctuations via population bottlenecks. The synthetic approach described here thus provides a way to study generic mechanisms of natural selection.},\n\tlanguage = {en},\n\tnumber = {5911},\n\turldate = {2022-02-03},\n\tjournal = {Science},\n\tauthor = {Chuang, John S. and Rivoire, Olivier and Leibler, Stanislas},\n\tmonth = jan,\n\tyear = {2009},\n\tkeywords = {read, public good, experimental, on website, ⛔ No INSPIRE recid found},\n\tpages = {272--275},\n\tfile = {Chuang et al. - 2009 - Simpson's Paradox in a Synthetic Microbial System.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\ETJQSFTC\\\\Chuang et al. - 2009 - Simpson's Paradox in a Synthetic Microbial System.pdf:application/pdf},\n}\n\n\n\n The maintenance of “public” or “common good” producers is a major question in the evolution of cooperation. Because nonproducers benefit from the shared resource without bearing its cost of production, they may proliferate faster than producers. We established a synthetic microbial system consisting of two Escherichia coli strains of common-good producers and nonproducers. Depending on the population structure, which was varied by forming groups with different initial compositions, an apparently paradoxical situation could be attained in which nonproducers grew faster within each group, yet producers increased overall. We show that a simple way to generate the variance required for this effect is through stochastic fluctuations via population bottlenecks. The synthetic approach described here thus provides a way to study generic mechanisms of natural selection.\n
\n\n\n\n \n\n \n \n \n \n \n \n The edge of neutral evolution in social dilemmas.\n \n \n \n \n\n\n \n Cremer, J.; Reichenbach, T.; and Frey, E.\n\n\n \n\n\n\n New Journal of Physics, 11(9): 093029. September 2009.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{cremer_edge_2009,\n\ttitle = {The edge of neutral evolution in social dilemmas},\n\tvolume = {11},\n\tissn = {1367-2630},\n\turl = {https://iopscience.iop.org/article/10.1088/1367-2630/11/9/093029},\n\tdoi = {10.1088/1367-2630/11/9/093029},\n\tabstract = {The functioning of animal as well as human societies fundamentally relies on cooperation. Yet, defection is often favorable for the selfish individual, and social dilemmas arise. Selection by individuals’ fitness, usually the basic driving force of evolution, quickly eliminates cooperators. However, evolution is also governed by fluctuations that can be of greater importance than fitness differences, and can render evolution effectively neutral. Here, we investigate the effects of selection versus fluctuations in social dilemmas.},\n\tlanguage = {en},\n\tnumber = {9},\n\turldate = {2022-06-20},\n\tjournal = {New Journal of Physics},\n\tauthor = {Cremer, Jonas and Reichenbach, Tobias and Frey, Erwin},\n\tmonth = sep,\n\tyear = {2009},\n\tkeywords = {read, fixation probability, coexistence, evolutionary game, fixation time, on website, ⛔ No INSPIRE recid found},\n\tpages = {093029},\n\tfile = {Cremer et al. - 2009 - The edge of neutral evolution in social dilemmas.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\YV6HPDK5\\\\Cremer et al. - 2009 - The edge of neutral evolution in social dilemmas.pdf:application/pdf},\n}\n\n\n\n The functioning of animal as well as human societies fundamentally relies on cooperation. Yet, defection is often favorable for the selfish individual, and social dilemmas arise. Selection by individuals’ fitness, usually the basic driving force of evolution, quickly eliminates cooperators. However, evolution is also governed by fluctuations that can be of greater importance than fitness differences, and can render evolution effectively neutral. Here, we investigate the effects of selection versus fluctuations in social dilemmas.\n
\n\n\n\n \n\n \n \n \n \n \n What determines species diversity?.\n \n \n \n\n\n \n Pennisi, E.\n\n\n \n\n\n\n Science (New York, N.Y.), 309: 90. 2009.\n \n\n\n\n
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\n\n\n\n@article{Pennisi09,\n\ttitle = {What determines species diversity?},\n\tvolume = {309},\n\tjournal = {Science (New York, N.Y.)},\n\tauthor = {Pennisi, E.},\n\tyear = {2009},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {90},\n\tfile = {Pennisi - 2009 - What determines species diversity.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\8C3T6PNS\\\\Pennisi - 2009 - What determines species diversity.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Microbial toxins: Current research and future trends.\n \n \n \n\n\n \n Proft, T.\n\n\n \n\n\n\n Caister Academic Press, 2009.\n \n\n\n\n
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\n\n\n\n@book{proft2009microbial,\n\ttitle = {Microbial toxins: {Current} research and future trends},\n\tpublisher = {Caister Academic Press},\n\tauthor = {Proft, T.},\n\tyear = {2009},\n\tkeywords = {⛔ No INSPIRE recid found},\n}\n\n\n\n \n\n \n \n \n \n \n An introduction to population genetics theory.\n \n \n \n\n\n \n Crow, J. F. F.; and Kimura, M.\n\n\n \n\n\n\n Blackburn Press, Caldwell, NJ, USA., 2009.\n \n\n\n\n
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\n\n\n\n@book{Kimura,\n\ttitle = {An introduction to population genetics theory},\n\tpublisher = {Blackburn Press, Caldwell, NJ, USA.},\n\tauthor = {Crow, J. F. F. and Kimura, M.},\n\tyear = {2009},\n\tkeywords = {⛔ No INSPIRE recid found},\n}\n\n\n\n
\n\n \n \n 2008\n \n \n (4)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Stochastic evolutionary game dynamics.\n \n \n \n \n\n\n \n Traulsen, A.; and Hauert, C.\n\n\n \n\n\n\n November 2008.\n Number: arXiv:0811.3538 arXiv:0811.3538 [q-bio]\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@misc{traulsen_stochastic_2008,\n\ttitle = {Stochastic evolutionary game dynamics},\n\turl = {http://arxiv.org/abs/0811.3538},\n\tabstract = {In this review, we summarize recent developments in stochastic evolutionary game dynamics of finite populations.},\n\tlanguage = {en},\n\turldate = {2022-05-27},\n\tpublisher = {arXiv},\n\tauthor = {Traulsen, Arne and Hauert, Christoph},\n\tmonth = nov,\n\tyear = {2008},\n\tnote = {Number: arXiv:0811.3538\narXiv:0811.3538 [q-bio]},\n\tkeywords = {unread, ⛔ No INSPIRE recid found},\n\tfile = {Traulsen and Hauert - 2008 - Stochastic evolutionary game dynamics.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\HY2PBSLR\\\\Traulsen and Hauert - 2008 - Stochastic evolutionary game dynamics.pdf:application/pdf},\n}\n\n\n\n In this review, we summarize recent developments in stochastic evolutionary game dynamics of finite populations.\n
\n\n\n\n \n\n \n \n \n \n \n \n Stochastic switching as a survival strategy in fluctuating environments.\n \n \n \n \n\n\n \n Acar, M.; Mettetal, J. T.; and van Oudenaarden, A.\n\n\n \n\n\n\n Nature Genetics, 40(4): 471–475. April 2008.\n Number: 4 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n\n
\n\n\n@article{acar_stochastic_2008,\n\ttitle = {Stochastic switching as a survival strategy in fluctuating environments},\n\tvolume = {40},\n\tcopyright = {2008 Nature Publishing Group},\n\tissn = {1546-1718},\n\turl = {https://www.nature.com/articles/ng.110},\n\tdoi = {10.1038/ng.110},\n\tabstract = {A classic problem in population and evolutionary biology is to understand how a population optimizes its fitness in fluctuating environments1,2,3,4. A population might enhance its fitness by allowing individual cells to stochastically transition among multiple phenotypes, thus ensuring that some cells are always prepared for an unforeseen environmental fluctuation. Here we experimentally explore how switching affects population growth by using the galactose utilization network of Saccharomyces cerevisiae. We engineered a strain that randomly transitions between two phenotypes as a result of stochastic gene expression5,6,7,8,9. Each phenotype was designed to confer a growth advantage over the other phenotype in a certain environment. When we compared the growth of two populations with different switching rates, we found that fast-switching populations outgrow slow switchers when the environment fluctuates rapidly, whereas slow-switching phenotypes outgrow fast switchers when the environment changes rarely. These results suggest that cells may tune inter-phenotype switching rates to the frequency of environmental changes.},\n\tlanguage = {en},\n\tnumber = {4},\n\turldate = {2023-03-10},\n\tjournal = {Nature Genetics},\n\tauthor = {Acar, Murat and Mettetal, Jerome T. and van Oudenaarden, Alexander},\n\tmonth = apr,\n\tyear = {2008},\n\tnote = {Number: 4\nPublisher: Nature Publishing Group},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {471--475},\n\tfile = {Acar et al. - 2008 - Stochastic switching as a survival strategy in flu.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\SI28SHYE\\\\Acar et al. - 2008 - Stochastic switching as a survival strategy in flu.pdf:application/pdf},\n}\n\n\n\n A classic problem in population and evolutionary biology is to understand how a population optimizes its fitness in fluctuating environments1,2,3,4. A population might enhance its fitness by allowing individual cells to stochastically transition among multiple phenotypes, thus ensuring that some cells are always prepared for an unforeseen environmental fluctuation. Here we experimentally explore how switching affects population growth by using the galactose utilization network of Saccharomyces cerevisiae. We engineered a strain that randomly transitions between two phenotypes as a result of stochastic gene expression5,6,7,8,9. Each phenotype was designed to confer a growth advantage over the other phenotype in a certain environment. When we compared the growth of two populations with different switching rates, we found that fast-switching populations outgrow slow switchers when the environment fluctuates rapidly, whereas slow-switching phenotypes outgrow fast switchers when the environment changes rarely. These results suggest that cells may tune inter-phenotype switching rates to the frequency of environmental changes.\n
\n\n\n\n \n\n \n \n \n \n \n \n Population extinction in a time-modulated environment.\n \n \n \n \n\n\n \n Assaf, M.; Kamenev, A.; and Meerson, B.\n\n\n \n\n\n\n Physical Review E, 78(4): 041123. October 2008.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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\n\n\n\n@article{assaf_population_2008,\n\ttitle = {Population extinction in a time-modulated environment},\n\tvolume = {78},\n\tissn = {1539-3755, 1550-2376},\n\turl = {https://link.aps.org/doi/10.1103/PhysRevE.78.041123},\n\tdoi = {10.1103/PhysRevE.78.041123},\n\tlanguage = {en},\n\tnumber = {4},\n\turldate = {2023-05-03},\n\tjournal = {Physical Review E},\n\tauthor = {Assaf, Michael and Kamenev, Alex and Meerson, Baruch},\n\tmonth = oct,\n\tyear = {2008},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {041123},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\NUJZKJ4V\\\\Assaf et al. - 2008 - Population extinction in a time-modulated environm.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Species synchrony and its drivers: Neutral and nonneutral community dynamics in fluctuating environments.\n \n \n \n\n\n \n Loreau, M.; and de Mazancourt, C.\n\n\n \n\n\n\n , 172: E48. 2008.\n \n\n\n\n
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\n\n\n\n@article{Loreau08,\n\ttitle = {Species synchrony and its drivers: {Neutral} and nonneutral community dynamics in fluctuating environments},\n\tvolume = {172},\n\tauthor = {Loreau, M. and de Mazancourt, C.},\n\tyear = {2008},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {E48},\n\tfile = {Loreau and de Mazancourt - 2008 - Species synchrony and its drivers Neutral and non.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\ZSYTXLTT\\\\Loreau and de Mazancourt - 2008 - Species synchrony and its drivers Neutral and non.pdf:application/pdf},\n}\n\n\n\n
\n\n \n \n 2007\n \n \n (4)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Stochastic models of evolution in genetics, ecology and linguistics.\n \n \n \n \n\n\n \n Blythe, R. A.; and McKane, A. J.\n\n\n \n\n\n\n Journal of Statistical Mechanics: Theory and Experiment, 2007(07): P07018–P07018. July 2007.\n Publisher: IOP Publishing\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n
\n\n\n@article{blythe_stochastic_2007,\n\ttitle = {Stochastic models of evolution in genetics, ecology and linguistics},\n\tvolume = {2007},\n\tissn = {1742-5468},\n\turl = {https://doi.org/10.1088/1742-5468/2007/07/p07018},\n\tdoi = {10.1088/1742-5468/2007/07/P07018},\n\tabstract = {We give an overview of stochastic models of evolution that have found applications in genetics, ecology and linguistics for an audience of non-specialists, especially statistical physicists. In particular, we focus mostly on neutral models in which no intrinsic advantage is ascribed to a particular type of the variable unit, for example a gene, appearing in the theory. In many cases these models are exactly solvable and furthermore go some way to describing observed features of genetic, ecological and linguistic systems.},\n\tlanguage = {en},\n\tnumber = {07},\n\turldate = {2022-03-09},\n\tjournal = {Journal of Statistical Mechanics: Theory and Experiment},\n\tauthor = {Blythe, R. A. and McKane, A. J.},\n\tmonth = jul,\n\tyear = {2007},\n\tnote = {Publisher: IOP Publishing},\n\tkeywords = {unread, Quantitative Biology - Populations and Evolution, Condensed Matter - Statistical Mechanics, ⛔ No INSPIRE recid found},\n\tpages = {P07018--P07018},\n\tfile = {arXiv Fulltext PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\EWU7QEPC\\\\Blythe and McKane - 2007 - Stochastic Models of Evolution in Genetics, Ecolog.pdf:application/pdf;arXiv.org Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\X2W79ZTP\\\\0703478.html:text/html;IOP Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\AFVVPGLU\\\\Blythe and McKane - 2007 - Stochastic models of evolution in genetics, ecolog.pdf:application/pdf;Submitted Version:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\DIMRHDPN\\\\Blythe and McKane - 2007 - Stochastic models of evolution in genetics, ecolog.pdf:application/pdf},\n}\n\n\n\n We give an overview of stochastic models of evolution that have found applications in genetics, ecology and linguistics for an audience of non-specialists, especially statistical physicists. In particular, we focus mostly on neutral models in which no intrinsic advantage is ascribed to a particular type of the variable unit, for example a gene, appearing in the theory. In many cases these models are exactly solvable and furthermore go some way to describing observed features of genetic, ecological and linguistic systems.\n
