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Nat Genet. 2017 Dec;49(12):1705-1713. doi: 10.1038/ng.3980. Epub 2017 Oct 30.

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

Author information

1
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
2
Center for Neurobehavioral Genetics, University of California, Los Angeles, Los Angeles, California, USA.
3
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
4
Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
5
Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
6
Department of Neurology, University of California, Los Angeles, Los Angeles, California, USA.
7
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
8
Department of Anthropology, Boston University, Boston, Massachusetts, USA.
9
Institut Pasteur, Unité HIPER, Paris, France.
10
Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation.
11
Medical Research Council (MRC), The Gambia Unit, The Gambia.
12
Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.
13
Department of Genetics, University of the Free State, Bloemfontein, South Africa.
14
Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
15
Department of Anthropology, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA.
16
McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, USA.

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.

PMID:
29083404
PMCID:
PMC5709169
DOI:
10.1038/ng.3980
[Indexed for MEDLINE]
Free PMC Article

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