title: The Genomic Signature of Population Reconnection Following Isolation: From Theory to HIV.
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.
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Lausanne CH-1015, Switzerland Department of Biology, Stanford University, Stanford, California 94305-5020 nalcala@stanford.edu.
authors.forename: Nicolas
authors.identifier: http://orcid.org/0000-0002-5961-5064
authors.initials: N
authors.lastname: Alcala
authors.affiliation: School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland.
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Jensen
authors.affiliation: Genomic Medicine, The J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037.
authors.forename: Amalio
authors.initials: A
authors.lastname: Telenti
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Lausanne CH-1015, Switzerland School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland Institute of Microbiology, University Hospital and University of Lausanne, Lausanne CH-1011, Switzerland.
authors.forename: Séverine
authors.initials: S
authors.lastname: Vuilleumier
mesh_terms: D019143:Evolution, Molecular; D014644:Genetic Variation; D005828:Genetics, Population; D016679:Genome, Viral; D023281:Genomics / Q000379:methods; D005838:Genotype; D015658:HIV Infections / Q000821:virology; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008962:Models, Theoretical; D016865:Reassortant Viruses; D011995:Recombination, Genetic
keywords: HIV; admixture; coalescent; migration; site frequency spectrum