\n\n\n\n \n\n \n \n \n \n \n \n A modified next reaction method for simulating chemical systems with time dependent propensities and delays.\n \n \n \n \n\n\n \n Anderson, D. F.\n\n\n \n\n\n\n The Journal of Chemical Physics, 127(21): 214107. December 2007.\n \n\n\n\n
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\n\n\n\n@article{anderson_modified_2007,\n\ttitle = {A modified next reaction method for simulating chemical systems with time dependent propensities and delays},\n\tvolume = {127},\n\tissn = {0021-9606, 1089-7690},\n\turl = {http://aip.scitation.org/doi/10.1063/1.2799998},\n\tdoi = {10.1063/1.2799998},\n\tlanguage = {en},\n\tnumber = {21},\n\turldate = {2022-05-11},\n\tjournal = {The Journal of Chemical Physics},\n\tauthor = {Anderson, David F.},\n\tmonth = dec,\n\tyear = {2007},\n\tkeywords = {read, simulation, on website, ⛔ No INSPIRE recid found},\n\tpages = {214107},\n\tfile = {Anderson - 2007 - A modified next reaction method for simulating che.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\C79H7UMV\\\\Anderson - 2007 - A modified next reaction method for simulating che.pdf:application/pdf;Anderson - 2007 - A modified next reaction method for simulating che.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\K2P4NVMD\\\\Anderson - 2007 - A modified next reaction method for simulating che.pdf:application/pdf;Submitted Version:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\EYU3VZ4F\\\\Anderson - 2007 - A modified next reaction method for simulating che.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n \n Cooperation Peaks at Intermediate Disturbance.\n \n \n \n \n\n\n \n Brockhurst, M. A.; Buckling, A.; and Gardner, A.\n\n\n \n\n\n\n Current Biology, 17(9): 761–765. May 2007.\n \n\n\n\n
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\n\n\n@article{brockhurst_cooperation_2007,\n\ttitle = {Cooperation {Peaks} at {Intermediate} {Disturbance}},\n\tvolume = {17},\n\tissn = {0960-9822},\n\turl = {https://www.sciencedirect.com/science/article/pii/S0960982207010664},\n\tdoi = {10.1016/j.cub.2007.02.057},\n\tabstract = {Explaining cooperation is a challenge for evolutionary biology 1, 2. Surprisingly, the role of extrinsic ecological parameters remains largely unconsidered. Disturbances 3, 4 are widespread in nature and have evolutionary consequences [5]. We develop a mathematical model predicting that cooperative traits most readily evolve at intermediate disturbance. Under infrequent disturbance, cooperation breaks down through the accumulation of evolved cheats. Higher rates of disturbance prevent this because the resulting bottlenecks increase genetic structuring (relatedness 6, 7, 8) promoting kin selection for cooperation. However, cooperation cannot be sustained under very frequent disturbance if population density remains below the level required for successful cooperation. We tested these predictions by using cooperative biofilm formation by the bacterium Pseudomonas fluorescens 9, 10. The proportion of biofilm-forming bacteria peaked at intermediate disturbance, in a manner consistent with model predictions. Under infrequent and intermediate disturbance, most bacteria occupied the biofilm, but the proportion of cheats was higher under less frequent disturbance. Under frequent disturbance, many bacteria did not occupy the biofilm, suggesting that biofilm dwelling was not as beneficial under frequent versus intermediate disturbance. Given the ubiquity of disturbances in nature, these results suggest that they may play a major role in the evolution of social traits in microbes.},\n\tlanguage = {en},\n\tnumber = {9},\n\turldate = {2022-07-10},\n\tjournal = {Current Biology},\n\tauthor = {Brockhurst, Michael A. and Buckling, Angus and Gardner, Andy},\n\tmonth = may,\n\tyear = {2007},\n\tkeywords = {unread, ⛔ No INSPIRE recid found},\n\tpages = {761--765},\n\tfile = {ScienceDirect Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\JY64TZPW\\\\Brockhurst et al. - 2007 - Cooperation Peaks at Intermediate Disturbance.pdf:application/pdf;ScienceDirect Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\55BWF9VD\\\\S0960982207010664.html:text/html},\n}\n\n\n\n Explaining cooperation is a challenge for evolutionary biology 1, 2. Surprisingly, the role of extrinsic ecological parameters remains largely unconsidered. Disturbances 3, 4 are widespread in nature and have evolutionary consequences [5]. We develop a mathematical model predicting that cooperative traits most readily evolve at intermediate disturbance. Under infrequent disturbance, cooperation breaks down through the accumulation of evolved cheats. Higher rates of disturbance prevent this because the resulting bottlenecks increase genetic structuring (relatedness 6, 7, 8) promoting kin selection for cooperation. However, cooperation cannot be sustained under very frequent disturbance if population density remains below the level required for successful cooperation. We tested these predictions by using cooperative biofilm formation by the bacterium Pseudomonas fluorescens 9, 10. The proportion of biofilm-forming bacteria peaked at intermediate disturbance, in a manner consistent with model predictions. Under infrequent and intermediate disturbance, most bacteria occupied the biofilm, but the proportion of cheats was higher under less frequent disturbance. Under frequent disturbance, many bacteria did not occupy the biofilm, suggesting that biofilm dwelling was not as beneficial under frequent versus intermediate disturbance. Given the ubiquity of disturbances in nature, these results suggest that they may play a major role in the evolution of social traits in microbes.\n
\n\n\n\n \n\n \n \n \n \n \n Mobility promotes and jeopardizes biodiversity in rock–paper–scissors games.\n \n \n \n\n\n \n Reichenbach, T.; Mobilia, M.; and Frey, E.\n\n\n \n\n\n\n Nature, 448: 1046–1049. 2007.\n Publisher: Nature Publishing Group\n\n\n\n
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\n\n\n\n@article{reich2007,\n\ttitle = {Mobility promotes and jeopardizes biodiversity in rock–paper–scissors games},\n\tvolume = {448},\n\tjournal = {Nature},\n\tauthor = {Reichenbach, T. and Mobilia, M. and Frey, E.},\n\tyear = {2007},\n\tnote = {Publisher: Nature Publishing Group},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {1046--1049},\n\tfile = {Reichenbach et al. - 2007 - Mobility promotes and jeopardizes biodiversity in .pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\AKQRJ8YP\\\\Reichenbach et al. - 2007 - Mobility promotes and jeopardizes biodiversity in .pdf:application/pdf},\n}\n\n\n\n
\n\n \n \n 2006\n \n \n (3)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Fixation of Strategies for an Evolutionary Game in Finite Populations.\n \n \n \n \n\n\n \n Antal, T.; and Scheuring, I.\n\n\n \n\n\n\n Bulletin of Mathematical Biology, 68(8): 1923–1944. November 2006.\n \n\n\n\n
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\n\n\n@article{antal_fixation_2006,\n\ttitle = {Fixation of {Strategies} for an {Evolutionary} {Game} in {Finite} {Populations}},\n\tvolume = {68},\n\tissn = {0092-8240, 1522-9602},\n\turl = {http://link.springer.com/10.1007/s11538-006-9061-4},\n\tdoi = {10.1007/s11538-006-9061-4},\n\tabstract = {A stochastic evolutionary dynamics of two strategies given by 2 × 2 matrix games is studied in finite populations. We focus on stochastic properties of fixation: how a strategy represented by a single individual wins over the entire population. The process is discussed in the framework of a random walk with site dependent hopping rates. The time of fixation is found to be identical for both strategies in any particular game. The asymptotic behavior of the fixation time and fixation probabilities in the large population size limit is also discussed. We show that fixation is fast when there is at least one pure evolutionary stable strategy (ESS) in the infinite population size limit, while fixation is slow when the ESS is the coexistence of the two strategies.},\n\tlanguage = {en},\n\tnumber = {8},\n\turldate = {2022-05-27},\n\tjournal = {Bulletin of Mathematical Biology},\n\tauthor = {Antal, Tibor and Scheuring, István},\n\tmonth = nov,\n\tyear = {2006},\n\tkeywords = {read, fixation probability, Moran model, coexistence, evolutionary game, fixation time, on website, ⛔ No INSPIRE recid found},\n\tpages = {1923--1944},\n\tfile = {Antal and Scheuring - 2006 - Fixation of Strategies for an Evolutionary Game in.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\CIMRBSUE\\\\Antal and Scheuring - 2006 - Fixation of Strategies for an Evolutionary Game in.pdf:application/pdf},\n}\n\n\n\n A stochastic evolutionary dynamics of two strategies given by 2 × 2 matrix games is studied in finite populations. We focus on stochastic properties of fixation: how a strategy represented by a single individual wins over the entire population. The process is discussed in the framework of a random walk with site dependent hopping rates. The time of fixation is found to be identical for both strategies in any particular game. The asymptotic behavior of the fixation time and fixation probabilities in the large population size limit is also discussed. We show that fixation is fast when there is at least one pure evolutionary stable strategy (ESS) in the infinite population size limit, while fixation is slow when the ESS is the coexistence of the two strategies.\n
\n\n\n\n \n\n \n \n \n \n \n Evolutionary dynamics.\n \n \n \n\n\n \n Nowak, M.\n\n\n \n\n\n\n Belknap Press, Cambridge, MA, USA, 2006.\n \n\n\n\n
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\n\n\n\n@book{Nowak,\n\ttitle = {Evolutionary dynamics},\n\tpublisher = {Belknap Press, Cambridge, MA, USA},\n\tauthor = {Nowak, M.A.},\n\tyear = {2006},\n\tkeywords = {⛔ No INSPIRE recid found},\n}\n\n\n\n \n\n \n \n \n \n \n Dichotomous Markov Noise: exact results for out-of-equilibrium systems.\n \n \n \n\n\n \n Bena, I.\n\n\n \n\n\n\n International Journal of Modern Physics B, 20: 2825. 2006.\n \n\n\n\n
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\n\n\n\n@article{bena2006,\n\ttitle = {Dichotomous {Markov} {Noise}: exact results for out-of-equilibrium systems},\n\tvolume = {20},\n\tdoi = {10.1142/S0217979206034881},\n\tjournal = {International Journal of Modern Physics B},\n\tauthor = {Bena, I.},\n\tyear = {2006},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {2825},\n\tfile = {Bena - 2006 - Dichotomous noise exact results for out-of-equili.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\ZG9BVAXM\\\\Bena - 2006 - Dichotomous noise exact results for out-of-equili.pdf:application/pdf},\n}\n\n\n\n
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\n \n \n\n \n \n \n \n \n \n Coevolutionary Dynamics: From Finite to Infinite Populations.\n \n \n \n \n\n\n \n Traulsen, A.; Claussen, J. C.; and Hauert, C.\n\n\n \n\n\n\n Physical Review Letters, 95(23): 238701. December 2005.\n \n\n\n\n
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\n\n\n\n@article{traulsen_coevolutionary_2005,\n\ttitle = {Coevolutionary {Dynamics}: {From} {Finite} to {Infinite} {Populations}},\n\tvolume = {95},\n\tissn = {0031-9007, 1079-7114},\n\tshorttitle = {Coevolutionary {Dynamics}},\n\turl = {https://link.aps.org/doi/10.1103/PhysRevLett.95.238701},\n\tdoi = {10.1103/PhysRevLett.95.238701},\n\tlanguage = {en},\n\tnumber = {23},\n\turldate = {2022-08-29},\n\tjournal = {Physical Review Letters},\n\tauthor = {Traulsen, Arne and Claussen, Jens Christian and Hauert, Christoph},\n\tmonth = dec,\n\tyear = {2005},\n\tkeywords = {read, on website, ⛔ No INSPIRE recid found},\n\tpages = {238701},\n\tfile = {Traulsen et al. - 2005 - Coevolutionary Dynamics From Finite to Infinite P.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\XQH3QZWD\\\\Traulsen et al. - 2005 - Coevolutionary Dynamics From Finite to Infinite P.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n \n Bacterial Persistence: A Model of Survival in Changing Environments.\n \n \n \n \n\n\n \n Kussell, E.; Kishony, R.; Balaban, N. Q; and Leibler, S.\n\n\n \n\n\n\n Genetics, 169(4): 1807–1814. April 2005.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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\n\n\n@article{kussell_bacterial_2005,\n\ttitle = {Bacterial {Persistence}: {A} {Model} of {Survival} in {Changing} {Environments}},\n\tvolume = {169},\n\tissn = {1943-2631},\n\tshorttitle = {Bacterial {Persistence}},\n\turl = {https://doi.org/10.1534/genetics.104.035352},\n\tdoi = {10.1534/genetics.104.035352},\n\tabstract = {The persistence phenotype is an epigenetic trait exhibited by a subpopulation of bacteria, characterized by slow growth coupled with an ability to survive antibiotic treatment. The phenotype is acquired via a spontaneous, reversible switch between normal and persister cells. These observations suggest that clonal bacterial populations may use persister cells, whose slow division rate under growth conditions leads to lower population fitness, as an “insurance policy” against antibiotic encounters. We present a model of Escherichia coli persistence, and using experimentally derived parameters for both wild type and a mutant strain (hipQ) with markedly different switching rates, we show how fitness loss due to slow persister growth pays off as a risk-reducing strategy. We demonstrate that wild-type persistence is suited for environments in which antibiotic stress is a rare event. The optimal rate of switching between normal and persister cells is found to depend strongly on the frequency of environmental changes and only weakly on the selective pressures of any given environment. In contrast to typical examples of adaptations to features of a single environment, persistence appears to constitute an adaptation that is tuned to the distribution of environmental change.},\n\tnumber = {4},\n\turldate = {2023-03-10},\n\tjournal = {Genetics},\n\tauthor = {Kussell, Edo and Kishony, Roy and Balaban, Nathalie Q and Leibler, Stanislas},\n\tmonth = apr,\n\tyear = {2005},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {1807--1814},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\6B4AXEC4\\\\Kussell et al. - 2005 - Bacterial Persistence A Model of Survival in Chan.pdf:application/pdf;Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\M96KELVZ\\\\6059501.html:text/html},\n}\n\n\n\n The persistence phenotype is an epigenetic trait exhibited by a subpopulation of bacteria, characterized by slow growth coupled with an ability to survive antibiotic treatment. The phenotype is acquired via a spontaneous, reversible switch between normal and persister cells. These observations suggest that clonal bacterial populations may use persister cells, whose slow division rate under growth conditions leads to lower population fitness, as an “insurance policy” against antibiotic encounters. We present a model of Escherichia coli persistence, and using experimentally derived parameters for both wild type and a mutant strain (hipQ) with markedly different switching rates, we show how fitness loss due to slow persister growth pays off as a risk-reducing strategy. We demonstrate that wild-type persistence is suited for environments in which antibiotic stress is a rare event. The optimal rate of switching between normal and persister cells is found to depend strongly on the frequency of environmental changes and only weakly on the selective pressures of any given environment. In contrast to typical examples of adaptations to features of a single environment, persistence appears to constitute an adaptation that is tuned to the distribution of environmental change.\n
