Evaluating the Impact of Genomic Data and Priors on Bayesian Estimates of the Angiosperm Evolutionary Timescale.
Identifieur interne : 000D38 ( PubMed/Curation ); précédent : 000D37; suivant : 000D39Evaluating the Impact of Genomic Data and Priors on Bayesian Estimates of the Angiosperm Evolutionary Timescale.
Auteurs : Charles S P. Foster [Australie] ; Hervê Sauquet [France] ; Marlien Van Der Merwe [Australie] ; Hannah Mcpherson [Australie] ; Maurizio Rossetto [Australie] ; Simon Y W. Ho [Australie]Source :
- Systematic biology [ 1076-836X ] ; 2017.
Abstract
The evolutionary timescale of angiosperms has long been a key question in biology. Molecular estimates of this timescale have shown considerable variation, being influenced by differences in taxon sampling, gene sampling, fossil calibrations, evolutionary models, and choices of priors. Here, we analyze a data set comprising 76 protein-coding genes from the chloroplast genomes of 195 taxa spanning 86 families, including novel genome sequences for 11 taxa, to evaluate the impact of models, priors, and gene sampling on Bayesian estimates of the angiosperm evolutionary timescale. Using a Bayesian relaxed molecular-clock method, with a core set of 35 minimum and two maximum fossil constraints, we estimated that crown angiosperms arose 221 (251-192) Ma during the Triassic. Based on a range of additional sensitivity and subsampling analyses, we found that our date estimates were generally robust to large changes in the parameters of the birth-death tree prior and of the model of rate variation across branches. We found an exception to this when we implemented fossil calibrations in the form of highly informative gamma priors rather than as uniform priors on node ages. Under all other calibration schemes, including trials of seven maximum age constraints, we consistently found that the earliest divergences of angiosperm clades substantially predate the oldest fossils that can be assigned unequivocally to their crown group. Overall, our results and experiments with genome-scale data suggest that reliable estimates of the angiosperm crown age will require increased taxon sampling, significant methodological changes, and new information from the fossil record. [Angiospermae, chloroplast, genome, molecular dating, Triassic.].
DOI: 10.1093/sysbio/syw086
PubMed: 27650175
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000D41
Links to Exploration step
pubmed:27650175Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Evaluating the Impact of Genomic Data and Priors on Bayesian Estimates of the Angiosperm Evolutionary Timescale.</title><author><name sortKey="Foster, Charles S P" sort="Foster, Charles S P" uniqKey="Foster C" first="Charles S P" last="Foster">Charles S P. Foster</name><affiliation wicri:level="1"><nlm:affiliation>School of Life and Environmental Sciences, Edgeworth David Building A11, University of Sydney, Sydney, New South Wales 2006, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>School of Life and Environmental Sciences, Edgeworth David Building A11, University of Sydney, Sydney, New South Wales 2006</wicri:regionArea></affiliation></author><author><name sortKey="Sauquet, Herve" sort="Sauquet, Herve" uniqKey="Sauquet H" first="Hervê" last="Sauquet">Hervê Sauquet</name><affiliation wicri:level="1"><nlm:affiliation>Laboratoire écologie, Systématique, évolution, Université Paris-Sud, CNRS UMR 8079, bat. 360, Orsay 91405, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire écologie, Systématique, évolution, Université Paris-Sud, CNRS UMR 8079, bat. 360, Orsay 91405</wicri:regionArea></affiliation></author><author><name sortKey="Van Der Merwe, Marlien" sort="Van Der Merwe, Marlien" uniqKey="Van Der Merwe M" first="Marlien" last="Van Der Merwe">Marlien Van Der Merwe</name><affiliation wicri:level="1"><nlm:affiliation>National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000</wicri:regionArea></affiliation></author><author><name sortKey="Mcpherson, Hannah" sort="Mcpherson, Hannah" uniqKey="Mcpherson H" first="Hannah" last="Mcpherson">Hannah Mcpherson</name><affiliation wicri:level="1"><nlm:affiliation>National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000</wicri:regionArea></affiliation></author><author><name sortKey="Rossetto, Maurizio" sort="Rossetto, Maurizio" uniqKey="Rossetto M" first="Maurizio" last="Rossetto">Maurizio Rossetto</name><affiliation wicri:level="1"><nlm:affiliation>National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000</wicri:regionArea></affiliation></author><author><name sortKey="Ho, Simon Y W" sort="Ho, Simon Y W" uniqKey="Ho S" first="Simon Y W" last="Ho">Simon Y W. Ho</name><affiliation wicri:level="1"><nlm:affiliation>School of Life and Environmental Sciences, Edgeworth David Building A11, University of Sydney, Sydney, New South Wales 2006, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>School of Life and Environmental Sciences, Edgeworth David Building A11, University of Sydney, Sydney, New South Wales 2006</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:27650175</idno><idno type="pmid">27650175</idno><idno type="doi">10.1093/sysbio/syw086</idno><idno type="wicri:Area/PubMed/Corpus">000D41</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000D41</idno><idno type="wicri:Area/PubMed/Curation">000D38</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000D38</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Evaluating the Impact of Genomic Data and Priors on Bayesian Estimates of the Angiosperm Evolutionary Timescale.