Selective Sweep in the Flotillin-2 Region of European Drosophila melanogaster

Annegret Werzner,Wolfgang Stephan,Stefan Laurent,Pavlos Pavlidis,Lino Ometto

doi:10.1371/journal.pone.0056629

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.

Highlights

Localizing genes that are subject to recent positive selection is a major goal of evolutionary biology
In the European sample the mean value of nucleotide variation in the Flotillin-2 gene (Flo-2) region is hE = 0.0024, which is significantly lower than the observed value for the entire X chromosome in European D. melanogaster
The corresponding genetic region in the African sample has a nucleotide diversity of hA = 0.0141, which matches the mean value of the entire X chromosome

Summary

Introduction

Localizing genes that are subject to recent positive selection is a major goal of evolutionary biology. Recent methodological and theoretical advances are facilitating their identification by allowing the shift from candidate-locus approaches to genome-wide analyses. The fixation of the beneficial mutation can have a joint effect on linked neutral sites, which are expected to increase in frequency This process, known as genetic hitchhiking [1], generates a signal of i) reduced genetic variation at the target of selection [2,3], ii) a skewed site frequency spectrum (SFS) due to an excess of rare and high-frequency derived alleles [4,5,6], and iii) increased linkage disequilibrium (LD) on both sides of the target of selection but reduced LD between them [7,8,9]

Methods

Results

Conclusion