Population genomic analysis uncovers African and European admixture inDrosophila melanogasterpopulations from the southeastern United States and Caribbean Islands

Abstract

Genome sequences from North American Drosophila melanogaster populations have become available to the scientific community. Deciphering the underlying population structure of these resources is crucial to make the most of these population genomic resources. Accepted models of North American colonization generally purport that several hundred years ago, flies from Africa and Europe were transported to the east coast United States and the Caribbean Islands respectively and thus current east coast US and Caribbean populations are an admixture of African and European ancestry. Theses models have been constructed 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 Winters, CA, (USA); Raleigh, NC (USA); Cameroon (Africa); and Montpellier (France) to uncover the underlying population structure of North American populations. We find that west coast US populations are most like European populations likely reflecting a rapid westward expansion upon first settlements into North America. We also find genomic evidence of African and European admixture in east coast US and Caribbean populations, with a clinal pattern of decreasing proportions of African ancestry with higher latitude further supporting the proposed demographic model of Caribbean flies being established by African ancestors. Our genomic analysis of Caribbean flies is the first study that exposes the source of previously reported novel African alleles found in east coast US populations.

A Thousand Fly Genomes: An ExpandedDrosophilaGenome Nexus

“…As previously indicated, genomic diversity is highest in Zambia and other southern African populations Lack et al 2015), and all sub-Saharan populations are more diverse than all others. Because North American populations have mainly European but partly African ancestry (Kao et al 2015;Pool 2015;Bergland et al 2016), they show somewhat higher diversity than European populations. Geographic structure is apparent, especially between sub-Saharan populations and all others, with the latter group showing a common reduced gene pool apparently resulting from a population bottleneck.…”

“…Campo et al (2013) studied 35 genomes from a California population. Kao et al (2015) added 23 genomes originating from 12 New World locations.…”

Comparative population genomics of latitudinal variation in Drosophila simulans and Drosophila melanogaster

“…; Kao et al . ). Although the D. melanogaster latitudinal clines are robust and some do seem to result from local adaptation, demography complicates the inference of selection.…”

Adaptive patterns of phenotypic plasticity in laboratory and field environments in Drosophila melanogaster

“…The presumed absence of population structure in D. melanogaster suggests that these clines are driven by natural selection and local adaptation; however, latitudinal clines may also be generated by demography and secondary contact (Kao et al. ; Bergland et al. ).…”