</title><author><name sortKey="Foster, Charles S P" sort="Foster, Charles S P" uniqKey="Foster C" first="Charles S P" last="Foster">Charles S P. Foster</name><affiliation wicri:level="1"><nlm:affiliation>School of Life and Environmental Sciences, Edgeworth David Building A11, University of Sydney, Sydney, New South Wales 2006, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>School of Life and Environmental Sciences, Edgeworth David Building A11, University of Sydney, Sydney, New South Wales 2006</wicri:regionArea></affiliation></author><author><name sortKey="Sauquet, Herve" sort="Sauquet, Herve" uniqKey="Sauquet H" first="Hervê" last="Sauquet">Hervê Sauquet</name><affiliation wicri:level="1"><nlm:affiliation>Laboratoire écologie, Systématique, évolution, Université Paris-Sud, CNRS UMR 8079, bat. 360, Orsay 91405, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire écologie, Systématique, évolution, Université Paris-Sud, CNRS UMR 8079, bat. 360, Orsay 91405</wicri:regionArea></affiliation></author><author><name sortKey="Van Der Merwe, Marlien" sort="Van Der Merwe, Marlien" uniqKey="Van Der Merwe M" first="Marlien" last="Van Der Merwe">Marlien Van Der Merwe</name><affiliation wicri:level="1"><nlm:affiliation>National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000</wicri:regionArea></affiliation></author><author><name sortKey="Mcpherson, Hannah" sort="Mcpherson, Hannah" uniqKey="Mcpherson H" first="Hannah" last="Mcpherson">Hannah Mcpherson</name><affiliation wicri:level="1"><nlm:affiliation>National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000</wicri:regionArea></affiliation></author><author><name sortKey="Rossetto, Maurizio" sort="Rossetto, Maurizio" uniqKey="Rossetto M" first="Maurizio" last="Rossetto">Maurizio Rossetto</name><affiliation wicri:level="1"><nlm:affiliation>National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000</wicri:regionArea></affiliation></author><author><name sortKey="Ho, Simon Y W" sort="Ho, Simon Y W" uniqKey="Ho S" first="Simon Y W" last="Ho">Simon Y W. Ho</name><affiliation wicri:level="1"><nlm:affiliation>School of Life and Environmental Sciences, Edgeworth David Building A11, University of Sydney, Sydney, New South Wales 2006, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>School of Life and Environmental Sciences, Edgeworth David Building A11, University of Sydney, Sydney, New South Wales 2006</wicri:regionArea></affiliation></author></analytic><series><title level="j">Systematic biology</title><idno type="eISSN">1076-836X</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The evolutionary timescale of angiosperms has long been a key question in biology. Molecular estimates of this timescale have shown considerable variation, being influenced by differences in taxon sampling, gene sampling, fossil calibrations, evolutionary models, and choices of priors. Here, we analyze a data set comprising 76 protein-coding genes from the chloroplast genomes of 195 taxa spanning 86 families, including novel genome sequences for 11 taxa, to evaluate the impact of models, priors, and gene sampling on Bayesian estimates of the angiosperm evolutionary timescale. Using a Bayesian relaxed molecular-clock method, with a core set of 35 minimum and two maximum fossil constraints, we estimated that crown angiosperms arose 221 (251-192) Ma during the Triassic. Based on a range of additional sensitivity and subsampling analyses, we found that our date estimates were generally robust to large changes in the parameters of the birth-death tree prior and of the model of rate variation across branches. We found an exception to this when we implemented fossil calibrations in the form of highly informative gamma priors rather than as uniform priors on node ages. Under all other calibration schemes, including trials of seven maximum age constraints, we consistently found that the earliest divergences of angiosperm clades substantially predate the oldest fossils that can be assigned unequivocally to their crown group. Overall, our results and experiments with genome-scale data suggest that reliable estimates of the angiosperm crown age will require increased taxon sampling, significant methodological changes, and new information from the fossil record. [Angiospermae, chloroplast, genome, molecular dating, Triassic.].