Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana

Abstract

Although it is well understood that selection shapes the polymorphism pattern in Drosophila, signatures of classic selective sweeps are scarce. Here, we focus on Drosophila mauritiana, an island endemic, which is closely related to Drosophila melanogaster. Based on a new, annotated genome sequence, we characterized the genome-wide polymorphism by sequencing pooled individuals (Pool-seq). We show that the interplay between selection and recombination results in a genome-wide polymorphism pattern characteristic for D. mauritiana. Two large genomic regions (>500 kb) showed the signature of almost complete selective sweeps. We propose that the absence of population structure and limited geographic distribution could explain why such pronounced sweep patterns are restricted to D. mauritiana. Further evidence for strong adaptive evolution was detected for several nucleoporin genes, some of which were not previously identified as genes involved in genomic conflict. Since this adaptive evolution is continuing after the split of D. mauritiana and Drosophila simulans, we conclude that genomic conflict is not restricted to short episodes, but rather an ongoing process in Drosophila.

Rapid evolutionary turnover underlies conserved lncRNA–genome interactions

“…All genome builds were obtained from FlyBase (http://www .flybase.org) with the following exceptions: Drosophila americana (genome assembly downloaded from the Jorge Vieira laboratory Web site, http://evolution.ibmc.up.pt), Drosophila suzukii (Spotted Wing FlyBase; Chiu et al 2013), and Drosophila mauritiana (Nolte et al 2013). For D. busckii, we downloaded the raw WGS reads from the NCBI Short Read Archive (SRP021047).…”

Genetics on the Fly: A Primer on theDrosophilaModel System

“…One goal of the modENCODE project has been to sequence the genomes of eight additional species with next-generation technology (Celniker et al 2009). Several more Drosophila species genomes are available through the efforts of individual labs (e.g., Garrigan et al 2012;Zhou and Bachtrog 2012;Nolte et al 2013;Guillen et al 2014) ( Figure 3B). The large number of sequenced Drosophila genomes provides an important resource for comparative genomics and offers a powerful approach to the discovery of functional elements in genomes and their evolution (Singh et al 2009), and ecological genomics (Markow 2015).…”

“…Owing to the abundance of new genetic and molecular tools, the field of speciation genetics is growing (reviewed in Presgraves 2010). Population genomic resources now exist for several species closely related to D. melanogaster, including D. simulans (Rogers et al 2014), D. mauritiana (Nolte et al 2013;Garrigan et al 2015), and D. yakuba (Rogers et al 2014) with several additional datasets on the way (http:// www.dpgp.org/1K_300genomes.html). Population-level data on transcriptomes (RNA sequence datasets) are also available for studying gene regulatory evolution and de novo genes (Zhao et al 2014).…”

Conflict on the Sex Chromosomes: Cause, Effect, and Complexity

“…Evidence consistent with this scenario is that sex ratio distorters may be responsible for very rapid selective sweeps (e.g., Nolte et al 2013). Spread of segregation distorters may also result in the hitchhiking of tightly linked genes that can potentially have dramatic fitness consequences.…”