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

Drosophila melanogaster is postulated to have colonized North America in the past several hundred 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 southeast 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 southeast 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 southeast 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 southeast 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 southeast US and the Caribbean island to be the admixture hot zone where distinctly African-like Caribbean flies become genomically more similar to European-like southeast 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）据推测在过去数百年间以两次浪潮的形式定居北美。源自欧洲的果蝇殖民了美国东海岸，而来自非洲的果蝇则栖息于加勒比地区；若该推论成立，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生接触带。该假说最初基于表型数据与有限的遗传资料提出。本研究对美国东南部及加勒比群岛种群的果蝇个体开展了全基因组测序，并结合美国西海岸、非洲与欧洲的种群基因组序列展开综合分析。研究发现，美国西海岸种群与欧洲种群亲缘关系紧密，这大概率反映了其首次定居北美后快速向西扩张的过程。我们还在美国东南部与加勒比种群的基因组中检测到非洲与欧洲血统的混合迹象，且呈现出随纬度升高非洲血统占比逐渐降低的渐变模式。对美国东南部及加勒比群岛黑腹果蝇种群的基因组分析，为“加勒比群岛是此前报道的美国东海岸其他种群中新型非洲等位基因的来源”这一观点提供了更多实证支持。我们还发现，美国东南部与加勒比群岛的交界地带属于基因混合热点区域：原本典型的类加勒比非洲果蝇，其基因组特征逐渐向类美国东南部欧洲果蝇靠拢。本研究结果对此前通过选择作用探究美国东海岸渐变格局形成机制的相关研究具有重要启示意义。