Natural selection on synonymous and nonsynonymous mutations shapes patterns of polymorphism in Populus tremula.
Identifieur interne : 003186 ( Main/Exploration ); précédent : 003185; suivant : 003187Natural selection on synonymous and nonsynonymous mutations shapes patterns of polymorphism in Populus tremula.
Auteurs : P R K. Ingvarsson [Suède]Source :
- Molecular biology and evolution [ 1537-1719 ] ; 2010.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Codon, Populus.
- méthodes : Biologie informatique.
- Adaptation biologique, Dynamique non linéaire, Mutation, Sélection génétique, Théorème de Bayes, Évolution moléculaire.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Codon.
- genetics : Populus.
- methods : Computational Biology.
- Adaptation, Biological, Bayes Theorem, Evolution, Molecular, Mutation, Nonlinear Dynamics, Selection, Genetic.
Abstract
One important goal of population genetics is to understand the relative importance of different evolutionary processes for shaping variation in natural populations. Here, I use multilocus data to show that natural selection on both synonymous and nonsynonymous mutations plays an important role in shaping levels of synonymous polymorphism in European aspen (Populus tremula). Previous studies have documented a preferential fixation of synonymous mutations encoding preferred codons in P. tremula. The results presented here show that this has resulted in an increase in codon bias in P. tremula, consistent with stronger selection acting on synonymous codon usage. In addition, positive selection on nonsynonymous mutations appears to be common in P. tremula, with approximately 30% of all mutations having been fixed by positive selection. In addition, the recurrent fixation of beneficial mutations also reduces standing levels of polymorphism as evidenced by a significantly negative relationship between the rate of protein evolution synonymous site diversity and silent site diversity. Finally, I use approximate Bayesian methods to estimate the strength of selection acting on beneficial substitutions. These calculations show that recurrent hitchhiking reduces polymorphism by, on average, 30%. The product of strength of selection acting on beneficial mutations and the rate by which these occur across the genome (2N(e)lambdas) equals 1.54x10( - 7), which is in line with estimates from Drosophila where recurrent hitchhiking has also been shown to have significant effects on standing levels of polymorphism.
DOI: 10.1093/molbev/msp255
PubMed: 19837657
Affiliations:
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Here, I use multilocus data to show that natural selection on both synonymous and nonsynonymous mutations plays an important role in shaping levels of synonymous polymorphism in European aspen (Populus tremula). Previous studies have documented a preferential fixation of synonymous mutations encoding preferred codons in P. tremula. The results presented here show that this has resulted in an increase in codon bias in P. tremula, consistent with stronger selection acting on synonymous codon usage. In addition, positive selection on nonsynonymous mutations appears to be common in P. tremula, with approximately 30% of all mutations having been fixed by positive selection. In addition, the recurrent fixation of beneficial mutations also reduces standing levels of polymorphism as evidenced by a significantly negative relationship between the rate of protein evolution synonymous site diversity and silent site diversity. Finally, I use approximate Bayesian methods to estimate the strength of selection acting on beneficial substitutions. These calculations show that recurrent hitchhiking reduces polymorphism by, on average, 30%. The product of strength of selection acting on beneficial mutations and the rate by which these occur across the genome (2N(e)lambdas) equals 1.54x10( - 7), which is in line with estimates from Drosophila where recurrent hitchhiking has also been shown to have significant effects on standing levels of polymorphism.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19837657</PMID><DateCompleted><Year>2010</Year><Month>05</Month><Day>12</Day></DateCompleted><DateRevised><Year>2010</Year><Month>02</Month><Day>17</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1537-1719</ISSN><JournalIssue CitedMedium="Internet"><Volume>27</Volume><Issue>3</Issue><PubDate><Year>2010</Year><Month>Mar</Month></PubDate></JournalIssue><Title>Molecular biology and evolution</Title><ISOAbbreviation>Mol Biol Evol</ISOAbbreviation></Journal><ArticleTitle>Natural selection on synonymous and nonsynonymous mutations shapes patterns of polymorphism in Populus tremula.</ArticleTitle><Pagination><MedlinePgn>650-60</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/molbev/msp255</ELocationID><Abstract><AbstractText>One important goal of population genetics is to understand the relative importance of different evolutionary processes for shaping variation in natural populations. Here, I use multilocus data to show that natural selection on both synonymous and nonsynonymous mutations plays an important role in shaping levels of synonymous polymorphism in European aspen (Populus tremula). Previous studies have documented a preferential fixation of synonymous mutations encoding preferred codons in P. tremula. The results presented here show that this has resulted in an increase in codon bias in P. tremula, consistent with stronger selection acting on synonymous codon usage. In addition, positive selection on nonsynonymous mutations appears to be common in P. tremula, with approximately 30% of all mutations having been fixed by positive selection. In addition, the recurrent fixation of beneficial mutations also reduces standing levels of polymorphism as evidenced by a significantly negative relationship between the rate of protein evolution synonymous site diversity and silent site diversity. Finally, I use approximate Bayesian methods to estimate the strength of selection acting on beneficial substitutions. These calculations show that recurrent hitchhiking reduces polymorphism by, on average, 30%. The product of strength of selection acting on beneficial mutations and the rate by which these occur across the genome (2N(e)lambdas) equals 1.54x10( - 7), which is in line with estimates from Drosophila where recurrent hitchhiking has also been shown to have significant effects on standing levels of polymorphism.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ingvarsson</LastName><ForeName>Pär K</ForeName><Initials>PK</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden. par.ingvarsson@emg.umu.se</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2009</Year><Month>10</Month><Day>16</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Mol Biol Evol</MedlineTA><NlmUniqueID>8501455</NlmUniqueID><ISSNLinking>0737-4038</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D003062">Codon</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000220" MajorTopicYN="N">Adaptation, Biological</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001499" MajorTopicYN="N">Bayes Theorem</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003062" MajorTopicYN="N">Codon</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="Y">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009154" MajorTopicYN="Y">Mutation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017711" MajorTopicYN="N">Nonlinear Dynamics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012641" MajorTopicYN="Y">Selection, Genetic</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2009</Year><Month>10</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2009</Year><Month>10</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2010</Year><Month>5</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">19837657</ArticleId><ArticleId IdType="pii">msp255</ArticleId><ArticleId IdType="doi">10.1093/molbev/msp255</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Suède</li></country></list><tree><country name="Suède"><noRegion><name sortKey="Ingvarsson, P R K" sort="Ingvarsson, P R K" uniqKey="Ingvarsson P" first="P R K" last="Ingvarsson">P R K. 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