A guide to phylogenetic metrics for conservation, community ecology and macroecology.
Identifieur interne : 000D40 ( PubMed/Curation ); précédent : 000D39; suivant : 000D41A guide to phylogenetic metrics for conservation, community ecology and macroecology.
Auteurs : Caroline M. Tucker [États-Unis] ; Marc W. Cadotte [Canada] ; Silvia B. Carvalho [Portugal] ; T Jonathan Davies [Canada] ; Simon Ferrier [Australie] ; Susanne A. Fritz [Allemagne] ; Rich Grenyer [Royaume-Uni] ; Matthew R. Helmus [Pays-Bas] ; Lanna S. Jin [Canada] ; Arne O. Mooers [Canada] ; Sandrine Pavoine [France] ; Oliver Purschke [Allemagne] ; David W. Redding [Royaume-Uni] ; Dan F. Rosauer [Australie] ; Marten Winter [Allemagne] ; Florent Mazel [France]Source :
- Biological reviews of the Cambridge Philosophical Society [ 1469-185X ] ; 2017.
Abstract
The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub-disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub-disciplines hampers potential meta-analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo-diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo-diversity metrics based on their mathematical form within these three dimensions and identify 'anchor' representatives: for α-diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices.
DOI: 10.1111/brv.12252
PubMed: 26785932
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Tucker</name><affiliation wicri:level="1"><nlm:affiliation>Department of Ecology and Evolutionary Biology, University of Colorado, Box 334, Boulder, CO, 80309-0334, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Ecology and Evolutionary Biology, University of Colorado, Box 334, Boulder, CO, 80309-0334</wicri:regionArea></affiliation></author><author><name sortKey="Cadotte, Marc W" sort="Cadotte, Marc W" uniqKey="Cadotte M" first="Marc W" last="Cadotte">Marc W. Cadotte</name><affiliation wicri:level="1"><nlm:affiliation>Biological Sciences, University of Toronto-Scarborough, Scarborough, M1C 1A4, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Biological Sciences, University of Toronto-Scarborough, Scarborough, M1C 1A4</wicri:regionArea></affiliation></author><author><name sortKey="Carvalho, Silvia B" sort="Carvalho, Silvia B" uniqKey="Carvalho S" first="Silvia B" last="Carvalho">Silvia B. Carvalho</name><affiliation wicri:level="1"><nlm:affiliation>CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, 4485-661, Vairão, Portugal.</nlm:affiliation><country xml:lang="fr">Portugal</country><wicri:regionArea>CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, 4485-661, Vairão</wicri:regionArea></affiliation></author><author><name sortKey="Davies, T Jonathan" sort="Davies, T Jonathan" uniqKey="Davies T" first="T Jonathan" last="Davies">T Jonathan Davies</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, McGill University, Montréal, H3A 1B1, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Biology, McGill University, Montréal, H3A 1B1</wicri:regionArea></affiliation></author><author><name sortKey="Ferrier, Simon" sort="Ferrier, Simon" uniqKey="Ferrier S" first="Simon" last="Ferrier">Simon Ferrier</name><affiliation wicri:level="1"><nlm:affiliation>CSIRO Ecosystem Sciences, Climate Adaptation Flagship, GPO BOX 1600, Canberra, 2601, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Ecosystem Sciences, Climate Adaptation Flagship, GPO BOX 1600, Canberra, 2601</wicri:regionArea></affiliation></author><author><name sortKey="Fritz, Susanne A" sort="Fritz, Susanne A" uniqKey="Fritz S" first="Susanne A" last="Fritz">Susanne A. Fritz</name><affiliation wicri:level="1"><nlm:affiliation>Biodiversity & Climate Research Centre (BiK-F) and Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt am Main, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Biodiversity & Climate Research Centre (BiK-F) and Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt am Main</wicri:regionArea></affiliation></author><author><name sortKey="Grenyer, Rich" sort="Grenyer, Rich" uniqKey="Grenyer R" first="Rich" last="Grenyer">Rich Grenyer</name><affiliation wicri:level="1"><nlm:affiliation>School of Geography and the Environment, University of Oxford, Oxford, OX1 3QY, U.K.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>School of Geography and the Environment, University of Oxford, Oxford, OX1 3QY</wicri:regionArea></affiliation></author><author><name sortKey="Helmus, Matthew R" sort="Helmus, Matthew R" uniqKey="Helmus M" first="Matthew R" last="Helmus">Matthew R. Helmus</name><affiliation wicri:level="1"><nlm:affiliation>Department of Ecological Sciences - Animal Ecology, Vrije Universiteit, Amsterdam, Netherlands.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Ecological Sciences - Animal Ecology, Vrije Universiteit, Amsterdam</wicri:regionArea></affiliation></author><author><name sortKey="Jin, Lanna S" sort="Jin, Lanna S" uniqKey="Jin L" first="Lanna S" last="Jin">Lanna S. Jin</name><affiliation wicri:level="1"><nlm:affiliation>Ecology & Evolutionary Biology, University of Toronto, Room 3055, Toronto, M5S 3B2, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Ecology & Evolutionary Biology, University of Toronto, Room 3055, Toronto, M5S 3B2</wicri:regionArea></affiliation></author><author><name sortKey="Mooers, Arne O" sort="Mooers, Arne O" uniqKey="Mooers A" first="Arne O" last="Mooers">Arne O. Mooers</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, Simon Fraser University, Burnaby, V5A 1S6, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Biology, Simon Fraser University, Burnaby, V5A 1S6</wicri:regionArea></affiliation></author><author><name sortKey="Pavoine, Sandrine" sort="Pavoine, Sandrine" uniqKey="Pavoine S" first="Sandrine" last="Pavoine">Sandrine Pavoine</name><affiliation wicri:level="1"><nlm:affiliation>Centre of Ecology and Conservation Sciences (UMR 7204 CESCO), Museum National d'Histoire Naturelle, Paris, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Centre of Ecology and Conservation Sciences (UMR 7204 CESCO), Museum National d'Histoire Naturelle, Paris</wicri:regionArea></affiliation></author><author><name sortKey="Purschke, Oliver" sort="Purschke, Oliver" uniqKey="Purschke O" first="Oliver" last="Purschke">Oliver Purschke</name><affiliation wicri:level="1"><nlm:affiliation>German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, DE-04103, Leipzig, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, DE-04103, Leipzig</wicri:regionArea></affiliation></author><author><name sortKey="Redding, David W" sort="Redding, David W" uniqKey="Redding D" first="David W" last="Redding">David W. Redding</name><affiliation wicri:level="1"><nlm:affiliation>Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, U.K.