The Genomic Signature of Population Reconnection Following Isolation: From Theory to HIV.

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Version: Final published version
Serval ID
serval:BIB_E3CDFF1685AC
Type
Article: article from journal or magazin.
Collection
Publications
Title
The Genomic Signature of Population Reconnection Following Isolation: From Theory to HIV.
Journal
G3 (bethesda, Md.)
Author(s)
Alcala N., Jensen J.D., Telenti A., Vuilleumier S.
ISSN
2160-1836 (Electronic)
ISSN-L
2160-1836
Publication state
Published
Issued date
2015
Volume
6
Number
1
Pages
107-120
Language
english
Notes
Publication types: Journal Article
Publication Status: epublish
Abstract
Ease of worldwide travel provides increased opportunities for organisms not only to colonize new environments but also to encounter related but diverged populations. Such events of reconnection and secondary contact of previously isolated populations are widely observed at different time scales. For example, during the quaternary glaciation, sea water level fluctuations caused temporal isolation of populations, often to be followed by secondary contact. At shorter time scales, population isolation and reconnection of viruses are commonly observed, and such events are often associated with epidemics and pandemics. Here, using coalescent theory and simulations, we describe the temporal impact of population reconnection after isolation on nucleotide differences and the site frequency spectrum, as well as common summary statistics of DNA variation. We identify robust genomic signatures of population reconnection after isolation. We utilize our development to infer the recent evolutionary history of human immunodeficiency virus 1 (HIV-1) in Asia and South America, successfully retrieving the successive HIV subtype colonization events in these regions. Our analysis reveals that divergent HIV-1 subtype populations are currently admixing in these regions, suggesting that HIV-1 may be undergoing a process of homogenization, contrary to popular belief.
Keywords
Evolution, Molecular, Genetic Variation, Genetics, Population, Genome, Viral, Genomics/methods, Genotype, HIV Infections/virology, HIV-1/genetics, Humans, Models, Theoretical, Reassortant Viruses, Recombination, Genetic
Pubmed
Web of science
Open Access
Yes
Create date
28/01/2016 15:37
Last modification date
20/08/2019 17:07
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