An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit
Identifieur interne : 000749 ( Main/Exploration ); précédent : 000748; suivant : 000750An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit
Auteurs : Jesse D. Bloom [États-Unis]Source :
- Molecular Biology and Evolution [ 0737-4038 ] ; 2014.
Abstract
All modern approaches to molecular phylogenetics require a quantitative model for how genes evolve. Unfortunately, existing evolutionary models do not realistically represent the site-heterogeneous selection that governs actual sequence change. Attempts to remedy this problem have involved augmenting these models with a burgeoning number of free parameters. Here, I demonstrate an alternative: Experimental determination of a parameter-free evolutionary model via mutagenesis, functional selection, and deep sequencing. Using this strategy, I create an evolutionary model for influenza nucleoprotein that describes the gene phylogeny far better than existing models with dozens or even hundreds of free parameters. Emerging high-throughput experimental strategies such as the one employed here provide fundamentally new information that has the potential to transform the sensitivity of phylogenetic and genetic analyses.
Url:
DOI: 10.1093/molbev/msu173
PubMed: 24859245
PubMed Central: 4104320
Affiliations:
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Bloom</name><affiliation wicri:level="2"><nlm:aff id="msu173-AFF1">Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Washington (État)</region></placeName><wicri:cityArea>Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle</wicri:cityArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24859245</idno><idno type="pmc">4104320</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104320</idno><idno type="RBID">PMC:4104320</idno><idno type="doi">10.1093/molbev/msu173</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000A28</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000A28</idno><idno type="wicri:Area/Pmc/Curation">000A28</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000A28</idno><idno type="wicri:Area/Pmc/Checkpoint">000534</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000534</idno><idno type="wicri:Area/Ncbi/Merge">000A49</idno><idno type="wicri:Area/Ncbi/Curation">000A49</idno><idno type="wicri:Area/Ncbi/Checkpoint">000A49</idno><idno type="wicri:doubleKey">0737-4038:2014:Bloom J:an:experimentally:determined</idno><idno type="wicri:Area/Main/Merge">000750</idno><idno type="wicri:Area/Main/Curation">000749</idno><idno type="wicri:Area/Main/Exploration">000749</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit</title><author><name sortKey="Bloom, Jesse D" sort="Bloom, Jesse D" uniqKey="Bloom J" first="Jesse D." last="Bloom">Jesse D. Bloom</name><affiliation wicri:level="2"><nlm:aff id="msu173-AFF1">Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Washington (État)</region></placeName><wicri:cityArea>Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle</wicri:cityArea></affiliation></author></analytic><series><title level="j">Molecular Biology and Evolution</title><idno type="ISSN">0737-4038</idno><idno type="eISSN">1537-1719</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>All modern approaches to molecular phylogenetics require a quantitative model for how genes evolve. Unfortunately, existing evolutionary models do not realistically represent the site-heterogeneous selection that governs actual sequence change. Attempts to remedy this problem have involved augmenting these models with a burgeoning number of free parameters. Here, I demonstrate an alternative: Experimental determination of a parameter-free evolutionary model via mutagenesis, functional selection, and deep sequencing. Using this strategy, I create an evolutionary model for influenza nucleoprotein that describes the gene phylogeny far better than existing models with dozens or even hundreds of free parameters. Emerging high-throughput experimental strategies such as the one employed here provide fundamentally new information that has the potential to transform the sensitivity of phylogenetic and genetic analyses.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Araya, Cl" uniqKey="Araya C">CL Araya</name></author><author><name sortKey="Fowler, Dm" uniqKey="Fowler D">DM Fowler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ashenberg, O" uniqKey="Ashenberg O">O Ashenberg</name></author><author><name sortKey="Gong, Li" uniqKey="Gong L">LI Gong</name></author><author><name sortKey="Bloom, Jd" uniqKey="Bloom J">JD Bloom</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bao, Y" uniqKey="Bao Y">Y Bao</name></author><author><name sortKey="Bolotov, P" uniqKey="Bolotov P">P Bolotov</name></author><author><name sortKey="Dernovoy, D" uniqKey="Dernovoy D">D 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Nielsen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ye, Q" uniqKey="Ye Q">Q Ye</name></author><author><name sortKey="Krug, Rm" uniqKey="Krug R">RM Krug</name></author><author><name sortKey="Tao, Yj" uniqKey="Tao Y">YJ Tao</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Washington (État)</li></region></list><tree><country name="États-Unis"><region name="Washington (État)"><name sortKey="Bloom, Jesse D" sort="Bloom, Jesse D" uniqKey="Bloom J" first="Jesse D." last="Bloom">Jesse D. 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