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

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

Author information

1
Department of Biology, University of Iowa, Iowa City, IA 52242, USA josep-comeron@uiowa.edu.
2
Interdisciplinary Program in Genetics, University of Iowa, Iowa City, IA 52242, USA.

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'.

KEYWORDS:

background selection; genetic hitchhiking; recombination; selective sweep

PMID:
29109230
PMCID:
PMC5698629
DOI:
10.1098/rstb.2016.0471
[Indexed for MEDLINE]
Free PMC Article

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