\n\n\n\n \n\n \n \n \n \n \n \n A framework for multidimensional modelling of activity and structure of multispecies biofilms.\n \n \n \n \n\n\n \n Xavier, J. B.; Picioreanu, C.; and Van Loosdrecht, M. C. M.\n\n\n \n\n\n\n Environmental Microbiology, 7(8): 1085–1103. 2005.\n _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1462-2920.2005.00787.x\n\n\n\n
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\n\n\n@article{xavier_framework_2005,\n\ttitle = {A framework for multidimensional modelling of activity and structure of multispecies biofilms},\n\tvolume = {7},\n\tissn = {1462-2920},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1462-2920.2005.00787.x},\n\tdoi = {10.1111/j.1462-2920.2005.00787.x},\n\tabstract = {Concepts from previous biofilm models were integrated to create a framework for the implementation of multidimensional (2D and 3D) multispecies biofilm models. The framework is here described at three levels: (i) mathematical representation of the processes involved in biofilm formation, (ii) numerical implementation into a computer program (freely available from our website http://www.biofilms.bt.tudelft.nl/frameworkMaterial) and (iii) using the program for the creation of biofilm models with multiple bacterial and solute species. An improved version of the individual-based modelling (IbM) that allows structured biomass was used. In this approach biomass composition may be discriminated into any number of particulate species, including extracellular polymeric substances (EPS) for which specific functionality was included. Detachment is also included, described as occurring at the biofilm surface with variable local rates derived from functions of state variables. The application of this modelling framework to a multispecies system with structured biomass is illustrated in a case study where the competition between an organism capable of accumulating polyhydroxybutyrate (PHB, an internal storage compound) and an EPS-producing organism in a two-species biofilm is analysed. Results illustrate that biofilms enriched in PHB-producing organisms may be obtained by supplying substrate intermittently in feast/famine cycles.},\n\tlanguage = {en},\n\tnumber = {8},\n\turldate = {2023-03-14},\n\tjournal = {Environmental Microbiology},\n\tauthor = {Xavier, Joao B. and Picioreanu, Cristian and Van Loosdrecht, Mark C. M.},\n\tyear = {2005},\n\tnote = {\\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1462-2920.2005.00787.x},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {1085--1103},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\6EGCAXIV\\\\Xavier et al. - 2005 - A framework for multidimensional modelling of acti.pdf:application/pdf;Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\V8G27BTL\\\\j.1462-2920.2005.00787.html:text/html},\n}\n\n\n\n Concepts from previous biofilm models were integrated to create a framework for the implementation of multidimensional (2D and 3D) multispecies biofilm models. The framework is here described at three levels: (i) mathematical representation of the processes involved in biofilm formation, (ii) numerical implementation into a computer program (freely available from our website http://www.biofilms.bt.tudelft.nl/frameworkMaterial) and (iii) using the program for the creation of biofilm models with multiple bacterial and solute species. An improved version of the individual-based modelling (IbM) that allows structured biomass was used. In this approach biomass composition may be discriminated into any number of particulate species, including extracellular polymeric substances (EPS) for which specific functionality was included. Detachment is also included, described as occurring at the biofilm surface with variable local rates derived from functions of state variables. The application of this modelling framework to a multispecies system with structured biomass is illustrated in a case study where the competition between an organism capable of accumulating polyhydroxybutyrate (PHB, an internal storage compound) and an EPS-producing organism in a two-species biofilm is analysed. Results illustrate that biofilms enriched in PHB-producing organisms may be obtained by supplying substrate intermittently in feast/famine cycles.\n
\n\n\n\n \n\n \n \n \n \n \n \n Effects of Biodiversity on Ecosystem Functioning: A Consensus of Current Knowledge.\n \n \n \n \n\n\n \n Hooper, D. U.; Chapin III, F. S.; Ewel, J. J.; Hector, A.; Inchausti, P.; Lavorel, S.; Lawton, J. H.; Lodge, D. M.; Loreau, M.; Naeem, S.; Schmid, B.; Setälä, H.; Symstad, A. J.; Vandermeer, J.; and Wardle, D. A.\n\n\n \n\n\n\n Ecological Monographs, 75(1): 3–35. 2005.\n _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1890/04-0922\n\n\n\n
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\n\n\n@article{hooper_effects_2005,\n\ttitle = {Effects of {Biodiversity} on {Ecosystem} {Functioning}: {A} {Consensus} of {Current} {Knowledge}},\n\tvolume = {75},\n\tissn = {1557-7015},\n\tshorttitle = {Effects of {Biodiversity} on {Ecosystem} {Functioning}},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1890/04-0922},\n\tdoi = {10.1890/04-0922},\n\tabstract = {Humans are altering the composition of biological communities through a variety of activities that increase rates of species invasions and species extinctions, at all scales, from local to global. These changes in components of the Earth's biodiversity cause concern for ethical and aesthetic reasons, but they also have a strong potential to alter ecosystem properties and the goods and services they provide to humanity. Ecological experiments, observations, and theoretical developments show that ecosystem properties depend greatly on biodiversity in terms of the functional characteristics of organisms present in the ecosystem and the distribution and abundance of those organisms over space and time. Species effects act in concert with the effects of climate, resource availability, and disturbance regimes in influencing ecosystem properties. Human activities can modify all of the above factors; here we focus on modification of these biotic controls. The scientific community has come to a broad consensus on many aspects of the relationship between biodiversity and ecosystem functioning, including many points relevant to management of ecosystems. Further progress will require integration of knowledge about biotic and abiotic controls on ecosystem properties, how ecological communities are structured, and the forces driving species extinctions and invasions. To strengthen links to policy and management, we also need to integrate our ecological knowledge with understanding of the social and economic constraints of potential management practices. Understanding this complexity, while taking strong steps to minimize current losses of species, is necessary for responsible management of Earth's ecosystems and the diverse biota they contain. Based on our review of the scientific literature, we are certain of the following conclusions: 1) Species' functional characteristics strongly influence ecosystem properties. Functional characteristics operate in a variety of contexts, including effects of dominant species, keystone species, ecological engineers, and interactions among species (e.g., competition, facilitation, mutualism, disease, and predation). Relative abundance alone is not always a good predictor of the ecosystem-level importance of a species, as even relatively rare species (e.g., a keystone predator) can strongly influence pathways of energy and material flows. 2) Alteration of biota in ecosystems via species invasions and extinctions caused by human activities has altered ecosystem goods and services in many well-documented cases. Many of these changes are difficult, expensive, or impossible to reverse or fix with technological solutions. 3) The effects of species loss or changes in composition, and the mechanisms by which the effects manifest themselves, can differ among ecosystem properties, ecosystem types, and pathways of potential community change. 4) Some ecosystem properties are initially insensitive to species loss because (a) ecosystems may have multiple species that carry out similar functional roles, (b) some species may contribute relatively little to ecosystem properties, or (c) properties may be primarily controlled by abiotic environmental conditions. 5) More species are needed to insure a stable supply of ecosystem goods and services as spatial and temporal variability increases, which typically occurs as longer time periods and larger areas are considered. We have high confidence in the following conclusions: 1) Certain combinations of species are complementary in their patterns of resource use and can increase average rates of productivity and nutrient retention. At the same time, environmental conditions can influence the importance of complementarity in structuring communities. Identification of which and how many species act in a complementary way in complex communities is just beginning. 2) Susceptibility to invasion by exotic species is strongly influenced by species composition and, under similar environmental conditions, generally decreases with increasing species richness. However, several other factors, such as propagule pressure, disturbance regime, and resource availability also strongly influence invasion success and often override effects of species richness in comparisons across different sites or ecosystems. 3) Having a range of species that respond differently to different environmental perturbations can stabilize ecosystem process rates in response to disturbances and variation in abiotic conditions. Using practices that maintain a diversity of organisms of different functional effect and functional response types will help preserve a range of management options. Uncertainties remain and further research is necessary in the following areas: 1) Further resolution of the relationships among taxonomic diversity, functional diversity, and community structure is important for identifying mechanisms of biodiversity effects. 2) Multiple trophic levels are common to ecosystems but have been understudied in biodiversity/ecosystem functioning research. The response of ecosystem properties to varying composition and diversity of consumer organisms is much more complex than responses seen in experiments that vary only the diversity of primary producers. 3) Theoretical work on stability has outpaced experimental work, especially field research. We need long-term experiments to be able to assess temporal stability, as well as experimental perturbations to assess response to and recovery from a variety of disturbances. Design and analysis of such experiments must account for several factors that covary with species diversity. 4) Because biodiversity both responds to and influences ecosystem properties, understanding the feedbacks involved is necessary to integrate results from experimental communities with patterns seen at broader scales. Likely patterns of extinction and invasion need to be linked to different drivers of global change, the forces that structure communities, and controls on ecosystem properties for the development of effective management and conservation strategies. 5) This paper focuses primarily on terrestrial systems, with some coverage of freshwater systems, because that is where most empirical and theoretical study has focused. While the fundamental principles described here should apply to marine systems, further study of that realm is necessary. Despite some uncertainties about the mechanisms and circumstances under which diversity influences ecosystem properties, incorporating diversity effects into policy and management is essential, especially in making decisions involving large temporal and spatial scales. Sacrificing those aspects of ecosystems that are difficult or impossible to reconstruct, such as diversity, simply because we are not yet certain about the extent and mechanisms by which they affect ecosystem properties, will restrict future management options even further. It is incumbent upon ecologists to communicate this need, and the values that can derive from such a perspective, to those charged with economic and policy decision-making.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-03-14},\n\tjournal = {Ecological Monographs},\n\tauthor = {Hooper, D. U. and Chapin III, F. S. and Ewel, J. J. and Hector, A. and Inchausti, P. and Lavorel, S. and Lawton, J. H. and Lodge, D. M. and Loreau, M. and Naeem, S. and Schmid, B. and Setälä, H. and Symstad, A. J. and Vandermeer, J. and Wardle, D. A.