Ancient hybridization and strong adaptation to viruses across African vervet monkey populations

Analysis of whole-genome sequencing data from 163 vervet monkeys from Africa and the Caribbean shows high diversity among taxa and identifies signatures of selection. Selection signals affect viral processes, and genes that show response to SIV in vervets but not macaques have elevated selection sco...

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Bibliographic Details
Published in:	Nature genetics Vol. 49; no. 12; pp. 1705 - 1713
Main Authors:	Svardal, Hannes, Jasinska, Anna J, Apetrei, Cristian, Coppola, Giovanni, Huang, Yu, Schmitt, Christopher A, Jacquelin, Beatrice, Ramensky, Vasily, Müller-Trutwin, Michaela, Antonio, Martin, Weinstock, George, Grobler, J Paul, Dewar, Ken, Wilson, Richard K, Turner, Trudy R, Warren, Wesley C, Freimer, Nelson B, Nordborg, Magnus
Format:	Journal Article
Language:	English
Published:	New York Nature Publishing Group US 01.12.2017 Nature Publishing Group
Subjects:	38 45 45/23 631/208/457 631/250/255/1901 Acquired immune deficiency syndrome Adaptation Adaptation, Physiological - genetics Africa Agriculture AIDS Animal Genetics and Genomics Animals Bioinformatics Biomedicine Cancer Research CD4-Positive T-Lymphocytes - metabolism CD4-Positive T-Lymphocytes - virology Chlorocebus Chlorocebus aethiops Chlorocebus aethiops - blood Chlorocebus aethiops - classification Chlorocebus aethiops - genetics Chlorocebus aethiops - virology Disease susceptibility Divergence Gene Expression Profiling Gene Function Gene Ontology Gene Regulatory Networks Gene sequencing Genes Genetic aspects Genetic Variation Genomes Genomics Health aspects HIV Host-Pathogen Interactions Human Genetics Human immunodeficiency virus Hybridization Hybridization, Genetic Infections Macaca mulatta - blood Macaca mulatta - genetics Macaca mulatta - virology Mitochondrial DNA Monkeys Monkeys & apes Morphology Phylogeny Primates Simian Acquired Immunodeficiency Syndrome - genetics Simian Acquired Immunodeficiency Syndrome - virology Simian immunodeficiency virus Simian Immunodeficiency Virus - classification Simian Immunodeficiency Virus - genetics Simian Immunodeficiency Virus - physiology Species Specificity Taxa Taxonomy Vaccines Vervet monkey Viruses Africa
ISSN:	1061-4036, 1546-1718, 1546-1718
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Summary:	Analysis of whole-genome sequencing data from 163 vervet monkeys from Africa and the Caribbean shows high diversity among taxa and identifies signatures of selection. Selection signals affect viral processes, and genes that show response to SIV in vervets but not macaques have elevated selection scores. Vervet monkeys are among the most widely distributed nonhuman primates, show considerable phenotypic diversity, and have long been an important biomedical model for a variety of human diseases and in vaccine research. Using whole-genome sequencing data from 163 vervets sampled from across Africa and the Caribbean, we find high diversity within and between taxa and clear evidence that taxonomic divergence was reticulate rather than following a simple branching pattern. A scan for diversifying selection across taxa identifies strong and highly polygenic selection signals affecting viral processes. Furthermore, selection scores are elevated in genes whose human orthologs interact with HIV and in genes that show a response to experimental simian immunodeficiency virus (SIV) infection in vervet monkeys but not in rhesus macaques, suggesting that part of the signal reflects taxon-specific adaptation to SIV.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Present address: Wellcome Trust Sanger Institute, Cambridge, UK Present address: Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
ISSN:	1061-4036 1546-1718 1546-1718
DOI:	10.1038/ng.3980