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Widespread Genomic Signatures of Natural Selection in Hominid Evolution
Open accessAbstract
Selection acting on genomic functional elements can be detected by its indirect effects on population diversity at linked neutral sites. To illuminate the selective forces that shaped hominid evolution, we analyzed the genomic distributions of human polymorphisms and sequence differences among five primate species relative to the locations of conserved sequence features. Neutral sequence diversity in human and ancestral hominid populations is substantially reduced near such features, resulting in a surprisingly large genome average diversity reduction due to selection of 19-26% on the autosomes and 12-40% on the X chromosome. The overall trends are broadly consistent with "background selection" or hitchhiking in ancestral populations acting to remove deleterious variants. Average selection is much stronger on exonic (both protein-coding and untranslated) conserved features than non-exonic features. Long term selection, rather than complex speciation scenarios, explains the large intragenomic variation in human/chimpanzee divergence. Our analyses reveal a dominant role for selection in shaping genomic diversity and divergence patterns, clarify hominid evolution, and provide a baseline for investigating specific selective events.
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“In particular, background selection (i.e., the selective removal of deleterious alleles across the genome) appears to play a primary role in shaping the highly polygenic architecture of human traits and diseases [1, 7–9].”
From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [1]
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“To ensure the observed differences between aSNPs and naSNPs were not caused by different levels of background selection we downloaded from https://github.com/gmcvicker/bkgd the bed file containing the list of pre-computed values for the B-statistic in hg19 coordinates [32].”
From Denisovan introgression has shaped the immune system of present-day Papuans (2022) · cites this paper as [32]
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“Genomic features related to natural selection are enriched for loci associated with complex traits [1, 7–9].”
From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [1]
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“Background Genetic variation across worldwide populations reflects the widespread impact of human evolutionary history, including processes related to natural selection and demographic history [1].”
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Metadata
- Authors
- McVicker, G., Gordon, D., Davis, C., & Green, P.
- Affiliations
- University of Washington (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- McVicker, Graham
- Green, Phil
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2009-05-08
- Volume
- 5
- Issue
- 5
- Pages
- e1000471
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC2669884
- OpenAlex
- W2032311106
- Cited by
- 456
- References
- 80
- Citations by year
- 2026: 24 · 2025: 25 · 2024: 37 · 2023: 34 · 2022: 23 · 2021: 29 · 2020: 38 · 2019: 33 · 2018: 33 · 2017: 23 · 2016: 25 · 2015: 25 · 2014: 30 · 2013: 16 · 2012: 25
- FWCI
- 11.83
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Howard Hughes Medical Institute
- Natural Sciences and Engineering Research Council of Canada
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- natural selection, hominid evolution, human polymorphism, background selection, hitchhiking, X chromosome, human-chimpanzee divergence
- MeSH terms
- Animals, Pan troglodytes, Humans, Markov Chains, Models, Genetic, Primates, Recombination, Genetic, Selection, Genetic, X Chromosome, Hominidae, Genome, Human, Confidence Intervals, Likelihood Functions, Conserved Sequence, Evolution, Molecular, Polymorphism, Single Nucleotide, Chromosomes, Human, X
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