},\n\tyear = {2005},\n\tnote = {\\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1890/04-0922},\n\tkeywords = {species richness, biodiversity, complementary resource use, ecosystem goods and services, ecosystem processes, ecosystem properties, functional characteristics, functional diversity, net primary production, sampling effect, species extinction, species invasions, stability, ⛔ No INSPIRE recid found},\n\tpages = {3--35},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\J74WKIZD\\\\Hooper et al. - 2005 - Effects of Biodiversity on Ecosystem Functioning .pdf:application/pdf;Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\CTYLJTBA\\\\04-0922.html:text/html},\n}\n\n\n\n Humans are altering the composition of biological communities through a variety of activities that increase rates of species invasions and species extinctions, at all scales, from local to global. These changes in components of the Earth's biodiversity cause concern for ethical and aesthetic reasons, but they also have a strong potential to alter ecosystem properties and the goods and services they provide to humanity. Ecological experiments, observations, and theoretical developments show that ecosystem properties depend greatly on biodiversity in terms of the functional characteristics of organisms present in the ecosystem and the distribution and abundance of those organisms over space and time. Species effects act in concert with the effects of climate, resource availability, and disturbance regimes in influencing ecosystem properties. Human activities can modify all of the above factors; here we focus on modification of these biotic controls. The scientific community has come to a broad consensus on many aspects of the relationship between biodiversity and ecosystem functioning, including many points relevant to management of ecosystems. Further progress will require integration of knowledge about biotic and abiotic controls on ecosystem properties, how ecological communities are structured, and the forces driving species extinctions and invasions. To strengthen links to policy and management, we also need to integrate our ecological knowledge with understanding of the social and economic constraints of potential management practices. Understanding this complexity, while taking strong steps to minimize current losses of species, is necessary for responsible management of Earth's ecosystems and the diverse biota they contain. Based on our review of the scientific literature, we are certain of the following conclusions: 1) Species' functional characteristics strongly influence ecosystem properties. Functional characteristics operate in a variety of contexts, including effects of dominant species, keystone species, ecological engineers, and interactions among species (e.g., competition, facilitation, mutualism, disease, and predation). Relative abundance alone is not always a good predictor of the ecosystem-level importance of a species, as even relatively rare species (e.g., a keystone predator) can strongly influence pathways of energy and material flows. 2) Alteration of biota in ecosystems via species invasions and extinctions caused by human activities has altered ecosystem goods and services in many well-documented cases. Many of these changes are difficult, expensive, or impossible to reverse or fix with technological solutions. 3) The effects of species loss or changes in composition, and the mechanisms by which the effects manifest themselves, can differ among ecosystem properties, ecosystem types, and pathways of potential community change. 4) Some ecosystem properties are initially insensitive to species loss because (a) ecosystems may have multiple species that carry out similar functional roles, (b) some species may contribute relatively little to ecosystem properties, or (c) properties may be primarily controlled by abiotic environmental conditions. 5) More species are needed to insure a stable supply of ecosystem goods and services as spatial and temporal variability increases, which typically occurs as longer time periods and larger areas are considered. We have high confidence in the following conclusions: 1) Certain combinations of species are complementary in their patterns of resource use and can increase average rates of productivity and nutrient retention. At the same time, environmental conditions can influence the importance of complementarity in structuring communities. Identification of which and how many species act in a complementary way in complex communities is just beginning. 2) Susceptibility to invasion by exotic species is strongly influenced by species composition and, under similar environmental conditions, generally decreases with increasing species richness. However, several other factors, such as propagule pressure, disturbance regime, and resource availability also strongly influence invasion success and often override effects of species richness in comparisons across different sites or ecosystems. 3) Having a range of species that respond differently to different environmental perturbations can stabilize ecosystem process rates in response to disturbances and variation in abiotic conditions. Using practices that maintain a diversity of organisms of different functional effect and functional response types will help preserve a range of management options. Uncertainties remain and further research is necessary in the following areas: 1) Further resolution of the relationships among taxonomic diversity, functional diversity, and community structure is important for identifying mechanisms of biodiversity effects. 2) Multiple trophic levels are common to ecosystems but have been understudied in biodiversity/ecosystem functioning research. The response of ecosystem properties to varying composition and diversity of consumer organisms is much more complex than responses seen in experiments that vary only the diversity of primary producers. 3) Theoretical work on stability has outpaced experimental work, especially field research. We need long-term experiments to be able to assess temporal stability, as well as experimental perturbations to assess response to and recovery from a variety of disturbances. Design and analysis of such experiments must account for several factors that covary with species diversity. 4) Because biodiversity both responds to and influences ecosystem properties, understanding the feedbacks involved is necessary to integrate results from experimental communities with patterns seen at broader scales. Likely patterns of extinction and invasion need to be linked to different drivers of global change, the forces that structure communities, and controls on ecosystem properties for the development of effective management and conservation strategies. 5) This paper focuses primarily on terrestrial systems, with some coverage of freshwater systems, because that is where most empirical and theoretical study has focused. While the fundamental principles described here should apply to marine systems, further study of that realm is necessary. Despite some uncertainties about the mechanisms and circumstances under which diversity influences ecosystem properties, incorporating diversity effects into policy and management is essential, especially in making decisions involving large temporal and spatial scales. Sacrificing those aspects of ecosystems that are difficult or impossible to reconstruct, such as diversity, simply because we are not yet certain about the extent and mechanisms by which they affect ecosystem properties, will restrict future management options even further. It is incumbent upon ecologists to communicate this need, and the values that can derive from such a perspective, to those charged with economic and policy decision-making.\n
\n\n\n\n \n\n \n \n \n \n \n \n Survival strategies of infectious biofilms.\n \n \n \n \n\n\n \n Fux, C. A.; Costerton, J. W.; Stewart, P. S.; and Stoodley, P.\n\n\n \n\n\n\n Trends in Microbiology, 13(1): 34–40. January 2005.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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\n\n\n@article{fux_survival_2005,\n\ttitle = {Survival strategies of infectious biofilms},\n\tvolume = {13},\n\tissn = {0966-842X},\n\turl = {https://www.sciencedirect.com/science/article/pii/S0966842X04002641},\n\tdoi = {10.1016/j.tim.2004.11.010},\n\tabstract = {Modern medicine is facing the spread of biofilm-related infections. Bacterial biofilms are difficult to detect in routine diagnostics and are inherently tolerant to host defenses and antibiotic therapies. In addition, biofilms facilitate the spread of antibiotic resistance by promoting horizontal gene transfer. We review current concepts of biofilm tolerance with special emphasis on the role of the biofilm matrix and the physiology of biofilm-embedded cells. The heterogeneity in metabolic and reproductive activity within a biofilm correlates with a non-uniform susceptibility of enclosed bacteria. Recent studies have documented similar heterogeneity in planktonic cultures. Nutritional starvation and high cell density, two key characteristics of biofilm physiology, also mediate antimicrobial tolerance in stationary-phase planktonic cultures. Advances in characterizing the role of stress response genes, quorum sensing and phase variation in stationary-phase planktonic cultures have shed new light on tolerance mechanisms within biofilm communities.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-04-04},\n\tjournal = {Trends in Microbiology},\n\tauthor = {Fux, C. A. and Costerton, J. W. and Stewart, P. S. and Stoodley, P.},\n\tmonth = jan,\n\tyear = {2005},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {34--40},\n\tfile = {Full Text:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\DMWR5A5E\\\\Fux et al. - 2005 - Survival strategies of infectious biofilms.pdf:application/pdf;ScienceDirect Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\ZASENWSH\\\\S0966842X04002641.html:text/html},\n}\n\n\n\n Modern medicine is facing the spread of biofilm-related infections. Bacterial biofilms are difficult to detect in routine diagnostics and are inherently tolerant to host defenses and antibiotic therapies. In addition, biofilms facilitate the spread of antibiotic resistance by promoting horizontal gene transfer. We review current concepts of biofilm tolerance with special emphasis on the role of the biofilm matrix and the physiology of biofilm-embedded cells. The heterogeneity in metabolic and reproductive activity within a biofilm correlates with a non-uniform susceptibility of enclosed bacteria. Recent studies have documented similar heterogeneity in planktonic cultures. Nutritional starvation and high cell density, two key characteristics of biofilm physiology, also mediate antimicrobial tolerance in stationary-phase planktonic cultures. Advances in characterizing the role of stress response genes, quorum sensing and phase variation in stationary-phase planktonic cultures have shed new light on tolerance mechanisms within biofilm communities.\n
\n\n\n\n \n\n \n \n \n \n \n \n Phenotypic Diversity, Population Growth, and Information in Fluctuating Environments.\n \n \n \n \n\n\n \n Kussell, E.; and Leibler, S.\n\n\n \n\n\n\n Science, 309(5743): 2075–2078. September 2005.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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\n\n\n@article{kussell_phenotypic_2005,\n\ttitle = {Phenotypic {Diversity}, {Population} {Growth}, and {Information} in {Fluctuating} {Environments}},\n\tvolume = {309},\n\tissn = {0036-8075, 1095-9203},\n\turl = {https://www.science.org/doi/10.1126/science.1114383},\n\tdoi = {10.1126/science.1114383},\n\tabstract = {Organisms in fluctuating environments must constantly adapt their behavior to survive. In clonal populations, this may be achieved through sensing followed by response or through the generation of diversity by stochastic phenotype switching. Here we show that stochastic switching can be favored over sensing when the environment changes infrequently. The optimal switching rates then mimic the statistics of environmental changes. We derive a relation between the long-term growth rate of the organism and the information available about its fluctuating environment.},\n\tlanguage = {en},\n\tnumber = {5743},\n\turldate = {2023-05-03},\n\tjournal = {Science},\n\tauthor = {Kussell, Edo and Leibler, Stanislas},\n\tmonth = sep,\n\tyear = {2005},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {2075--2078},\n\tfile = {Kussell and Leibler - 2005 - Phenotypic Diversity, Population Growth, and Infor.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\46GIDIHM\\\\Kussell and Leibler - 2005 - Phenotypic Diversity, Population Growth, and Infor.pdf:application/pdf},\n}\n\n\n\n Organisms in fluctuating environments must constantly adapt their behavior to survive. In clonal populations, this may be achieved through sensing followed by response or through the generation of diversity by stochastic phenotype switching. Here we show that stochastic switching can be favored over sensing when the environment changes infrequently. The optimal switching rates then mimic the statistics of environmental changes. We derive a relation between the long-term growth rate of the organism and the information available about its fluctuating environment.\n
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\n \n \n\n \n \n \n \n \n \n Clinical Relevance of Bacteriostatic versus Bactericidal Mechanisms of Action in the Treatment of Gram-Positive Bacterial Infections.\n \n \n \n \n\n\n \n Pankey, G. A.; and Sabath, L. D.\n\n\n \n\n\n\n Clinical Infectious Diseases, 38(6): 864–870. March 2004.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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\n\n\n@article{pankey_clinical_2004,\n\ttitle = {Clinical {Relevance} of {Bacteriostatic} versus {Bactericidal} {Mechanisms} of {Action} in the {Treatment} of {Gram}-{Positive} {Bacterial} {Infections}},\n\tvolume = {38},\n\tissn = {1058-4838},\n\turl = {https://doi.org/10.1086/381972},\n\tdoi = {10.1086/381972},\n\tabstract = {The distinction between bactericidal and bacteriostatic agents appears to be clear according to the in vitro definition, but this only applies under strict laboratory conditions and is inconsistent for a particular agent against all bacteria. The distinction is more arbitrary when agents are categorized in clinical situations. The supposed superiority of bactericidal agents over bacteriostatic agents is of little relevance when treating the vast majority of infections with gram-positive bacteria, particularly in patients with uncomplicated infections and noncompromised immune systems. Bacteriostatic agents (e.g., chloramphenicol, clindamycin, and linezolid) have been effectively used for treatment of endocarditis, meningitis, and osteomyelitis—indications that are often considered to require bactericidal activity. Although bacteriostatic/bactericidal data may provide valuable information on the potential action of antibacterial agents in vitro, it is necessary to combine this information with pharmacokinetic and pharmacodynamic data to provide more meaningful prediction of efficacy in vivo. The ultimate guide to treatment of any infection must be clinical outcome.},\n\tnumber = {6},\n\turldate = {2023-03-31},\n\tjournal = {Clinical Infectious Diseases},\n\tauthor = {Pankey, G. A. and Sabath, L. D.},\n\tmonth = mar,\n\tyear = {2004},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {864--870},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\SMNTJUP7\\\\Pankey and Sabath - 2004 - Clinical Relevance of Bacteriostatic versus Bacter.pdf:application/pdf},\n}\n\n\n\n The distinction between bactericidal and bacteriostatic agents appears to be clear according to the in vitro definition, but this only applies under strict laboratory conditions and is inconsistent for a particular agent against all bacteria. The distinction is more arbitrary when agents are categorized in clinical situations. The supposed superiority of bactericidal agents over bacteriostatic agents is of little relevance when treating the vast majority of infections with gram-positive bacteria, particularly in patients with uncomplicated infections and noncompromised immune systems. Bacteriostatic agents (e.g., chloramphenicol, clindamycin, and linezolid) have been effectively used for treatment of endocarditis, meningitis, and osteomyelitis—indications that are often considered to require bactericidal activity. Although bacteriostatic/bactericidal data may provide valuable information on the potential action of antibacterial agents in vitro, it is necessary to combine this information with pharmacokinetic and pharmacodynamic data to provide more meaningful prediction of efficacy in vivo. The ultimate guide to treatment of any infection must be clinical outcome.\n
