History and Structure of Sub-Saharan Populations ofDrosophila melanogaster

Abstract

Drosophila melanogaster is an important model organism in evolutionary genetics, yet little is known about the population structure and the demographic history of this species within sub-Saharan Africa, which is thought to contain its ancestral range. We surveyed nucleotide variation at four 1-kb fragments in 240 individual lines representing 21 sub-Saharan and 4 Palearctic population samples of D. melanogaster. In agreement with recent studies, we find a small but significant level of genetic differentiation within subSaharan Africa. A clear geographic pattern is observed, with eastern and western African populations composing two genetically distinct groups. This pattern may have resulted from a relatively recent establishment of D. melanogaster in western Africa. Eastern populations show greater evidence for longterm stability, consistent with the hypothesis that eastern Africa contains the ancestral range of the species. Three sub-Saharan populations show evidence for cosmopolitan introgression. Apart from those cases, the closest relationships between Palearctic and sub-Saharan populations involve a sample from the rift zone (Uganda), suggesting that the progenitors of Palearctic D. melanogaster might have come from this region. Finally, we find a large excess of singleton polymorphisms in the full data set, which is best explained by a combination of population growth and purifying selection.

Surprising Differences in the Variability of Y Chromosomes in African and Cosmopolitan Populations ofDrosophila melanogaster

“…Moreover, Pennsylvania and Tasmania Y chromosomes are nearly indistinguishable ( Figure 2 and Table 2). Consistent with several surveys of population differentiation showing considerable population structure in Asia (Hale and Singh 1991;Baudry et al 2004;Pool and Aquadro 2006;Schlötterer et al 2006), the Beijing Y chromosome is highly differentiated from the rest of the populations. There is no evidence of substructuring within the Beijing population on the Y chromosome ( Figure 2B).…”

“…There is no evidence of substructuring within the Beijing population on the Y chromosome ( Figure 2B). Outside of the clustering of Zimbabwe and Netherlands Y chromosomes, these results are consistent with the population structure of autosomal, X chromosomal, and mitochondrial loci from these or similar populations (Hale and Singh 1991;Baudry et al 2004;Haddrill et al 2005;Pool and Aquadro 2006;Schlötterer et al 2006). Genomic sequences from non-Y-linked loci exclude the possibility that the similarity of Netherlands and Zimbabwe Y chromosomes are explained by contamination in our fly lines (A.G. Clark, unpublished results).…”

“…We used the average u X estimated from Haddrill et al (2005) for the following populations: Zimbabwe (0.01327); Netherlands (0.00414); and Pennsylvania (0.00557). For Uganda and Beijing, we used estimates of u X from Pool and Aquadro (2006), 0.012 and 0.0036, respectively (Table S1). Because comparable X-linked data (PCR resequence data from noncoding X-linked loci) are not currently available for Tasmania, we assumed a uniform range of u X values that encompass the Cosmopolitan samples that we have considered [u X U(0.0020-0.0045)].…”

“…Briefly, Pool and Aquadro (2006) surveyed 10 lines of flies from a China and Uganda population at 4 noncoding X-linked loci at least 10 kb from coding loci in regions of high recombination (Table S1). Haddrill et al (2005) surveyed the introns of 10 X-linked genes across regions of the X chromosome with high recombination in Zimbabwe, Netherlands, and Pennsylvania populations (Table S1).…”

“…Moreover, Pool and Aquadro (2006) hypothesized that the ancestral source population for the Out-of-Africa migration to Europe was similar to a Uganda population based on X-linked variation data.…”