Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches
Identifieur interne : 000076 ( Ncbi/Curation ); précédent : 000075; suivant : 000077Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches
Auteurs : Stephen A. Smith [États-Unis] ; Jeremy M. Beaulieu [États-Unis] ; Michael J. Donoghue [États-Unis]Source :
- BMC Evolutionary Biology [ 1471-2148 ] ; 2009.
Abstract
Biology has increasingly recognized the necessity to build and utilize larger phylogenies to address broad evolutionary questions. Large phylogenies have facilitated the discovery of differential rates of molecular evolution between trees and herbs. They have helped us understand the diversification patterns of mammals as well as the patterns of seed evolution. In addition to these broad evolutionary questions there is increasing awareness of the importance of large phylogenies for addressing conservation issues such as biodiversity hotspots and response to global change. Two major classes of methods have been employed to accomplish the large tree-building task: supertrees and supermatrices. Although these methods are continually being developed, they have yet to be made fully accessible to comparative biologists making extremely large trees rare.
Here we describe and demonstrate a modified supermatrix method termed mega-phylogeny that uses databased sequences as well as taxonomic hierarchies to make extremely large trees with denser matrices than supermatrices. The two major challenges facing large-scale supermatrix phylogenetics are assembling large data matrices from databases and reconstructing trees from those datasets. The mega-phylogeny approach addresses the former as the latter is accomplished by employing recently developed methods that have greatly reduced the run time of large phylogeny construction. We present an algorithm that requires relatively little human intervention. The implemented algorithm is demonstrated with a dataset and phylogeny for Asterales (within Campanulidae) containing 4954 species and 12,033 sites and an
By examining much larger phylogenies, patterns emerge that were otherwise unseen. The phylogeny of Viridiplantae successfully reconstructs major relationships of vascular plants that previously required many more genes. These demonstrations underscore the importance of using large phylogenies to uncover important evolutionary patterns and we present a fast and simple method for constructing these phylogenies.
Url:
DOI: 10.1186/1471-2148-9-37
PubMed: 19210768
PubMed Central: 2645364
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000215
- to stream Pmc, to step Curation: Pour aller vers cette notice dans l'étape Curation :000215
- to stream Pmc, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :000631
- to stream Ncbi, to step Merge: Pour aller vers cette notice dans l'étape Curation :000076
Links to Exploration step
PMC:2645364Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches</title>
<author><name sortKey="Smith, Stephen A" sort="Smith, Stephen A" uniqKey="Smith S" first="Stephen A" last="Smith">Stephen A. Smith</name>
<affiliation wicri:level="2"><nlm:aff id="I1">National Evolutionary Synthesis Center, 2024 W Main St A200, Durham, NC 27705, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>National Evolutionary Synthesis Center, 2024 W Main St A200, Durham, NC 27705</wicri:regionArea>
<placeName><region type="state">Caroline du Nord</region>
</placeName>
</affiliation>
<affiliation wicri:level="2"><nlm:aff id="I2">Department of Ecology and Evolutionary Biology, Yale University, PO Box 208105, New Haven, CT 06520, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Ecology and Evolutionary Biology, Yale University, PO Box 208105, New Haven, CT 06520</wicri:regionArea>
<placeName><region type="state">Connecticut</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Beaulieu, Jeremy M" sort="Beaulieu, Jeremy M" uniqKey="Beaulieu J" first="Jeremy M" last="Beaulieu">Jeremy M. Beaulieu</name>
<affiliation wicri:level="2"><nlm:aff id="I2">Department of Ecology and Evolutionary Biology, Yale University, PO Box 208105, New Haven, CT 06520, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Ecology and Evolutionary Biology, Yale University, PO Box 208105, New Haven, CT 06520</wicri:regionArea>
<placeName><region type="state">Connecticut</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Donoghue, Michael J" sort="Donoghue, Michael J" uniqKey="Donoghue M" first="Michael J" last="Donoghue">Michael J. Donoghue</name>
<affiliation wicri:level="2"><nlm:aff id="I2">Department of Ecology and Evolutionary Biology, Yale University, PO Box 208105, New Haven, CT 06520, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Ecology and Evolutionary Biology, Yale University, PO Box 208105, New Haven, CT 06520</wicri:regionArea>
<placeName><region type="state">Connecticut</region>
</placeName>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">19210768</idno>
<idno type="pmc">2645364</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2645364</idno>
<idno type="RBID">PMC:2645364</idno>
<idno type="doi">10.1186/1471-2148-9-37</idno>
<date when="2009">2009</date>
<idno type="wicri:Area/Pmc/Corpus">000215</idno>
<idno type="wicri:Area/Pmc/Curation">000215</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000631</idno>
