Background selection as null hypothesis in population genomics: insights and challenges from Drosophila studies

Philos Trans R Soc Lond B Biol Sci. 2017 Dec 19;372(1736):20160471. doi: 10.1098/rstb.2016.0471.


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'.

Keywords: background selection; genetic hitchhiking; recombination; selective sweep.

MeSH terms

  • Animals
  • Drosophila / genetics*
  • Evolution, Molecular*
  • Genetics, Population
  • Genome, Insect*
  • Models, Genetic
  • Recombination, Genetic*