Data from: Population genomic analysis uncovers African and European admixture in Drosophila melanogaster populations from the southeastern United States and Caribbean Islands

Drosophila melanogaster is postulated to have colonized North America in the past several 100 years in two waves. Flies from Europe colonized the east coast United States while flies from Africa inhabited the Caribbean, which if true, make the south-east US and Caribbean Islands a secondary contact zone for African and European D. melanogaster. This scenario has been proposed based on phenotypes and limited genetic data. In our study, we have sequenced individual whole genomes of flies from populations in the south-east US and Caribbean Islands and examined these populations in conjunction with population sequences from the west coast US, Africa, and Europe. We find that west coast US populations are closely related to the European population, likely reflecting a rapid westward expansion upon first settlements into North America. We also find genomic evidence of African and European admixture in south-east US and Caribbean populations, with a clinal pattern of decreasing proportions of African ancestry with higher latitude. Our genomic analysis of D. melanogaster populations from the south-east US and Caribbean Islands provides more evidence for the Caribbean Islands as the source of previously reported novel African alleles found in other east coast US populations. We also find the border between the south-east US and the Caribbean island to be the admixture hot zone where distinctly African-like Caribbean flies become genomically more similar to European-like south-east US flies. Our findings have important implications for previous studies examining the generation of east coast US clines via selection.黑腹果蝇（Drosophila melanogaster）被推测在过去数百年间通过两次定殖浪潮入侵北美。来自欧洲的果蝇定殖了美国东海岸，而来自非洲的果蝇则定殖于加勒比地区；若该假说成立，则美国东南部与加勒比群岛将成为非洲与欧洲黑腹果蝇的次级接触带。该情景最初基于表型数据与有限的遗传数据被提出。 本研究对美国东南部及加勒比群岛的果蝇群体开展了个体全基因组测序，并结合美国西海岸、非洲及欧洲的群体基因组序列对上述群体进行联合分析。研究发现，美国西海岸群体与欧洲群体亲缘关系紧密，这大概率反映了其首次定殖北美后快速向西扩张的过程。同时，我们在美东南部与加勒比群体中检测到非洲与欧洲血统的遗传混合信号，且呈现出随纬度升高非洲血统占比逐渐降低的渐变群模式。 我们针对美国东南部及加勒比群岛黑腹果蝇群体的基因组分析，为“加勒比群岛是此前报道的美国东海岸群体中发现的新型非洲等位基因的来源”这一结论提供了更多实证支持。此外，我们发现美国东南部与加勒比群岛的交界区域为混合热点区，在此处原本具有典型非洲血统特征的加勒比果蝇，在基因组层面逐渐与具有欧洲血统特征的美国东南部果蝇趋于相似。 本研究结果对此前通过选择作用解析美国东海岸群体渐变群特征的相关研究具有重要的启示意义。