Journal article
Background selection as null hypothesis in population genomics: insights and challenges from Drosophila studies
Philosophical transactions. Biological sciences, Vol.372(1736), pp.20160471-20160471
12/19/2017
DOI: 10.1098/rstb.2016.0471
PMCID: PMC5698629
PMID: 29109230
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 (
) 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
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
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'.
Details
- Title: Subtitle
- Background selection as null hypothesis in population genomics: insights and challenges from Drosophila studies
- Creators
- Josep M Comeron - Interdisciplinary Program in Genetics, University of Iowa, Iowa City, IA 52242, USA
- Resource Type
- Journal article
- Publication Details
- Philosophical transactions. Biological sciences, Vol.372(1736), pp.20160471-20160471
- Publisher
- England
- DOI
- 10.1098/rstb.2016.0471
- PMID
- 29109230
- PMCID
- PMC5698629
- ISSN
- 1471-2970
- eISSN
- 1471-2970
- Grant note
- DOI: 10.13039/100000155, name: Division of Environmental Biology, award: DEB1354921
- Language
- English
- Date published
- 12/19/2017
- Academic Unit
- Biology
- Record Identifier
- 9983991933902771
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