1. Ancient hybridization and strong adaptation to viruses across African vervet monkey populations.
- Author
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Svardal H, Jasinska AJ, Apetrei C, Coppola G, Huang Y, Schmitt CA, Jacquelin B, Ramensky V, Müller-Trutwin M, Antonio M, Weinstock G, Grobler JP, Dewar K, Wilson RK, Turner TR, Warren WC, Freimer NB, and Nordborg M
- Subjects
- Africa, Animals, CD4-Positive T-Lymphocytes metabolism, CD4-Positive T-Lymphocytes virology, Chlorocebus aethiops blood, Chlorocebus aethiops classification, Chlorocebus aethiops genetics, Gene Expression Profiling, Gene Ontology, Gene Regulatory Networks, Genetic Variation, Host-Pathogen Interactions, Hybridization, Genetic, Macaca mulatta blood, Macaca mulatta genetics, Macaca mulatta virology, Phylogeny, Simian Acquired Immunodeficiency Syndrome genetics, Simian Immunodeficiency Virus classification, Simian Immunodeficiency Virus genetics, Species Specificity, Adaptation, Physiological genetics, Chlorocebus aethiops virology, Simian Acquired Immunodeficiency Syndrome virology, Simian Immunodeficiency Virus physiology
- Abstract
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.
- Published
- 2017
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