\n\n\n\n \n\n \n \n \n \n \n \n Bacterial Persistence as a Phenotypic Switch.\n \n \n \n \n\n\n \n Balaban, N. Q.; Merrin, J.; Chait, R.; Kowalik, L.; and Leibler, S.\n\n\n \n\n\n\n Science, 305(5690): 1622–1625. September 2004.\n Publisher: American Association for the Advancement of Science\n\n\n\n
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\n\n\n@article{balaban_bacterial_2004,\n\ttitle = {Bacterial {Persistence} as a {Phenotypic} {Switch}},\n\tvolume = {305},\n\turl = {https://www.science.org/doi/10.1126/science.1099390},\n\tdoi = {10.1126/science.1099390},\n\tabstract = {A fraction of a genetically homogeneous microbial population may survive exposure to stress such as antibiotic treatment. Unlike resistant mutants, cells regrown from such persistent bacteria remain sensitive to the antibiotic. We investigated the persistence of single cells of Escherichia coli with the use of microfluidic devices. Persistence was linked to preexisting heterogeneity in bacterial populations because phenotypic switching occurred between normally growing cells and persister cells having reduced growth rates. Quantitative measurements led to a simple mathematical description of the persistence switch. Inherent heterogeneity of bacterial populations may be important in adaptation to fluctuating environments and in the persistence of bacterial infections.},\n\tnumber = {5690},\n\turldate = {2023-05-03},\n\tjournal = {Science},\n\tauthor = {Balaban, Nathalie Q. and Merrin, Jack and Chait, Remy and Kowalik, Lukasz and Leibler, Stanislas},\n\tmonth = sep,\n\tyear = {2004},\n\tnote = {Publisher: American Association for the Advancement of Science},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {1622--1625},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\TFEN8BRM\\\\Balaban et al. - 2004 - Bacterial Persistence as a Phenotypic Switch.pdf:application/pdf},\n}\n\n\n\n A fraction of a genetically homogeneous microbial population may survive exposure to stress such as antibiotic treatment. Unlike resistant mutants, cells regrown from such persistent bacteria remain sensitive to the antibiotic. We investigated the persistence of single cells of Escherichia coli with the use of microfluidic devices. Persistence was linked to preexisting heterogeneity in bacterial populations because phenotypic switching occurred between normally growing cells and persister cells having reduced growth rates. Quantitative measurements led to a simple mathematical description of the persistence switch. Inherent heterogeneity of bacterial populations may be important in adaptation to fluctuating environments and in the persistence of bacterial infections.\n
\n\n\n\n \n\n \n \n \n \n \n Stochastic gene expression in fluctuating environments.\n \n \n \n\n\n \n Thattai, M.; and Van Oudenaarden, A.\n\n\n \n\n\n\n Genetics, 167: 523. 2004.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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\n\n\n\n@article{Thattai04,\n\ttitle = {Stochastic gene expression in fluctuating environments},\n\tvolume = {167},\n\tjournal = {Genetics},\n\tauthor = {Thattai, M. and Van Oudenaarden, A.},\n\tyear = {2004},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {523},\n\tfile = {Thattai and Van Oudenaarden - 2004 - Stochastic gene expression in fluctuating environm.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\HM5T5WPS\\\\Thattai and Van Oudenaarden - 2004 - Stochastic gene expression in fluctuating environm.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Mathematical population genetics.\n \n \n \n\n\n \n Ewens, W. J.\n\n\n \n\n\n\n Springer, New York, USA, 2004.\n \n\n\n\n
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\n\n\n\n@book{Ewens,\n\ttitle = {Mathematical population genetics},\n\tpublisher = {Springer, New York, USA},\n\tauthor = {Ewens, W. J.},\n\tyear = {2004},\n\tkeywords = {⛔ No INSPIRE recid found},\n}\n\n\n\n
\n\n \n \n 2003\n \n \n (1)\n \n \n
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\n \n \n\n \n \n \n \n \n \n The Impact of Antimicrobial Resistance on Health and Economic Outcomes.\n \n \n \n \n\n\n \n Eliopoulos, G. M.; Cosgrove, S. E.; and Carmeli, Y.\n\n\n \n\n\n\n Clinical Infectious Diseases, 36(11): 1433–1437. June 2003.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n\n
\n\n\n@article{eliopoulos_impact_2003,\n\ttitle = {The {Impact} of {Antimicrobial} {Resistance} on {Health} and {Economic} {Outcomes}},\n\tvolume = {36},\n\tissn = {1058-4838},\n\turl = {https://doi.org/10.1086/375081},\n\tdoi = {10.1086/375081},\n\tabstract = {Despite an increasing prevalence of antimicrobial-resistant pathogens, the health and economic impact of colonization and infection with these organisms has not been fully elucidated. We explore how antimicrobial resistance can affect patient outcomes by enhancing virulence, causing a delay in the administration of appropriate therapy, and limiting available therapy. Next, we examine the different perspectives held by hospitals, third-party payers, patients, and society on the impact of resistance. Finally, we review methodological issues in designing and assessing studies that address the clinical outcomes for patients infected or colonized with resistant pathogens, including adjustment for important confounding variables, control group selection, and the quantification of economic outcomes.},\n\tnumber = {11},\n\turldate = {2023-03-07},\n\tjournal = {Clinical Infectious Diseases},\n\tauthor = {Eliopoulos, George M. and Cosgrove, Sara E. and Carmeli, Yehuda},\n\tmonth = jun,\n\tyear = {2003},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {1433--1437},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\4UVIBEAQ\\\\Eliopoulos et al. - 2003 - The Impact of Antimicrobial Resistance on Health a.pdf:application/pdf;Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\8KAZBERC\\\\304950.html:text/html},\n}\n\n\n\n Despite an increasing prevalence of antimicrobial-resistant pathogens, the health and economic impact of colonization and infection with these organisms has not been fully elucidated. We explore how antimicrobial resistance can affect patient outcomes by enhancing virulence, causing a delay in the administration of appropriate therapy, and limiting available therapy. Next, we examine the different perspectives held by hospitals, third-party payers, patients, and society on the impact of resistance. Finally, we review methodological issues in designing and assessing studies that address the clinical outcomes for patients infected or colonized with resistant pathogens, including adjustment for important confounding variables, control group selection, and the quantification of economic outcomes.\n
\n\n\n\n
\n\n \n \n 2002\n \n \n (1)\n \n \n
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\n \n \n\n \n \n \n \n \n Handbook of stochastic methods.\n \n \n \n\n\n \n Gardiner, C. W\n\n\n \n\n\n\n Springer, USA, 2002.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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\n\n\n\n@book{Gardiner,\n\ttitle = {Handbook of stochastic methods},\n\tpublisher = {Springer, USA},\n\tauthor = {Gardiner, C. W},\n\tyear = {2002},\n\tkeywords = {⛔ No INSPIRE recid found},\n}\n\n\n\n
\n\n \n \n 2001\n \n \n (3)\n \n \n
\n \n \n \n
\n \n \n\n \n \n \n \n \n \n The rise and fall of antimicrobial resistance.\n \n \n \n \n\n\n \n Lipsitch, M.\n\n\n \n\n\n\n Trends in Microbiology, 9(9): 438–444. September 2001.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n
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Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n\n
\n\n\n\n@article{lipsitch_rise_2001,\n\ttitle = {The rise and fall of antimicrobial resistance},\n\tvolume = {9},\n\tissn = {0966842X},\n\turl = {https://linkinghub.elsevier.com/retrieve/pii/S0966842X01021308},\n\tdoi = {10.1016/S0966-842X(01)02130-8},\n\tlanguage = {en},\n\tnumber = {9},\n\turldate = {2022-09-15},\n\tjournal = {Trends in Microbiology},\n\tauthor = {Lipsitch, Marc},\n\tmonth = sep,\n\tyear = {2001},\n\tkeywords = {unread, ⛔ No INSPIRE recid found},\n\tpages = {438--444},\n\tfile = {Lipsitch - 2001 - The rise and fall of antimicrobial resistance.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\NQT57GNB\\\\Lipsitch - 2001 - The rise and fall of antimicrobial resistance.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n \n The Diversity–Disturbance Relationship: Is It Generally Strong and Peaked?.\n \n \n \n \n\n\n \n Mackey, R. L.; and Currie, D. J.\n\n\n \n\n\n\n Ecology, 82(12): 3479–3492. 2001.\n _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1890/0012-9658%282001%29082%5B3479%3ATDDRII%5D2.0.CO%3B2\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n
\n\n\n@article{mackey_diversitydisturbance_2001,\n\ttitle = {The {Diversity}–{Disturbance} {Relationship}: {Is} {It} {Generally} {Strong} and {Peaked}?},\n\tvolume = {82},\n\tissn = {1939-9170},\n\tshorttitle = {The {Diversity}–{Disturbance} {Relationship}},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1890/0012-9658%282001%29082%5B3479%3ATDDRII%5D2.0.CO%3B2},\n\tdoi = {10.2307/2680166},\n\tabstract = {The contemporary literature accepts that disturbance strongly influences patterns of species diversity, and that the relationship is peaked, with a maximum at intermediate levels of disturbance. We tested this hypothesis using a compilation of published species diversity–disturbance relationships that were gleaned from a literature search of papers published from 1985 through 1996 and from references therein. We identified 116 species richness–, 53 diversity–, and 28 evenness–disturbance relationships in the literature, which we grouped according to shape of relationship (nonsignificant, peaked, negative monotonic, positive monotonic, or U-shaped). We tested the relationships between the strength and shapes of these relationships and attributes of the community, disturbance, and sampling and study design. Nonsignificant relationships were the most common, comprising 35\\% of richness, 28\\% of diversity, and 50\\% of evenness studies. Peaked responses were reported in only 16\\% of richness, 19\\% of diversity, and 11\\% of evenness cases. Explained variation in the three measures of diversity was variable among studies but averaged ∼50\\%. It was higher when few samples and few disturbance levels were examined and when organisms within the samples were not exhaustively censused, suggesting that procedural artifact contributes to these relationships. Explained variation was also higher in studies in which disturbance was measured as a gradient of time passed since the last disturbance (meanr2 = 61\\%), vs. studies of spatial variation in richness (meanr2 = 42\\%). Peaked richness relationships had the greatest odds of being observed when sampled area and actual evapotranspiration were small, when disturbances were natural rather than anthropogenic in origin, and when few disturbance levels were examined. Thus, on average, diversity–disturbance relationships do not have consistently highr2 and are not as consistently peaked as the contemporary consensus would suggest.},\n\tlanguage = {en},\n\tnumber = {12},\n\turldate = {2023-03-07},\n\tjournal = {Ecology},\n\tauthor = {Mackey, Robin L. and Currie, David J.},\n\tyear = {2001},\n\tnote = {\\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1890/0012-9658\\%282001\\%29082\\%5B3479\\%3ATDDRII\\%5D2.0.CO\\%3B2},\n\tkeywords = {unread, disturbance, diversity, diversity–disturbance relationship, intermediate-disturbance hypothesis, meta-analyses, sampling artifacts, sampling intensity, species diversity, species richness, temporal and spatial patterns, ⛔ No INSPIRE recid found},\n\tpages = {3479--3492},\n\tfile = {Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\UXBX6PPS\\\\0012-9658(2001)082[3479TDDRII]2.0.html:text/html},\n}\n\n\n\n The contemporary literature accepts that disturbance strongly influences patterns of species diversity, and that the relationship is peaked, with a maximum at intermediate levels of disturbance. We tested this hypothesis using a compilation of published species diversity–disturbance relationships that were gleaned from a literature search of papers published from 1985 through 1996 and from references therein. We identified 116 species richness–, 53 diversity–, and 28 evenness–disturbance relationships in the literature, which we grouped according to shape of relationship (nonsignificant, peaked, negative monotonic, positive monotonic, or U-shaped). We tested the relationships between the strength and shapes of these relationships and attributes of the community, disturbance, and sampling and study design. Nonsignificant relationships were the most common, comprising 35% of richness, 28% of diversity, and 50% of evenness studies. Peaked responses were reported in only 16% of richness, 19% of diversity, and 11% of evenness cases. Explained variation in the three measures of diversity was variable among studies but averaged ∼50%. It was higher when few samples and few disturbance levels were examined and when organisms within the samples were not exhaustively censused, suggesting that procedural artifact contributes to these relationships. Explained variation was also higher in studies in which disturbance was measured as a gradient of time passed since the last disturbance (meanr2 = 61%), vs. studies of spatial variation in richness (meanr2 = 42%). Peaked richness relationships had the greatest odds of being observed when sampled area and actual evapotranspiration were small, when disturbances were natural rather than anthropogenic in origin, and when few disturbance levels were examined. Thus, on average, diversity–disturbance relationships do not have consistently highr2 and are not as consistently peaked as the contemporary consensus would suggest.\n
