RT Journal Article SR Electronic T1 Rate and cost of adaptation in the Drosophila genome JF bioRxiv FD Cold Spring Harbor Laboratory SP 008680 DO 10.1101/008680 A1 Stephan Schiffels A1 Michael Lässig A1 Ville Mustonen YR 2014 UL http://biorxiv.org/content/early/2014/09/02/008680.abstract AB Recent studies have consistently inferred high rates of adaptive molecular evolution between Drosophila species. At the same time, the Drosophila genome evolves under different rates of recombination, which results in partial genetic linkage between alleles at neighboring genomic loci. Here we analyze how linkage correlations affect adaptive evolution. We develop a new inference method for adaptation that takes into account the effect on an allele at a focal site caused by neighboring deleterious alleles (background selection) and by neighboring adaptive substitutions (hitchhiking). Using complete genome sequence data and fine-scale recombination maps, we infer a highly heterogeneous scenario of adaptation in Drosophila. In high-recombining regions, about 50% of all amino acid substitutions are adaptive, together with about 20% of all substitutions in proximal intergenic regions. In low-recombining regions, only a small fraction of the amino acid substitutions are adaptive, while hitchhiking accounts for the majority of these changes. Hitchhiking of deleterious alleles generates a substantial collateral cost of adaptation, leading to a fitness decline of about 30/2N per gene and per million years in the lowest-recombining regions. Our results show how recombination shapes rate and efficacy of the adaptive dynamics in eukaryotic genomes.Author Summary Because recombination takes place at a limited rate, alleles at neighboring sites in a genome can remain genetically linked over evolutionary periods. In this paper, we show that evolutionary forces generated by genetic linkage have drastic consequences for the adaptive dynamics in low-recombining parts of the Drosophila genome. Our study is based on a new method to analyze allele frequencies that is applicable to genome data at both high and low rates of recombination. We show that genes in low-recombining regions of the Drosophila genome incur a substantial cost of adaptation, because deleterious alleles get fixed more frequently than under high recombination. This cost reduces rate and power of the adaptive process. Our results suggest that the Drosophila genome has evolved to minimize this cost by placing genes under high adaptive pressure in high-recombining regions.