Academic journal article Genetics

Elevated Linkage Disequilibrium and Signatures of Soft Sweeps Are Common in Drosophila Melanogaster

Academic journal article Genetics

Elevated Linkage Disequilibrium and Signatures of Soft Sweeps Are Common in Drosophila Melanogaster

Article excerpt

DISENTANGLING the effects of demography and selection on patterns of genomic variation remains a central challenge in evolutionary biology. Until recently, inference of demography and selection primarily relied on short genomic fragments sampled from a limited number of individuals (e.g., Pritchard et al. 2000; Molina et al. 2001; Li and Stephan 2006; Thornton and Andolfatto 2006; Gutenkunst et al. 2009; Duchen et al. 2013). While these studies provided important insights into the evolutionary forces acting on populations, they were ultimately limited by both sample size and the physical scale in which patterns of polymorphism and linkage could be investigated. The recent availability of wholegenome sequences from multiple individuals with populations in a variety of species (e.g., Abecasis et al. 2010; Cao et al. 2011; Mackay et al. 2012) is enabling us to examine long-range patterns of linkage disequilibrium (LD) (^10 kb), measured either as correlations between pairs of sites or as haplotype homozygosity. LD offers powerful insights into selective and demographic processes shaping genetic variation in a natural population, such as bottleneck or admixture events (Andolfatto and Przeworski 2000; Wall and Pritchard 2003; Pennings and Hermisson 2006; Pokalyuk 2012). In addition, haplotype homozygosity is very sensitive to recent and strong adaptation leading to both classical hard and soft selective sweeps (Pennings and Hermisson 2006; Garud et al. 2015; Garud and Rosenberg 2015).

In the case of Drosophila melanogaster, the most recent demographic models were inferred using short intergenic and intronic sequence fragments on the X chromosome of lengths no longer than a few hundred base pairs in tens of individuals (Duchen et al. 2013). Because the data were so sparse, models assuming independence between polymorphic sites were fit to statistics sensitive to the site frequency spectrum (SFS) and to short-scale LD measuring the correlation between polymorphic sites separated by short distances (Duchen et al. 2013).

The availability of the Drosophila Genetic Reference Panel (DGRP) (version 1), consisting of 168 fully-sequenced D. melanogaster strains from a single population in Raleigh, North Carolina (Mackay et al. 2012), offered the opportunity to study genome-wide signatures of demography and selection in a deep sample. Recently, we analyzed patterns of LD and haplotype homozygosity at distances of ^10 kb in the DGRP data set (Garud et al. 2015) and compared these patterns with neutral expectations generated under several demographic models of North American D. melanogaster, including two constant Ne models, two bottleneck models, and two recently inferred admixture models (Duchen et al. 2013), one of which is considered to be the most accurate model of the admixture between the European and African flies founding North American D. melanogaster. We found that LD and haplotype homozygosity in the DGRP data are elevated relative to expectations under any of the demographic models tested and that this elevation remained even after controlling for several potential sources of elevated LD, including close relatedness between individuals, presence of genomic inversions, recombination rate variation, and population substructure.

Inaddition, we identifiedregions in the DGRP data withthe elevated haplotype homozygosity, measured using statistic H12, designed to detect both hard and soft sweeps (Garud et al. 2015). H12 calculates haplotype homozygosity after combining the frequencies of the first- and second-most common haplotypes in order to increase the power to detect soft sweeps. Among the three highest-ranking candidates in the H12 scan were the prominent known cases of soft sweeps at the loci Ace, Cyp6g1, and CHKov1 (Karasov et al. 2010; Schmidt et al. 2010; Magwire et al. 2011). All 50 outlier H12 peaks in the DGRP data showed signatures of partial soft sweeps, suggesting that soft sweeps were common in the DGRP data (but see Schrider et al. …

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