\n\n\n\n \n\n \n \n \n \n \n \n Intrinsic noise in gene regulatory networks.\n \n \n \n \n\n\n \n Thattai, M.; and van Oudenaarden, A.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences, 98(15): 8614–8619. July 2001.\n Publisher: Proceedings of the National Academy of Sciences\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n\n
\n\n\n@article{thattai_intrinsic_2001,\n\ttitle = {Intrinsic noise in gene regulatory networks},\n\tvolume = {98},\n\turl = {https://www.pnas.org/doi/10.1073/pnas.151588598},\n\tdoi = {10.1073/pnas.151588598},\n\tabstract = {Cells are intrinsically noisy biochemical reactors: low reactant numbers can lead to significant statistical fluctuations in molecule numbers and reaction rates. Here we use an analytic model to investigate the emergent noise properties of genetic systems. We find for a single gene that noise is essentially determined at the translational level, and that the mean and variance of protein concentration can be independently controlled. The noise strength immediately following single gene induction is almost twice the final steady-state value. We find that fluctuations in the concentrations of a regulatory protein can propagate through a genetic cascade; translational noise control could explain the inefficient translation rates observed for genes encoding such regulatory proteins. For an autoregulatory protein, we demonstrate that negative feedback efficiently decreases system noise. The model can be used to predict the noise characteristics of networks of arbitrary connectivity. The general procedure is further illustrated for an autocatalytic protein and a bistable genetic switch. The analysis of intrinsic noise reveals biological roles of gene network structures and can lead to a deeper understanding of their evolutionary origin.},\n\tnumber = {15},\n\turldate = {2023-05-03},\n\tjournal = {Proceedings of the National Academy of Sciences},\n\tauthor = {Thattai, Mukund and van Oudenaarden, Alexander},\n\tmonth = jul,\n\tyear = {2001},\n\tnote = {Publisher: Proceedings of the National Academy of Sciences},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {8614--8619},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\RJFJN9TT\\\\Thattai and van Oudenaarden - 2001 - Intrinsic noise in gene regulatory networks.pdf:application/pdf},\n}\n\n\n\n Cells are intrinsically noisy biochemical reactors: low reactant numbers can lead to significant statistical fluctuations in molecule numbers and reaction rates. Here we use an analytic model to investigate the emergent noise properties of genetic systems. We find for a single gene that noise is essentially determined at the translational level, and that the mean and variance of protein concentration can be independently controlled. The noise strength immediately following single gene induction is almost twice the final steady-state value. We find that fluctuations in the concentrations of a regulatory protein can propagate through a genetic cascade; translational noise control could explain the inefficient translation rates observed for genes encoding such regulatory proteins. For an autoregulatory protein, we demonstrate that negative feedback efficiently decreases system noise. The model can be used to predict the noise characteristics of networks of arbitrary connectivity. The general procedure is further illustrated for an autocatalytic protein and a bistable genetic switch. The analysis of intrinsic noise reveals biological roles of gene network structures and can lead to a deeper understanding of their evolutionary origin.\n
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\n\n \n \n 2000\n \n \n (3)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels.\n \n \n \n \n\n\n \n Gibson, M. A.; and Bruck, J.\n\n\n \n\n\n\n The Journal of Physical Chemistry A, 104(9): 1876–1889. March 2000.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n
\n\n\n\n@article{gibson_efficient_2000,\n\ttitle = {Efficient {Exact} {Stochastic} {Simulation} of {Chemical} {Systems} with {Many} {Species} and {Many} {Channels}},\n\tvolume = {104},\n\tissn = {1089-5639, 1520-5215},\n\turl = {https://pubs.acs.org/doi/10.1021/jp993732q},\n\tdoi = {10.1021/jp993732q},\n\tlanguage = {en},\n\tnumber = {9},\n\turldate = {2022-05-11},\n\tjournal = {The Journal of Physical Chemistry A},\n\tauthor = {Gibson, Michael A. and Bruck, Jehoshua},\n\tmonth = mar,\n\tyear = {2000},\n\tkeywords = {read, simulation, on website, ⛔ No INSPIRE recid found},\n\tpages = {1876--1889},\n\tfile = {Gibson and Bruck - 2000 - Efficient Exact Stochastic Simulation of Chemical .pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\466KGCYS\\\\Gibson and Bruck - 2000 - Efficient Exact Stochastic Simulation of Chemical .pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n General theory of competitive coexistence in spatially-varying environments.\n \n \n \n\n\n \n Chesson, P.\n\n\n \n\n\n\n Theoretical Population Biology, 58: 211. 2000.\n \n\n\n\n
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\n\n\n\n@article{Chesson00b,\n\ttitle = {General theory of competitive coexistence in spatially-varying environments.},\n\tvolume = {58},\n\tdoi = {10.1006/tpbi.2000.1486},\n\tjournal = {Theoretical Population Biology},\n\tauthor = {Chesson, P.},\n\tyear = {2000},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {211},\n\tfile = {Chesson - 2000 - General theory of competitive coexistence in spati.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\ZX7NW4L9\\\\Chesson - 2000 - General theory of competitive coexistence in spati.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Mechanisms of maintenance of species diversity.\n \n \n \n\n\n \n Chesson, P.\n\n\n \n\n\n\n , 31: 343. 2000.\n \n\n\n\n
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\n\n\n\n@article{Chesson00a,\n\ttitle = {Mechanisms of maintenance of species diversity},\n\tvolume = {31},\n\tdoi = {10.1146/annurev.ecolsys.31.1.343},\n\tauthor = {Chesson, P.},\n\tyear = {2000},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {343},\n\tfile = {Chesson - 2000 - Mechanisms of maintenance of species diversity.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\DUAPF2J8\\\\Chesson - 2000 - Mechanisms of maintenance of species diversity.pdf:application/pdf},\n}\n\n\n\n
\n\n \n \n 1998\n \n \n (1)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Cycles of famine and feast: the starvation and outgrowth strategies of a marineVibrio.\n \n \n \n \n\n\n \n Srinivasan, S.; and Kjelleberg, S.\n\n\n \n\n\n\n Journal of Biosciences, 23(4): 501–511. October 1998.\n \n\n\n\n
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\n\n\n@article{srinivasan_cycles_1998,\n\ttitle = {Cycles of famine and feast: the starvation and outgrowth strategies of a {marineVibrio}},\n\tvolume = {23},\n\tissn = {0973-7138},\n\tshorttitle = {Cycles of famine and feast},\n\turl = {https://doi.org/10.1007/BF02936144},\n\tdoi = {10.1007/BF02936144},\n\tabstract = {Studies of starvation survival in non-differentiating bacteria have largely focused on physiological changes and regulatory aspects of a few master regulators such as the signal molecule ppGpp and the stationary phase alternative sigma factor, sigma S. Recent findings have implicated a series of novel key events for the entry as well as exit from starvation. The importance of alternative sigma factors other than sigma S is emerging. In addition, low molecular weight extracellular signals have been demonstrated to be essential for the induction and mediation of several adaptive responses. The importance of mRNA modification and stability for starvation survival as well as outgrowth is receiving renewedinterest. In this paper, we present the results obtained from studies of starvation survival and recovery ofVibrio sp. strain S14.},\n\tlanguage = {en},\n\tnumber = {4},\n\turldate = {2023-03-14},\n\tjournal = {Journal of Biosciences},\n\tauthor = {Srinivasan, Sujatha and Kjelleberg, Staffan},\n\tmonth = oct,\n\tyear = {1998},\n\tkeywords = {carbon starvation, extracellular signals, MarineVibrio, outgrowth, recovery, stringent response, ⛔ No INSPIRE recid found},\n\tpages = {501--511},\n\tfile = {Srinivasan and Kjelleberg - 1998 - Cycles of famine and feast the starvation and out.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\QI2TBTTT\\\\Srinivasan and Kjelleberg - 1998 - Cycles of famine and feast the starvation and out.pdf:application/pdf},\n}\n\n\n\n Studies of starvation survival in non-differentiating bacteria have largely focused on physiological changes and regulatory aspects of a few master regulators such as the signal molecule ppGpp and the stationary phase alternative sigma factor, sigma S. Recent findings have implicated a series of novel key events for the entry as well as exit from starvation. The importance of alternative sigma factors other than sigma S is emerging. In addition, low molecular weight extracellular signals have been demonstrated to be essential for the induction and mediation of several adaptive responses. The importance of mRNA modification and stability for starvation survival as well as outgrowth is receiving renewedinterest. In this paper, we present the results obtained from studies of starvation survival and recovery ofVibrio sp. strain S14.\n
\n\n\n\n
\n\n \n \n 1997\n \n \n (1)\n \n \n
\n \n \n \n
\n \n \n\n \n \n \n \n \n \n Adaptation to the fitness costs of antibiotic resistance in Escherichia coli.\n \n \n \n \n\n\n \n Schrag, S J; Perrot, V; and Levin, B R\n\n\n \n\n\n\n Proceedings of the Royal Society B: Biological Sciences, 264(1386): 1287–1291. September 1997.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n
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Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n\n
\n\n\n@article{schrag_adaptation_1997,\n\ttitle = {Adaptation to the fitness costs of antibiotic resistance in {Escherichia} coli.},\n\tvolume = {264},\n\tissn = {0962-8452},\n\turl = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1688596/},\n\tdoi = {10.1098/rspb.1997.0178},\n\tabstract = {Policies aimed at alleviating the growing problem of drug-resistant pathogens by restricting antimicrobial usage implicitly assume that resistance reduces the Darwinian fitness of pathogens in the absence of drugs. While fitness costs have been demonstrated for bacteria and viruses resistant to some chemotherapeutic agents, these costs are anticipated to decline during subsequent evolution. This has recently been observed in pathogens as diverse as HIV and Escherichia coli. Here we present evidence that these gentic adaptations to the costs of resistance can virtually preclude resistant lineages from reverting to sensitivity. We show that second site mutations which compensate for the substantial (14 and 18\\% per generation) fitness costs of streptomycin resistant (rpsL) mutations in E. coli create a genetic background in which streptomycin sensitive, rpsL+ alleles have a 4-30\\% per generation selective disadvantage relative to adapted, resistant strains. We also present evidence that similar compensatory mutations have been fixed in long-term streptomycin-resistant laboratory strains of E. coli and may account for the persistence of rpsL streptomycin resistance in populations maintained for more than 10,000 generations in the absence of the antibiotic. We discuss the public health implications of these and other experimental results that question whether the more prudent use of antimicrobial chemotherapy will lead to declines in the incidence of drug-resistant pathogenic microbes.},\n\tnumber = {1386},\n\turldate = {2022-06-28},\n\tjournal = {Proceedings of the Royal Society B: Biological Sciences},\n\tauthor = {Schrag, S J and Perrot, V and Levin, B R},\n\tmonth = sep,\n\tyear = {1997},\n\tpmid = {9332013},\n\tpmcid = {PMC1688596},\n\tkeywords = {read, on website, ⛔ No INSPIRE recid found},\n\tpages = {1287--1291},\n\tfile = {PubMed Central Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\BCJ4AG7M\\\\Schrag et al. - 1997 - Adaptation to the fitness costs of antibiotic resi.pdf:application/pdf},\n}\n\n\n\n Policies aimed at alleviating the growing problem of drug-resistant pathogens by restricting antimicrobial usage implicitly assume that resistance reduces the Darwinian fitness of pathogens in the absence of drugs. While fitness costs have been demonstrated for bacteria and viruses resistant to some chemotherapeutic agents, these costs are anticipated to decline during subsequent evolution. This has recently been observed in pathogens as diverse as HIV and Escherichia coli. Here we present evidence that these gentic adaptations to the costs of resistance can virtually preclude resistant lineages from reverting to sensitivity. We show that second site mutations which compensate for the substantial (14 and 18% per generation) fitness costs of streptomycin resistant (rpsL) mutations in E. coli create a genetic background in which streptomycin sensitive, rpsL+ alleles have a 4-30% per generation selective disadvantage relative to adapted, resistant strains. We also present evidence that similar compensatory mutations have been fixed in long-term streptomycin-resistant laboratory strains of E. coli and may account for the persistence of rpsL streptomycin resistance in populations maintained for more than 10,000 generations in the absence of the antibiotic. We discuss the public health implications of these and other experimental results that question whether the more prudent use of antimicrobial chemotherapy will lead to declines in the incidence of drug-resistant pathogenic microbes.\n
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\n\n \n \n 1994\n \n \n (2)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Long-Term Experimental Evolution in Escherichia coli. II. Changes in Life-History Traits During Adaptation to a Seasonal Environment.\n \n \n \n \n\n\n \n Vasi, F.; Travisano, M.; and Lenski, R. E.\n\n\n \n\n\n\n The American Naturalist, 144(3): 432–456. September 1994.\n Publisher: The University of Chicago Press\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