</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">27650175</PMID><DateCreated><Year>2016</Year><Month>09</Month><Day>21</Day></DateCreated><DateRevised><Year>2017</Year><Month>04</Month><Day>20</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1076-836X</ISSN><JournalIssue CitedMedium="Internet"><Volume>66</Volume><Issue>3</Issue><PubDate><Year>2017</Year><Month>May</Month><Day>01</Day></PubDate></JournalIssue><Title>Systematic biology</Title><ISOAbbreviation>Syst. Biol.</ISOAbbreviation></Journal><ArticleTitle>Evaluating the Impact of Genomic Data and Priors on Bayesian Estimates of the Angiosperm Evolutionary Timescale.</ArticleTitle><Pagination><MedlinePgn>338-351</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/sysbio/syw086</ELocationID><Abstract><AbstractText>The evolutionary timescale of angiosperms has long been a key question in biology. Molecular estimates of this timescale have shown considerable variation, being influenced by differences in taxon sampling, gene sampling, fossil calibrations, evolutionary models, and choices of priors. Here, we analyze a data set comprising 76 protein-coding genes from the chloroplast genomes of 195 taxa spanning 86 families, including novel genome sequences for 11 taxa, to evaluate the impact of models, priors, and gene sampling on Bayesian estimates of the angiosperm evolutionary timescale. Using a Bayesian relaxed molecular-clock method, with a core set of 35 minimum and two maximum fossil constraints, we estimated that crown angiosperms arose 221 (251-192) Ma during the Triassic. Based on a range of additional sensitivity and subsampling analyses, we found that our date estimates were generally robust to large changes in the parameters of the birth-death tree prior and of the model of rate variation across branches. We found an exception to this when we implemented fossil calibrations in the form of highly informative gamma priors rather than as uniform priors on node ages. Under all other calibration schemes, including trials of seven maximum age constraints, we consistently found that the earliest divergences of angiosperm clades substantially predate the oldest fossils that can be assigned unequivocally to their crown group. Overall, our results and experiments with genome-scale data suggest that reliable estimates of the angiosperm crown age will require increased taxon sampling, significant methodological changes, and new information from the fossil record. [Angiospermae, chloroplast, genome, molecular dating, Triassic.].</AbstractText><CopyrightInformation>© The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Foster</LastName><ForeName>Charles S P</ForeName><Initials>CSP</Initials><AffiliationInfo><Affiliation>School of Life and Environmental Sciences, Edgeworth David Building A11, University of Sydney, Sydney, New South Wales 2006, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sauquet</LastName><ForeName>Hervê</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Laboratoire écologie, Systématique, évolution, Université Paris-Sud, CNRS UMR 8079, bat. 360, Orsay 91405, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>van der Merwe</LastName><ForeName>Marlien</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>McPherson</LastName><ForeName>Hannah</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rossetto</LastName><ForeName>Maurizio</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ho</LastName><ForeName>Simon Y W</ForeName><Initials>SYW</Initials><AffiliationInfo><Affiliation>School of Life and Environmental Sciences, Edgeworth David Building A11, University of Sydney, Sydney, New South Wales 2006, Australia.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Syst Biol</MedlineTA><NlmUniqueID>9302532</NlmUniqueID><ISSNLinking>1063-5157</ISSNLinking></MedlineJournalInfo></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>08</Month><Day>07</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>09</Month><Day>10</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>9</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>9</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>9</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27650175</ArticleId><ArticleId IdType="pii">syw086</ArticleId><ArticleId IdType="doi">10.1093/sysbio/syw086</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Asie/explor/AustralieFrV1/Data/PubMed/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000D38 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Curation/biblio.hfd -nk 000D38 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Asie
|area= AustralieFrV1
|flux= PubMed
|étape= Curation
|type= RBID
|clé= pubmed:27650175
|texte= Evaluating the Impact of Genomic Data and Priors on Bayesian Estimates of the Angiosperm Evolutionary Timescale.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Curation/RBID.i -Sk "pubmed:27650175" \
| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Curation/biblio.hfd \
| NlmPubMed2Wicri -a AustralieFrV1
| This area was generated with Dilib version V0.6.33. |  |