The recombination landscape of the Khoe-San likely represents the upper limits of recombination divergence in humans. van Eeden, G., Uren, C., Pless, E., Mastoras, M., van der Spuy, G. D., Tromp, G., Henn, B. M., & Möller, M. Genome Biology, 23(1):172, August, 2022. doi abstract bibtex BACKGROUND: Recombination maps are important resources for epidemiological and evolutionary analyses; however, there are currently no recombination maps representing any African population outside of those with West African ancestry. We infer the demographic history for the Nama, an indigenous Khoe-San population of southern Africa, and derive a novel, population-specific recombination map from the whole genome sequencing of 54 Nama individuals. We hypothesise that there are no publicly available recombination maps representative of the Nama, considering the deep population divergence and subsequent isolation of the Khoe-San from other African groups. RESULTS: We show that the recombination landscape of the Nama does not cluster with any continental groups with publicly available representative recombination maps. Finally, we use selection scans as an example of how fine-scale differences between the Nama recombination map and the combined Phase II HapMap recombination map can impact the outcome of selection scans. CONCLUSIONS: Fine-scale differences in recombination can meaningfully alter the results of a selection scan. The recombination map we infer likely represents an upper bound on the extent of divergence we expect to see for a recombination map in humans and would be of interest to any researcher that wants to test the sensitivity of population genetic or GWAS analysis to recombination map input.
@article{van_eeden_recombination_2022,
title = {The recombination landscape of the {Khoe}-{San} likely represents the upper limits of recombination divergence in humans},
volume = {23},
issn = {1474-760X},
doi = {10.1186/s13059-022-02744-5},
abstract = {BACKGROUND: Recombination maps are important resources for epidemiological and evolutionary analyses; however, there are currently no recombination maps representing any African population outside of those with West African ancestry. We infer the demographic history for the Nama, an indigenous Khoe-San population of southern Africa, and derive a novel, population-specific recombination map from the whole genome sequencing of 54 Nama individuals. We hypothesise that there are no publicly available recombination maps representative of the Nama, considering the deep population divergence and subsequent isolation of the Khoe-San from other African groups.
RESULTS: We show that the recombination landscape of the Nama does not cluster with any continental groups with publicly available representative recombination maps. Finally, we use selection scans as an example of how fine-scale differences between the Nama recombination map and the combined Phase II HapMap recombination map can impact the outcome of selection scans.
CONCLUSIONS: Fine-scale differences in recombination can meaningfully alter the results of a selection scan. The recombination map we infer likely represents an upper bound on the extent of divergence we expect to see for a recombination map in humans and would be of interest to any researcher that wants to test the sensitivity of population genetic or GWAS analysis to recombination map input.},
language = {eng},
number = {1},
journal = {Genome Biology},
author = {van Eeden, Gerald and Uren, Caitlin and Pless, Evlyn and Mastoras, Mira and van der Spuy, Gian D. and Tromp, Gerard and Henn, Brenna M. and Möller, Marlo},
month = aug,
year = {2022},
pmid = {35945619},
pmcid = {PMC9361568},
keywords = {Africa, Southern, Biological Evolution, Black People, Genetic map, Genetics, Population, Haplotypes, Humans, Khoe-San, Recombination map, Recombination rate, Selection scan},
pages = {172},
}
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We infer the demographic history for the Nama, an indigenous Khoe-San population of southern Africa, and derive a novel, population-specific recombination map from the whole genome sequencing of 54 Nama individuals. We hypothesise that there are no publicly available recombination maps representative of the Nama, considering the deep population divergence and subsequent isolation of the Khoe-San from other African groups. RESULTS: We show that the recombination landscape of the Nama does not cluster with any continental groups with publicly available representative recombination maps. Finally, we use selection scans as an example of how fine-scale differences between the Nama recombination map and the combined Phase II HapMap recombination map can impact the outcome of selection scans. CONCLUSIONS: Fine-scale differences in recombination can meaningfully alter the results of a selection scan. The recombination map we infer likely represents an upper bound on the extent of divergence we expect to see for a recombination map in humans and would be of interest to any researcher that wants to test the sensitivity of population genetic or GWAS analysis to recombination map input.","language":"eng","number":"1","journal":"Genome Biology","author":[{"propositions":["van"],"lastnames":["Eeden"],"firstnames":["Gerald"],"suffixes":[]},{"propositions":[],"lastnames":["Uren"],"firstnames":["Caitlin"],"suffixes":[]},{"propositions":[],"lastnames":["Pless"],"firstnames":["Evlyn"],"suffixes":[]},{"propositions":[],"lastnames":["Mastoras"],"firstnames":["Mira"],"suffixes":[]},{"propositions":["van","der"],"lastnames":["Spuy"],"firstnames":["Gian","D."],"suffixes":[]},{"propositions":[],"lastnames":["Tromp"],"firstnames":["Gerard"],"suffixes":[]},{"propositions":[],"lastnames":["Henn"],"firstnames":["Brenna","M."],"suffixes":[]},{"propositions":[],"lastnames":["Möller"],"firstnames":["Marlo"],"suffixes":[]}],"month":"August","year":"2022","pmid":"35945619","pmcid":"PMC9361568","keywords":"Africa, Southern, Biological Evolution, Black People, Genetic map, Genetics, Population, Haplotypes, Humans, Khoe-San, Recombination map, Recombination rate, Selection scan","pages":"172","bibtex":"@article{van_eeden_recombination_2022,\n\ttitle = {The recombination landscape of the {Khoe}-{San} likely represents the upper limits of recombination divergence in humans},\n\tvolume = {23},\n\tissn = {1474-760X},\n\tdoi = {10.1186/s13059-022-02744-5},\n\tabstract = {BACKGROUND: Recombination maps are important resources for epidemiological and evolutionary analyses; however, there are currently no recombination maps representing any African population outside of those with West African ancestry. We infer the demographic history for the Nama, an indigenous Khoe-San population of southern Africa, and derive a novel, population-specific recombination map from the whole genome sequencing of 54 Nama individuals. We hypothesise that there are no publicly available recombination maps representative of the Nama, considering the deep population divergence and subsequent isolation of the Khoe-San from other African groups.\nRESULTS: We show that the recombination landscape of the Nama does not cluster with any continental groups with publicly available representative recombination maps. Finally, we use selection scans as an example of how fine-scale differences between the Nama recombination map and the combined Phase II HapMap recombination map can impact the outcome of selection scans.\nCONCLUSIONS: Fine-scale differences in recombination can meaningfully alter the results of a selection scan. 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