\n\n\n \n\n\n\n \n \n
Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n\n
\n\n\n@article{vasi_long-term_1994,\n\ttitle = {Long-{Term} {Experimental} {Evolution} in {Escherichia} coli. {II}. {Changes} in {Life}-{History} {Traits} {During} {Adaptation} to a {Seasonal} {Environment}},\n\tvolume = {144},\n\tissn = {0003-0147},\n\turl = {https://www.journals.uchicago.edu/doi/10.1086/285685},\n\tdoi = {10.1086/285685},\n\tabstract = {Twelve populations of the bacterium Escherichia coli were propagated for 2,000 generations in a seasonal environment, which consisted of alternating periods of feast and famine. The mean fitness of the derived genotypes increased by ∼35\\% relative to their common ancestor, based on competition experiments in the same environment. The bacteria could have adapted, in principle, by decreasing their lag prior to growth upon transfer to fresh medium (L), increasing their maximum growth rate (Vm), reducing the concentration of resource required to support growth at half the maximum rate (Ks), and reducing their death rate after the limiting resource was exhausted (D). We estimated these parameters for the ancestor and then calculated the opportunity for selection on each parameter. The inferred selection gradients for Vm and L were much steeper than for Ks and D. The derived genotypes showed significant improvement in Vm and L but not in Ks or D. Also, the numerical yield in pure culture of the derived genotypes was significantly lower than the yield of the common ancestor, but the average cell size was much larger. The independently derived genotypes are somewhat more variable in these life-history traits than in their relative fitnesses, which indicates that they acquired different genetic adaptations to the seasonal environment. Nonetheless, the evolutionary changes in life-history traits exhibit substantial parallelism among the replicate populations.},\n\tnumber = {3},\n\turldate = {2023-03-14},\n\tjournal = {The American Naturalist},\n\tauthor = {Vasi, Farida and Travisano, Michael and Lenski, Richard E.},\n\tmonth = sep,\n\tyear = {1994},\n\tnote = {Publisher: The University of Chicago Press},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {432--456},\n\tfile = {Vasi et al. - 1994 - Long-Term Experimental Evolution in Escherichia co.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\CWERELF4\\\\Vasi et al. - 1994 - Long-Term Experimental Evolution in Escherichia co.pdf:application/pdf},\n}\n\n\n\n Twelve populations of the bacterium Escherichia coli were propagated for 2,000 generations in a seasonal environment, which consisted of alternating periods of feast and famine. The mean fitness of the derived genotypes increased by ∼35% relative to their common ancestor, based on competition experiments in the same environment. The bacteria could have adapted, in principle, by decreasing their lag prior to growth upon transfer to fresh medium (L), increasing their maximum growth rate (Vm), reducing the concentration of resource required to support growth at half the maximum rate (Ks), and reducing their death rate after the limiting resource was exhausted (D). We estimated these parameters for the ancestor and then calculated the opportunity for selection on each parameter. The inferred selection gradients for Vm and L were much steeper than for Ks and D. The derived genotypes showed significant improvement in Vm and L but not in Ks or D. Also, the numerical yield in pure culture of the derived genotypes was significantly lower than the yield of the common ancestor, but the average cell size was much larger. The independently derived genotypes are somewhat more variable in these life-history traits than in their relative fitnesses, which indicates that they acquired different genetic adaptations to the seasonal environment. Nonetheless, the evolutionary changes in life-history traits exhibit substantial parallelism among the replicate populations.\n
\n\n\n\n \n\n \n \n \n \n \n Multispecies competition in variable environments.\n \n \n \n\n\n \n Chesson, P.\n\n\n \n\n\n\n Theoretical Population Biology, 45: 227. 1994.\n \n\n\n\n
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\n\n\n\n@article{Chesson94,\n\ttitle = {Multispecies competition in variable environments},\n\tvolume = {45},\n\tdoi = {10.1006/tpbi.1994.1013},\n\tjournal = {Theoretical Population Biology},\n\tauthor = {Chesson, P.},\n\tyear = {1994},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {227},\n\tfile = {Chesson - 1994 - Multispecies competition in variable environments.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\RAW29CNU\\\\Chesson - 1994 - Multispecies competition in variable environments.pdf:application/pdf},\n}\n\n\n\n
\n\n \n \n 1993\n \n \n (1)\n \n \n
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\n \n \n\n \n \n \n \n \n Survival of hunger and stress: The role of rpoS in early stationary phase gene regulation in E. coli.\n \n \n \n\n\n \n Hengge-Aronis, R.\n\n\n \n\n\n\n Cell, 72(2): 165–168. 1993.\n \n\n\n\n
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\n\n\n\n@article{hengge-aronis_survival_1993,\n\ttitle = {Survival of hunger and stress: {The} role of {rpoS} in early stationary phase gene regulation in {E}. coli},\n\tvolume = {72},\n\tnumber = {2},\n\tjournal = {Cell},\n\tauthor = {Hengge-Aronis, Regine},\n\tyear = {1993},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {165--168},\n\tfile = {Hengge-Aronis - 1993 - Survival of hunger and stress The role of rpoS in.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\ITIFBHW6\\\\Hengge-Aronis - 1993 - Survival of hunger and stress The role of rpoS in.pdf:application/pdf},\n}\n\n\n\n
\n\n \n \n 1992\n \n \n (1)\n \n \n
\n \n \n \n
\n \n \n\n \n \n \n \n \n Stochastic processes in physics and chemistry.\n \n \n \n\n\n \n van Kampen, N. G\n\n\n \n\n\n\n North-Holland, Amsterdam, 1992.\n \n\n\n\n
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\n\n\n\n@book{VanKampen,\n\ttitle = {Stochastic processes in physics and chemistry},\n\tpublisher = {North-Holland, Amsterdam},\n\tauthor = {van Kampen, N. G},\n\tyear = {1992},\n\tkeywords = {⛔ No INSPIRE recid found},\n}\n\n\n\n
\n\n \n \n 1991\n \n \n (1)\n \n \n
\n \n \n \n
\n \n \n\n \n \n \n \n \n \n The Role of Abiotic Factors in Community Organization.\n \n \n \n \n\n\n \n Dunson, W. A.; and Travis, J.\n\n\n \n\n\n\n The American Naturalist, 138(5): 1067–1091. 1991.\n Publisher: [University of Chicago Press, American Society of Naturalists]\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n\n
\n\n\n@article{dunson_role_1991,\n\ttitle = {The {Role} of {Abiotic} {Factors} in {Community} {Organization}},\n\tvolume = {138},\n\tissn = {0003-0147},\n\turl = {https://www.jstor.org/stable/2462508},\n\tabstract = {Very few ecological studies have attempted to fully test the integrative role of abiotic and biotic factors in interspecific interactions. There is little if any dispute about the value of such an approach in community ecology. However, there is great disagreement over the present direction of the field; we advocate a reemphasis of the integrative role of abiotic and biotic factors. By using literature examples and data on the role of salinity in reversing the competitive relations between fish of the genus Lucania, we have suggested a reemphasis on these interactions. This represents a blend of the traditional fields of ecology, physiology, and toxicology and could facilitate progress in community ecology. As such it could also be a significant part of the new direction sought for the field of physiological ecology. Finally, we are not arguing that abiotic parameters are necessarily more important than any of a group of multiple factors that may be involved in regulating community structure, only that they must be included as possible controlling variables in any complete study.},\n\tnumber = {5},\n\turldate = {2023-03-14},\n\tjournal = {The American Naturalist},\n\tauthor = {Dunson, William A. and Travis, Joseph},\n\tyear = {1991},\n\tnote = {Publisher: [University of Chicago Press, American Society of Naturalists]},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {1067--1091},\n\tfile = {Dunson and Travis - 1991 - The Role of Abiotic Factors in Community Organizat.pdf:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\5GP4B4ZE\\\\Dunson and Travis - 1991 - The Role of Abiotic Factors in Community Organizat.pdf:application/pdf},\n}\n\n\n\n Very few ecological studies have attempted to fully test the integrative role of abiotic and biotic factors in interspecific interactions. There is little if any dispute about the value of such an approach in community ecology. However, there is great disagreement over the present direction of the field; we advocate a reemphasis of the integrative role of abiotic and biotic factors. By using literature examples and data on the role of salinity in reversing the competitive relations between fish of the genus Lucania, we have suggested a reemphasis on these interactions. This represents a blend of the traditional fields of ecology, physiology, and toxicology and could facilitate progress in community ecology. As such it could also be a significant part of the new direction sought for the field of physiological ecology. Finally, we are not arguing that abiotic parameters are necessarily more important than any of a group of multiple factors that may be involved in regulating community structure, only that they must be included as possible controlling variables in any complete study.\n
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\n\n \n \n 1990\n \n \n (1)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Evolution in a Variable Environment.\n \n \n \n \n\n\n \n Frank, S. A.; and Slatkin, M.\n\n\n \n\n\n\n The American Naturalist, 136(2): 244–260. August 1990.\n Publisher: The University of Chicago Press\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n\n
\n\n\n@article{frank_evolution_1990,\n\ttitle = {Evolution in a {Variable} {Environment}},\n\tvolume = {136},\n\tissn = {0003-0147},\n\turl = {https://www.journals.uchicago.edu/doi/abs/10.1086/285094},\n\tdoi = {10.1086/285094},\n\tabstract = {We develop a general model for the effects of variation in reproductive success on gene-frequency change and phenotypic evolution. Our approach is based on distinguishing among individual, genotypic, and population-level reproductive success and on relating these three levels through correlations. For example, the variance of genotypic reproductive success can be expressed by individual-level variance and by the correlations among individuals. We use these correlations to show the simple relationship among earlier models of selection on the variance of reproductive success, of temporal variation in selection, of spatial variation in selection, and of variation in behavioral traits. Our approach also applies to diploid individuals by regarding diploidy as a way to induce correlations in reproductive success between pairs of alleles. We apply our method to patterns of developmental homeostasis, the evolution of iteroparity, and the effects of variability in resource acquisition under nonlinear gains. Finally, we discuss the uses and limitations of the geometric-mean principle, and we provide a precise description and formal methods of analysis for bet hedging and risk aversion},\n\tnumber = {2},\n\turldate = {2023-03-14},\n\tjournal = {The American Naturalist},\n\tauthor = {Frank, Steven A. and Slatkin, Montgomery},\n\tmonth = aug,\n\tyear = {1990},\n\tnote = {Publisher: The University of Chicago Press},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {244--260},\n\tfile = {JSTOR Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\QQXHD2QL\\\\Frank and Slatkin - 1990 - Evolution in a Variable Environment.pdf:application/pdf},\n}\n\n\n\n We develop a general model for the effects of variation in reproductive success on gene-frequency change and phenotypic evolution. Our approach is based on distinguishing among individual, genotypic, and population-level reproductive success and on relating these three levels through correlations. For example, the variance of genotypic reproductive success can be expressed by individual-level variance and by the correlations among individuals. We use these correlations to show the simple relationship among earlier models of selection on the variance of reproductive success, of temporal variation in selection, of spatial variation in selection, and of variation in behavioral traits. Our approach also applies to diploid individuals by regarding diploidy as a way to induce correlations in reproductive success between pairs of alleles. We apply our method to patterns of developmental homeostasis, the evolution of iteroparity, and the effects of variability in resource acquisition under nonlinear gains. Finally, we discuss the uses and limitations of the geometric-mean principle, and we provide a precise description and formal methods of analysis for bet hedging and risk aversion\n
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\n\n \n \n 1984\n \n \n (2)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Piecewise-Deterministic Markov Processes: A General Class of Non-Diffusion Stochastic Models.\n \n \n \n \n\n\n \n Davis, M. H. A.\n\n\n \n\n\n\n Journal of the Royal Statistical Society. Series B (Methodological), 46(3): 353–388. 1984.\n Publisher: [Royal Statistical Society, Wiley]\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n
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Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n\n
