A population genetics-phylogenetics approach to inferring natural selection in coding sequences.
Through an analysis of polymorphism within and divergence between species, we can hope to learn about the distribution of selective effects of mutations in the genome, changes in the fitness landscape that occur over time, and the location of sites involved in key adaptations that distinguish modern...
| Main Authors: | , , , |
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| Format: | Journal article |
| Language: | English |
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Public Library of Science
2011
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| _version_ | 1797085509831360512 |
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| author | Wilson, D Hernandez, R Andolfatto, P Przeworski, M |
| author_facet | Wilson, D Hernandez, R Andolfatto, P Przeworski, M |
| author_sort | Wilson, D |
| collection | OXFORD |
| description | Through an analysis of polymorphism within and divergence between species, we can hope to learn about the distribution of selective effects of mutations in the genome, changes in the fitness landscape that occur over time, and the location of sites involved in key adaptations that distinguish modern-day species. We introduce a novel method for the analysis of variation in selection pressures within and between species, spatially along the genome and temporally between lineages. We model codon evolution explicitly using a joint population genetics-phylogenetics approach that we developed for the construction of multiallelic models with mutation, selection, and drift. Our approach has the advantage of performing direct inference on coding sequences, inferring ancestral states probabilistically, utilizing allele frequency information, and generalizing to multiple species. We use a Bayesian sliding window model for intragenic variation in selection coefficients that efficiently combines information across sites and captures spatial clustering within the genome. To demonstrate the utility of the method, we infer selective pressures acting in Drosophila melanogaster and D. simulans from polymorphism and divergence data for 100 X-linked coding regions. |
| first_indexed | 2024-03-07T02:09:46Z |
| format | Journal article |
| id | oxford-uuid:a0384a57-d89d-49d9-aef3-f9074159716c |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T02:09:46Z |
| publishDate | 2011 |
| publisher | Public Library of Science |
| record_format | dspace |
| spelling | oxford-uuid:a0384a57-d89d-49d9-aef3-f9074159716c2022-03-27T02:03:54ZA population genetics-phylogenetics approach to inferring natural selection in coding sequences.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:a0384a57-d89d-49d9-aef3-f9074159716cEnglishSymplectic Elements at OxfordPublic Library of Science2011Wilson, DHernandez, RAndolfatto, PPrzeworski, MThrough an analysis of polymorphism within and divergence between species, we can hope to learn about the distribution of selective effects of mutations in the genome, changes in the fitness landscape that occur over time, and the location of sites involved in key adaptations that distinguish modern-day species. We introduce a novel method for the analysis of variation in selection pressures within and between species, spatially along the genome and temporally between lineages. We model codon evolution explicitly using a joint population genetics-phylogenetics approach that we developed for the construction of multiallelic models with mutation, selection, and drift. Our approach has the advantage of performing direct inference on coding sequences, inferring ancestral states probabilistically, utilizing allele frequency information, and generalizing to multiple species. We use a Bayesian sliding window model for intragenic variation in selection coefficients that efficiently combines information across sites and captures spatial clustering within the genome. To demonstrate the utility of the method, we infer selective pressures acting in Drosophila melanogaster and D. simulans from polymorphism and divergence data for 100 X-linked coding regions. |
| spellingShingle | Wilson, D Hernandez, R Andolfatto, P Przeworski, M A population genetics-phylogenetics approach to inferring natural selection in coding sequences. |
| title | A population genetics-phylogenetics approach to inferring natural selection in coding sequences. |
| title_full | A population genetics-phylogenetics approach to inferring natural selection in coding sequences. |
| title_fullStr | A population genetics-phylogenetics approach to inferring natural selection in coding sequences. |
| title_full_unstemmed | A population genetics-phylogenetics approach to inferring natural selection in coding sequences. |
| title_short | A population genetics-phylogenetics approach to inferring natural selection in coding sequences. |
| title_sort | population genetics phylogenetics approach to inferring natural selection in coding sequences |
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