Selective sweep in the Flotillin-2 region of European Drosophila melanogaster

Abstract

Localizing genes that are subject to recent positive selection is a major goal of evolutionary biology. In the model organism Drosophila melanogaster many attempts have been made in recent years to identify such genes by conducting so-called genome scans of selection. These analyses consisted in typing a large number of genetic markers along the genomes of a sample of individuals and then identifying those loci that harbor patterns of genetic variation, which are compatible with the ones generated by a selective sweep. In this study we conduct an in-depth analysis of a genomic region located on the X chromosome of D. melanogaster that was identified as a potential target of recent positive selection by a previous genome scan of selection. To this end we re-sequenced 20 kilobases around the Flotillin-2 gene (Flo-2) and conducted a detailed analysis of the allele frequencies and linkage disequilibria observed in this new dataset. The results of this analysis reveal eight genetic novelties that are specific to temperate populations of D. melanogaster and that may have arisen during the expansion of the species outside its ancestral sub-Saharan habitat since about 16,000 years ago.

Figure 1. Nucleotide variation of the Flo-2 region in an African and European sample of D. melanogaster.

A) The valley of reduced genetic variation in a European sample of D. melanogaster compared to an ancestral population sample from Africa (solid lines; first y-axis, θ_W). The fully sequenced 20,011-bp fragment of the Flo-2 region is connected with an adjacent fragment of Ometto et al. , indicated by squares at coordinate 0 (white square-Africa; black square-Europe, distance to the fully sequenced Flo-2 region around 3,000 bp, θ_W values were interpolated between the two fragments). The x-axis shows the relative position on the X-chromosome. The dashed horizontal lines show the average nucleotide variation of the X-chromosome for the African population sample (wide dashed line, θ_AX = 0.0131) and the European population sample (dashed line, θ_EX = 0.0047). Black triangles show the position of indels; black diamonds indicate fixed nucleotide differences between both samples. The second y-axis corresponds to divergence of D. melanogaster to D. sechellia (dashed line). The gene map gives the name and the position of the coding sequence of all genes located within the valley of reduced variation. These genes are Eo, CG9503 CG32591, pdgy (partly) and eight different transcripts of Flo-2. B) Tajima’s D statistic (solid lines) is shown for the African and European sample of D. melanogaster (white square-Africa; black square-Europe). The horizontal lines show the average value of Tajima’s D for the X chromosome of the African population sample (wide dashed line, D _XA = −0.608) and the European population sample (dashed line, D _XE = −0.103). Significance values are indicated as follows: # P<0.10; *P<0.05; **P<0.01.

Figure 2. The sweep analysis reveals two profiles: the solid line shows the CLR of SweepFinder, the dashed line shows the result of the ω statistic.

The horizontal lines give the 5% significance threshold for the CLR test (solid line, TH_CLR = 32.3) and the ω statistic (dashed line, TH_ω = 65.2).