\n\n\n@article{davis_piecewise-deterministic_1984,\n\ttitle = {Piecewise-{Deterministic} {Markov} {Processes}: {A} {General} {Class} of {Non}-{Diffusion} {Stochastic} {Models}},\n\tvolume = {46},\n\tissn = {0035-9246},\n\tshorttitle = {Piecewise-{Deterministic} {Markov} {Processes}},\n\turl = {https://www.jstor.org/stable/2345677},\n\tabstract = {A general class of non-diffusion stochastic model is introduced with a view to providing a framework for studying optimization problems arising in queueing systems, inventory theory, resource allocation and other areas. The corresponding stochastic processes are Markov processes consisting of a mixture of deterministic motion and random jumps. Stochastic calculus for these processes is developed and a complete characterization of the extended generator is given; this is the main technical result of the paper. The relevance of the extended generator concept in applied problems is discussed and some recent results on optimal control of piecewise-deterministic processes are described.},\n\tnumber = {3},\n\turldate = {2023-04-02},\n\tjournal = {Journal of the Royal Statistical Society. Series B (Methodological)},\n\tauthor = {Davis, M. H. A.},\n\tyear = {1984},\n\tnote = {Publisher: [Royal Statistical Society, Wiley]},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {353--388},\n\tfile = {JSTOR Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\QHKD4J7U\\\\Davis - 1984 - Piecewise-Deterministic Markov Processes A Genera.pdf:application/pdf},\n}\n\n\n\n A general class of non-diffusion stochastic model is introduced with a view to providing a framework for studying optimization problems arising in queueing systems, inventory theory, resource allocation and other areas. The corresponding stochastic processes are Markov processes consisting of a mixture of deterministic motion and random jumps. Stochastic calculus for these processes is developed and a complete characterization of the extended generator is given; this is the main technical result of the paper. The relevance of the extended generator concept in applied problems is discussed and some recent results on optimal control of piecewise-deterministic processes are described.\n
\n\n\n\n \n\n \n \n \n \n \n .\n \n \n \n\n\n \n Horsthemke, W.; and René, L.\n\n\n \n\n\n\n In Noise-induced transitions, pages 258–292. Springer, Berlin, Heidelberg, 1984.\n \n\n\n\n
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\n\n\n\n@incollection{horsthemke_lefever,\n\taddress = {Berlin, Heidelberg},\n\tbooktitle = {Noise-induced transitions},\n\tpublisher = {Springer},\n\tauthor = {Horsthemke, W. and René, Lefever},\n\tyear = {1984},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {258--292},\n}\n\n\n\n
\n\n \n \n 1981\n \n \n (1)\n \n \n
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\n \n \n\n \n \n \n \n \n Environmental Variability Promotes Coexistence in Lottery Competitive Systems.\n \n \n \n\n\n \n Chesson, P.; and Warner, R. R.\n\n\n \n\n\n\n The American Naturalist, 117(6): 923–943. June 1981.\n MAG ID: 1996991785\n\n\n\n
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\n\n\n@article{chesson_environmental_1981,\n\ttitle = {Environmental {Variability} {Promotes} {Coexistence} in {Lottery} {Competitive} {Systems}},\n\tvolume = {117},\n\tdoi = {10.1086/283778},\n\tabstract = {In deterministic approaches to modeling, two species are generally regarded as capable of coexistence if the model has a stable equilibrium with both species in positive numbers. Temporal environmental variability is assumed to reduce the likelihood of coexistence by keeping species abundances away from equilibrium. Here we present a contrasting view based on a model of competition for space among coral reef fishes, or any similarly territorial animals. The model has no stable equilibrium point with both species in positive abundance, yet both species persist in the system provided environmental variability in birth rates is sufficiently high. In general the higher the environmental variability the more likely it is that coexistence will occur. This conclusion is not affected by one species having a mean advantage over the other. Not all kinds of environmental variability necessarily lead to coexistence, however, for when the death rates of the two species are highly variable and negatively correlated, th...},\n\tnumber = {6},\n\tjournal = {The American Naturalist},\n\tauthor = {Chesson, Peter and Warner, Robert R.},\n\tmonth = jun,\n\tyear = {1981},\n\tdoi = {10.1086/283778},\n\tnote = {MAG ID: 1996991785},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {923--943},\n\tfile = {JSTOR Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\I862Q8X2\\\\Chesson and Warner - 1981 - Environmental Variability Promotes Coexistence in .pdf:application/pdf},\n}\n\n\n\n In deterministic approaches to modeling, two species are generally regarded as capable of coexistence if the model has a stable equilibrium with both species in positive numbers. Temporal environmental variability is assumed to reduce the likelihood of coexistence by keeping species abundances away from equilibrium. Here we present a contrasting view based on a model of competition for space among coral reef fishes, or any similarly territorial animals. The model has no stable equilibrium point with both species in positive abundance, yet both species persist in the system provided environmental variability in birth rates is sufficiently high. In general the higher the environmental variability the more likely it is that coexistence will occur. This conclusion is not affected by one species having a mean advantage over the other. Not all kinds of environmental variability necessarily lead to coexistence, however, for when the death rates of the two species are highly variable and negatively correlated, th...\n
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\n\n \n \n 1979\n \n \n (2)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Nest Guard Replacement in the Antarctic Fish Harpagifer bispinis: Possible Altruistic Behavior.\n \n \n \n \n\n\n \n Daniels, R. A.\n\n\n \n\n\n\n Science, 205(4408): 831–833. August 1979.\n Publisher: American Association for the Advancement of Science\n\n\n\n
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\n\n\n\n@article{daniels_nest_1979,\n\ttitle = {Nest {Guard} {Replacement} in the {Antarctic} {Fish} {Harpagifer} bispinis: {Possible} {Altruistic} {Behavior}},\n\tvolume = {205},\n\tshorttitle = {Nest {Guard} {Replacement} in the {Antarctic} {Fish} {Harpagifer} bispinis},\n\turl = {https://www.science.org/doi/10.1126/science.205.4408.831},\n\tdoi = {10.1126/science.205.4408.831},\n\tnumber = {4408},\n\turldate = {2022-06-29},\n\tjournal = {Science},\n\tauthor = {Daniels, Robert A.},\n\tmonth = aug,\n\tyear = {1979},\n\tnote = {Publisher: American Association for the Advancement of Science},\n\tkeywords = {unread, ⛔ No INSPIRE recid found},\n\tpages = {831--833},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\C26JQ2FT\\\\Daniels - 1979 - Nest Guard Replacement in the Antarctic Fish Harpa.pdf:application/pdf},\n}\n\n\n\n \n\n \n \n \n \n \n Theory of population genetics and evolutionary ecology: An introduction.\n \n \n \n\n\n \n Roughgarden, J.\n\n\n \n\n\n\n Macmillan, New York, USA, 1979.\n \n\n\n\n
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\n\n\n\n@book{Roughgarden,\n\ttitle = {Theory of population genetics and evolutionary ecology: {An} introduction},\n\tpublisher = {Macmillan, New York, USA},\n\tauthor = {Roughgarden, J.},\n\tyear = {1979},\n\tkeywords = {⛔ No INSPIRE recid found},\n}\n\n\n\n
\n\n \n \n 1978\n \n \n (1)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Diversity in Tropical Rain Forests and Coral Reefs.\n \n \n \n \n\n\n \n Connell, J. H.\n\n\n \n\n\n\n Science, 199(4335): 1302–1310. March 1978.\n Publisher: American Association for the Advancement of Science\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n
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Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n\n
\n\n\n@article{connell_diversity_1978,\n\ttitle = {Diversity in {Tropical} {Rain} {Forests} and {Coral} {Reefs}},\n\tvolume = {199},\n\turl = {https://www.science.org/doi/10.1126/science.199.4335.1302},\n\tdoi = {10.1126/science.199.4335.1302},\n\tabstract = {The commonly observed high diversity of trees in tropical rain forests and corals on tropical reefs is a nonequilibrium state which, if not disturbed further, will progress toward a low-diversity equilibrium community. This may not happen if gradual changes in climate favor different species. If equilibrium is reached, a lesser degree of diversity may be sustained by niche diversification or by a compensatory mortality that favors inferior competitors. However, tropical forests and reefs are subject to severe disturbances often enough that equilibrium may never be attained.},\n\tnumber = {4335},\n\turldate = {2023-03-07},\n\tjournal = {Science},\n\tauthor = {Connell, Joseph H.},\n\tmonth = mar,\n\tyear = {1978},\n\tnote = {Publisher: American Association for the Advancement of Science},\n\tkeywords = {unread, ⛔ No INSPIRE recid found},\n\tpages = {1302--1310},\n}\n\n\n\n The commonly observed high diversity of trees in tropical rain forests and corals on tropical reefs is a nonequilibrium state which, if not disturbed further, will progress toward a low-diversity equilibrium community. This may not happen if gradual changes in climate favor different species. If equilibrium is reached, a lesser degree of diversity may be sustained by niche diversification or by a compensatory mortality that favors inferior competitors. However, tropical forests and reefs are subject to severe disturbances often enough that equilibrium may never be attained.\n
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\n\n \n \n 1974\n \n \n (1)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Temporal fluctuations in selection intensities: Case of small population size.\n \n \n \n \n\n\n \n Karlin, S.; and Levikson, B.\n\n\n \n\n\n\n Theoretical Population Biology, 6(3): 383–412. December 1974.\n \n\n\n\n
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\n\n\n\n@article{karlin_temporal_1974,\n\ttitle = {Temporal fluctuations in selection intensities: {Case} of small population size},\n\tvolume = {6},\n\tissn = {0040-5809},\n\tshorttitle = {Temporal fluctuations in selection intensities},\n\turl = {https://www.sciencedirect.com/science/article/pii/0040580974900173},\n\tdoi = {10.1016/0040-5809(74)90017-3},\n\tlanguage = {en},\n\tnumber = {3},\n\turldate = {2023-05-03},\n\tjournal = {Theoretical Population Biology},\n\tauthor = {Karlin, Samuel and Levikson, Benny},\n\tmonth = dec,\n\tyear = {1974},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {383--412},\n\tfile = {ScienceDirect Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\3E8ILPQG\\\\Karlin and Levikson - 1974 - Temporal fluctuations in selection intensities Ca.pdf:application/pdf;ScienceDirect Snapshot:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\P35Q7SKA\\\\0040580974900173.html:text/html},\n}\n\n\n\n
\n\n \n \n 1973\n \n \n (2)\n \n \n
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\n \n \n\n \n \n \n \n \n \n Competitive Exclusion in Herbaceous Vegetation.\n \n \n \n \n\n\n \n Grime, J. P.\n\n\n \n\n\n\n Nature, 242(5396): 344–347. March 1973.\n Number: 5396 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n
\n\n\n@article{grime_competitive_1973,\n\ttitle = {Competitive {Exclusion} in {Herbaceous} {Vegetation}},\n\tvolume = {242},\n\tcopyright = {1973 Nature Publishing Group},\n\tissn = {1476-4687},\n\turl = {https://www.nature.com/articles/242344a0},\n\tdoi = {10.1038/242344a0},\n\tabstract = {IN maintaining or reconstructing types of herbaceous vegetation in which the density of flowering plants exceeds 20 species/m2—the so-called “species-rich” communities, success is often frustrated by competitive exclusion. Here I describe an attempt to identify criteria with which to assess or anticipate the effect of competitive exclusion both at individual sites and in different types of vegetation.},\n\tlanguage = {en},\n\tnumber = {5396},\n\turldate = {2023-03-07},\n\tjournal = {Nature},\n\tauthor = {Grime, J. P.},\n\tmonth = mar,\n\tyear = {1973},\n\tnote = {Number: 5396\nPublisher: Nature Publishing Group},\n\tkeywords = {unread, Humanities and Social Sciences, multidisciplinary, Science, ⛔ No INSPIRE recid found},\n\tpages = {344--347},\n}\n\n\n\n IN maintaining or reconstructing types of herbaceous vegetation in which the density of flowering plants exceeds 20 species/m2—the so-called “species-rich” communities, success is often frustrated by competitive exclusion. Here I describe an attempt to identify criteria with which to assess or anticipate the effect of competitive exclusion both at individual sites and in different types of vegetation.\n
\n\n\n\n \n\n \n \n \n \n \n Stability and complexity in model ecosystems.\n \n \n \n\n\n \n May, R. M.\n\n\n \n\n\n\n Princeton University Press, Princeton, NJ, USA, 1973.\n \n\n\n\n
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\n\n\n\n@book{May,\n\ttitle = {Stability and complexity in model ecosystems},\n\tpublisher = {Princeton University Press, Princeton, NJ, USA},\n\tauthor = {May, R. M.},\n\tyear = {1973},\n\tkeywords = {⛔ No INSPIRE recid found},\n}\n\n\n\n
\n\n\n\n\n \n \n 1969\n \n \n (1)\n \n \n
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\n \n \n\n \n \n \n \n \n \n On population growth in a randomly varying environment.\n \n \n \n \n\n\n \n Lewontin, R. C.; and Cohen, D.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences, 62(4): 1056–1060. April 1969.\n Publisher: Proceedings of the National Academy of Sciences\n\n\n\n
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Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n\n
\n\n\n@article{lewontin_population_1969,\n\ttitle = {On population growth in a randomly varying environment},\n\tvolume = {62},\n\turl = {https://www.pnas.org/doi/10.1073/pnas.62.4.1056},\n\tdoi = {10.1073/pnas.62.4.1056},\n\tabstract = {If a population is growing in a randomly varying environment, such that the finite rate of increase per generation is a random variable with no serial autocorrelation, the logarithm of population size at any time t is normally distributed. Even though the expectation of population size may grow infinitely large with time, the probability of extinction may approach unity, owing to the difference between the geometric and arithmetic mean growth rates.},\n\tnumber = {4},\n\turldate = {2023-03-14},\n\tjournal = {Proceedings of the National Academy of Sciences},\n\tauthor = {Lewontin, R. C. and Cohen, D.},\n\tmonth = apr,\n\tyear = {1969},\n\tnote = {Publisher: Proceedings of the National Academy of Sciences},\n\tkeywords = {⛔ No INSPIRE recid found},\n\tpages = {1056--1060},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\matth\\\\Zotero\\\\storage\\\\H7S6AKE8\\\\Lewontin and Cohen - 1969 - On population growth in a randomly varying environ.pdf:application/pdf},\n}\n\n\n\n If a population is growing in a randomly varying environment, such that the finite rate of increase per generation is a random variable with no serial autocorrelation, the logarithm of population size at any time t is normally distributed. Even though the expectation of population size may grow infinitely large with time, the probability of extinction may approach unity, owing to the difference between the geometric and arithmetic mean growth rates.\n
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