Broad-scale variation in human genetic diversity levels is predicted by purifying selection on coding and non-coding elements
- Oklahoma Medical Research Foundation, United States
- Columbia University, United States
Abstract
Analyses of genetic variation in many taxa have established that neutral genetic diversity is shaped by natural selection at linked sites. Whether the mode of selection is primarily the fixation of strongly beneficial alleles (selective sweeps) or purifying selection on deleterious mutations (background selection) remains unknown, however. We address this question in humans by fitting a model of the joint effects of selective sweeps and background selection to autosomal polymorphism data from the 1000 Genomes Project. After controlling for variation in mutation rates along the genome, a model of background selection alone explains ~60% of the variance in diversity levels at the megabase scale. Adding the effects of selective sweeps driven by adaptive substitutions to the model does not improve the fit, and when both modes of selection are considered jointly, selective sweeps are estimated to have had little or no effect on linked neutral diversity. The regions under purifying selection are best predicted by phylogenetic conservation, with ~80% of the deleterious mutations affecting neutral diversity occurring in non-exonic regions. Thus, background selection is the dominant mode of linked selection in humans, with marked effects on diversity levels throughout autosomes.
Data availability
Shared data can be found at github.com/sellalab/HumanLinkedSelectionMaps. This repository includes fully documented code for: downloading and processing public datasets used, running inferences, analyzing results, and generating all figures from the manuscript. This repository also includes B-maps for all "best-fitting" models described in the manuscript. Customized CADD scores with bStatistic removed are available on Data Dryad at https://doi.org/10.5061/dryad.n8pk0p2x0.
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data from: Broad-scale variation in human genetic diversity levels is predicted by purifying selection on coding and non-coding elementsDryad Digital Repository, doi:10.5061/dryad.n8pk0p2x0.
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Data from: A global reference for human genetic variationdoi:10.1038/nature15393.
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Data from: The UCSC Table Browser data retrieval tooldoi:10.1093/nar/gkh103.
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Data from: The landscape of recombination in African Americansdoi:10.1038/nature10336.
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Data from: Expanded encyclopaedias of DNA elements in the human and mouse genomesdoi:10.1038/s41586-020-2493-4.
Article and author information
Author details
Funding
NIH (GM115889)
- Guy Sella
NIH (T32GM008798)
- David A Murphy
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Magnus Nordborg, Gregor Mendel Institute, Austria
Version history
- Preprint posted: July 2, 2021 (view preprint)
- Received: December 3, 2021
- Accepted: August 22, 2022
- Accepted Manuscript published: October 5, 2022 (version 1)
- Version of Record published: June 23, 2023 (version 2)
Copyright
© 2022, Murphy et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Broad-scale variation in human genetic diversity levels is predicted by purifying selection on coding and non-coding elements
eLife 11:e76065.
https://doi.org/10.7554/eLife.76065
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