Abstract

The consequences of selection at linked sites are multiple and widespread across the genomes of most species. Here, I first review the main concepts behind models of selection and linkage in recombining genomes, present the difficulty in parametrizing these models simply as a reduction in effective population size (Ne) and discuss the predicted impact of recombination rates on levels of diversity across genomes. Arguments are then put forward in favour of using a model of selection and linkage with neutral and deleterious mutations (i.e. the background selection model, BGS) as a sensible null hypothesis for investigating the presence of other forms of selection, such as balancing or positive. I also describe and compare two studies that have generated high-resolution landscapes of the predicted consequences of selection at linked sites in Drosophila melanogaster. Both studies show that BGS can explain a very large fraction of the observed variation in diversity across the whole genome, thus supporting its use as null model. Finally, I identify and discuss a number of caveats and challenges in studies of genetic hitchhiking that have been often overlooked, with several of them sharing a potential bias towards overestimating the evidence supporting recent selective sweeps to the detriment of a BGS explanation. One potential source of bias is the analysis of non-equilibrium populations: it is precisely because models of selection and linkage predict variation in Ne across chromosomes that demographic dynamics are not expected to be equivalent chromosome- or genome-wide. Other challenges include the use of incomplete genome annotations, the assumption of temporally stable recombination landscapes, the presence of genes under balancing selection and the consequences of ignoring non-crossover (gene conversion) recombination events.This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.

Highlights

  • Selection at a given genomic site has evolutionary consequences for genetically linked sites, either neutral or under selection themselves

  • The results showed that background selection model (BGS) is a realistic explanation for the observed reduction in neutral diversity on the fourth achiasmate chromosome and near centromeres of recombining chromosomes, when the deleterious consequences of transposable element (TE) insertions were taken into account [3]

  • Neutral mutations in 6 regions with lower density of sites under selection tend to show a more negative Tajima’s D than those in regions with more sites under selection when recombination rates are equivalent. These results suggest that neutral sites embedded in genomic regions with low BGS may exhibit patterns reminiscent of those caused by selective sweeps when compared with neutral sites under relatively stronger BGS as a consequence of the predicted longer periods of time to equilibrium in the former regions

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Summary

Introduction

Selection at a given genomic site has evolutionary consequences for genetically linked sites, either neutral or under selection themselves. This study used highresolution recombination rates [40] and explored the influence of crossover (CO) and non-crossover (NCO, or gene conversion) recombination events on the distribution of BGS effects (see below) This comprehensive approach generated wholegenome high-resolution landscapes of the consequences of selection at linked sites under BGS (i.e. BGS landscapes or B-maps) that were used to evaluate the general fit to the observed levels of neutral diversity and to identify outlier regions [79]. Controlled thinning strategies may help to identify and lessen potential biases in species, or genomic regions, with high levels of nucleotide diversity

Conclusion
Findings
58. Stevison LS et al 2016 The time scale of
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