A new test suggests hundreds of amino acid polymorphisms in humans are subject to balancing selection
The role that balancing selection plays in the maintenance of genetic diversity remains unresolved. Here, we introduce a new test, based on the McDonald–Kreitman test, in which the number of polymorphisms that are shared between populations is contrasted to those that are private at selected and neu...
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| Vydáno v: | PLoS biology Ročník 20; číslo 6; s. e3001645 |
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| Hlavní autoři: | , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
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United States
Public Library of Science
02.06.2022
Public Library of Science (PLoS) |
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| ISSN: | 1545-7885, 1544-9173, 1545-7885 |
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| Abstract | The role that balancing selection plays in the maintenance of genetic diversity remains unresolved. Here, we introduce a new test, based on the McDonald–Kreitman test, in which the number of polymorphisms that are shared between populations is contrasted to those that are private at selected and neutral sites. We show that this simple test is robust to a variety of demographic changes, and that it can also give a direct estimate of the number of shared polymorphisms that are directly maintained by balancing selection. We apply our method to population genomic data from humans and provide some evidence that hundreds of nonsynonymous polymorphisms are subject to balancing selection. |
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| AbstractList | The role that balancing selection plays in the maintenance of genetic diversity remains unresolved. Here, we introduce a new test, based on the McDonald–Kreitman test, in which the number of polymorphisms that are shared between populations is contrasted to those that are private at selected and neutral sites. We show that this simple test is robust to a variety of demographic changes, and that it can also give a direct estimate of the number of shared polymorphisms that are directly maintained by balancing selection. We apply our method to population genomic data from humans and provide some evidence that hundreds of nonsynonymous polymorphisms are subject to balancing selection. The role that balancing selection plays in the maintenance of genetic diversity remains unresolved. Here, we introduce a new test, based on the McDonald-Kreitman test, in which the number of polymorphisms that are shared between populations is contrasted to those that are private at selected and neutral sites. We show that this simple test is robust to a variety of demographic changes, and that it can also give a direct estimate of the number of shared polymorphisms that are directly maintained by balancing selection. We apply our method to population genomic data from humans and provide some evidence that hundreds of nonsynonymous polymorphisms are subject to balancing selection.The role that balancing selection plays in the maintenance of genetic diversity remains unresolved. Here, we introduce a new test, based on the McDonald-Kreitman test, in which the number of polymorphisms that are shared between populations is contrasted to those that are private at selected and neutral sites. We show that this simple test is robust to a variety of demographic changes, and that it can also give a direct estimate of the number of shared polymorphisms that are directly maintained by balancing selection. We apply our method to population genomic data from humans and provide some evidence that hundreds of nonsynonymous polymorphisms are subject to balancing selection. The role that balancing selection plays in the maintenance of genetic diversity remains unresolved. Here, we introduce a new test, based on the McDonald–Kreitman test, in which the number of polymorphisms that are shared between populations is contrasted to those that are private at selected and neutral sites. We show that this simple test is robust to a variety of demographic changes, and that it can also give a direct estimate of the number of shared polymorphisms that are directly maintained by balancing selection. We apply our method to population genomic data from humans and provide some evidence that hundreds of nonsynonymous polymorphisms are subject to balancing selection. What maintains genetic variation remains an unresolved mystery. This study describes the development of a new test and its application to human population genomic data, suggesting that natural selection may have a much more important role than previously thought, with hundreds of non-synonymous polymorphisms subject to balancing selection. |
| Audience | Academic |
| Author | Eyre-Walker, Adam Soni, Vivak Vos, Michiel |
| AuthorAffiliation | 2 European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn, United Kingdom Institute of Science and Technology Austria (IST Austria), AUSTRIA 1 School of Life Sciences, University of Sussex, Brighton, United Kingdom |
| AuthorAffiliation_xml | – name: 1 School of Life Sciences, University of Sussex, Brighton, United Kingdom – name: 2 European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn, United Kingdom – name: Institute of Science and Technology Austria (IST Austria), AUSTRIA |
| Author_xml | – sequence: 1 givenname: Vivak orcidid: 0000-0002-9496-9562 surname: Soni fullname: Soni, Vivak – sequence: 2 givenname: Michiel orcidid: 0000-0002-3917-8151 surname: Vos fullname: Vos, Michiel – sequence: 3 givenname: Adam orcidid: 0000-0001-5527-8729 surname: Eyre-Walker fullname: Eyre-Walker, Adam |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/35653351$$D View this record in MEDLINE/PubMed |
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| CitedBy_id | crossref_primary_10_1111_eva_70085 crossref_primary_10_1016_j_tig_2023_02_004 crossref_primary_10_1038_s41467_024_54603_5 crossref_primary_10_1111_mec_17632 crossref_primary_10_7554_eLife_79111 crossref_primary_10_1016_j_evolhumbehav_2024_106596 crossref_primary_10_1093_g3journal_jkae069 crossref_primary_10_1093_genetics_iyaf128 |
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| Copyright | COPYRIGHT 2022 Public Library of Science 2022 Soni et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 2022 Soni et al 2022 Soni et al |
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| SubjectTerms | Amino acids Balancing Biology and Life Sciences Evolution & development Genetic aspects Genetic diversity Genetic polymorphisms Methods and Resources Mutation Physiological aspects Polymorphism Population Quantitative genetics Research and Analysis Methods Simulation |
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| Title | A new test suggests hundreds of amino acid polymorphisms in humans are subject to balancing selection |
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