Alcala Nicolas, Jensen Jeffrey D, Telenti Amalio, Vuilleumier Séverine
Department of Ecology and Evolution, University of Lausanne, Lausanne CH-1015, Switzerland Department of Biology, Stanford University, Stanford, California 94305-5020
School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland.
G3 (Bethesda). 2015 Nov 6;6(1):107-20. doi: 10.1534/g3.115.024208.
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.
全球旅行的便利性不仅为生物体提供了更多在新环境中定殖的机会，也使其有更多机会接触到相关但有差异的种群。在不同的时间尺度上，广泛观察到先前隔离的种群重新连接和二次接触的此类事件。例如，在第四纪冰川期，海平面波动导致种群的暂时隔离，随后往往是二次接触。在较短的时间尺度上，病毒的种群隔离和重新连接很常见，而且此类事件通常与流行病和大流行有关。在这里，我们使用溯祖理论和模拟，描述了隔离后种群重新连接对核苷酸差异、位点频率谱以及DNA变异的常见汇总统计量的时间影响。我们确定了隔离后种群重新连接的稳健基因组特征。我们利用我们的研究成果推断亚洲和南美洲人类免疫缺陷病毒1型（HIV-1）的近期进化历史，成功检索到这些地区连续的HIV亚型定殖事件。我们的分析表明，不同的HIV-1亚型种群目前正在这些地区混合，这表明HIV-1可能正在经历同质化过程，这与普遍看法相反。