<idno type="wicri:Area/Ncbi/Merge">000076</idno>
<idno type="wicri:Area/Ncbi/Curation">000076</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches</title>
<author><name sortKey="Smith, Stephen A" sort="Smith, Stephen A" uniqKey="Smith S" first="Stephen A" last="Smith">Stephen A. Smith</name>
<affiliation wicri:level="2"><nlm:aff id="I1">National Evolutionary Synthesis Center, 2024 W Main St A200, Durham, NC 27705, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>National Evolutionary Synthesis Center, 2024 W Main St A200, Durham, NC 27705</wicri:regionArea>
<placeName><region type="state">Caroline du Nord</region>
</placeName>
</affiliation>
<affiliation wicri:level="2"><nlm:aff id="I2">Department of Ecology and Evolutionary Biology, Yale University, PO Box 208105, New Haven, CT 06520, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Ecology and Evolutionary Biology, Yale University, PO Box 208105, New Haven, CT 06520</wicri:regionArea>
<placeName><region type="state">Connecticut</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Beaulieu, Jeremy M" sort="Beaulieu, Jeremy M" uniqKey="Beaulieu J" first="Jeremy M" last="Beaulieu">Jeremy M. Beaulieu</name>
<affiliation wicri:level="2"><nlm:aff id="I2">Department of Ecology and Evolutionary Biology, Yale University, PO Box 208105, New Haven, CT 06520, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Ecology and Evolutionary Biology, Yale University, PO Box 208105, New Haven, CT 06520</wicri:regionArea>
<placeName><region type="state">Connecticut</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Donoghue, Michael J" sort="Donoghue, Michael J" uniqKey="Donoghue M" first="Michael J" last="Donoghue">Michael J. Donoghue</name>
<affiliation wicri:level="2"><nlm:aff id="I2">Department of Ecology and Evolutionary Biology, Yale University, PO Box 208105, New Haven, CT 06520, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Ecology and Evolutionary Biology, Yale University, PO Box 208105, New Haven, CT 06520</wicri:regionArea>
<placeName><region type="state">Connecticut</region>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j">BMC Evolutionary Biology</title>
<idno type="eISSN">1471-2148</idno>
<imprint><date when="2009">2009</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Biology has increasingly recognized the necessity to build and utilize larger phylogenies to address broad evolutionary questions. Large phylogenies have facilitated the discovery of differential rates of molecular evolution between trees and herbs. They have helped us understand the diversification patterns of mammals as well as the patterns of seed evolution. In addition to these broad evolutionary questions there is increasing awareness of the importance of large phylogenies for addressing conservation issues such as biodiversity hotspots and response to global change. Two major classes of methods have been employed to accomplish the large tree-building task: supertrees and supermatrices. Although these methods are continually being developed, they have yet to be made fully accessible to comparative biologists making extremely large trees rare.</p>
</sec>
<sec><title>Results</title>
<p>Here we describe and demonstrate a modified supermatrix method termed mega-phylogeny that uses databased sequences as well as taxonomic hierarchies to make extremely large trees with denser matrices than supermatrices. The two major challenges facing large-scale supermatrix phylogenetics are assembling large data matrices from databases and reconstructing trees from those datasets. The mega-phylogeny approach addresses the former as the latter is accomplished by employing recently developed methods that have greatly reduced the run time of large phylogeny construction. We present an algorithm that requires relatively little human intervention. The implemented algorithm is demonstrated with a dataset and phylogeny for Asterales (within Campanulidae) containing 4954 species and 12,033 sites and an <italic>rbcL </italic>
matrix for green plants (Viridiplantae) with 13,533 species and 1,401 sites.</p>
</sec>
<sec><title>Conclusion</title>
<p>By examining much larger phylogenies, patterns emerge that were otherwise unseen. The phylogeny of Viridiplantae successfully reconstructs major relationships of vascular plants that previously required many more genes. These demonstrations underscore the importance of using large phylogenies to uncover important evolutionary patterns and we present a fast and simple method for constructing these phylogenies.</p>
</sec>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
</listBibl>
</div1>
</back>
</TEI>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Ncbi/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000076 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd -nk 000076 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Ticri/CIDE |area= CyberinfraV1 |flux= Ncbi |étape= Curation |type= RBID |clé= PMC:2645364 |texte= Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/RBID.i -Sk "pubmed:19210768" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd \ | NlmPubMed2Wicri -a CyberinfraV1
This area was generated with Dilib version V0.6.25. |