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT</wicri:regionArea></affiliation></author><author><name sortKey="Rosauer, Dan F" sort="Rosauer, Dan F" uniqKey="Rosauer D" first="Dan F" last="Rosauer">Dan F. Rosauer</name><affiliation wicri:level="1"><nlm:affiliation>Research School of Biology, Australian National University, Acton, 2601, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Research School of Biology, Australian National University, Acton, 2601</wicri:regionArea></affiliation></author><author><name sortKey="Winter, Marten" sort="Winter, Marten" uniqKey="Winter M" first="Marten" last="Winter">Marten Winter</name><affiliation wicri:level="1"><nlm:affiliation>German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, DE-04103, Leipzig, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, DE-04103, Leipzig</wicri:regionArea></affiliation></author><author><name sortKey="Mazel, Florent" sort="Mazel, Florent" uniqKey="Mazel F" first="Florent" last="Mazel">Florent Mazel</name><affiliation wicri:level="1"><nlm:affiliation>Laboratoire d'Ecologie Alpine (LECA), CNRS - Université Grenoble Alpes (UMR 5553), BP 53, 38041, Grenoble Cedex 9, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire d'Ecologie Alpine (LECA), CNRS - Université Grenoble Alpes (UMR 5553), BP 53, 38041, Grenoble Cedex 9</wicri:regionArea></affiliation></author></analytic><series><title level="j">Biological reviews of the Cambridge Philosophical Society</title><idno type="eISSN">1469-185X</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 use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub-disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub-disciplines hampers potential meta-analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo-diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo-diversity metrics based on their mathematical form within these three dimensions and identify 'anchor' representatives: for α-diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">26785932</PMID><DateCreated><Year>2016</Year><Month>03</Month><Day>14</Day></DateCreated><DateRevised><Year>2017</Year><Month>09</Month><Day>22</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1469-185X</ISSN><JournalIssue CitedMedium="Internet"><Volume>92</Volume><Issue>2</Issue><PubDate><Year>2017</Year><Month>May</Month></PubDate></JournalIssue><Title>Biological reviews of the Cambridge Philosophical Society</Title><ISOAbbreviation>Biol Rev Camb Philos Soc</ISOAbbreviation></Journal><ArticleTitle>A guide to phylogenetic metrics for conservation, community ecology and macroecology.</ArticleTitle><Pagination><MedlinePgn>698-715</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/brv.12252</ELocationID><Abstract><AbstractText>The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub-disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub-disciplines hampers potential meta-analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo-diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo-diversity metrics based on their mathematical form within these three dimensions and identify 'anchor' representatives: for α-diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices.</AbstractText><CopyrightInformation>© 2016 The Authors. Biological Reviews published by John Wiley © Sons Ltd on behalf of Cambridge Philosophical Society.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tucker</LastName><ForeName>Caroline M</ForeName><Initials>CM</Initials><AffiliationInfo><Affiliation>Department of Ecology and Evolutionary Biology, University of Colorado, Box 334, Boulder, CO, 80309-0334, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cadotte</LastName><ForeName>Marc W</ForeName><Initials>MW</Initials><AffiliationInfo><Affiliation>Biological Sciences, University of Toronto-Scarborough, Scarborough, M1C 1A4, Canada.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Stake Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong, Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Carvalho</LastName><ForeName>Silvia B</ForeName><Initials>SB</Initials><AffiliationInfo><Affiliation>CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, 4485-661, Vairão, Portugal.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Davies</LastName><ForeName>T Jonathan</ForeName><Initials>TJ</Initials><AffiliationInfo><Affiliation>Department of Biology, McGill University, Montréal, H3A 1B1, Canada.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>African Centre for DNA Barcoding, University of Johannesburg, PO Box 524, Johannesburg, 2006, South Africa.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ferrier</LastName><ForeName>Simon</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>CSIRO Ecosystem Sciences, Climate Adaptation Flagship, GPO BOX 1600, Canberra, 2601, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fritz</LastName><ForeName>Susanne A</ForeName><Initials>SA</Initials><AffiliationInfo><Affiliation>Biodiversity & Climate Research Centre (BiK-F) and Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt am Main, Germany.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institute of Ecology, Evolution and Diversity, Goethe University, 60438, Frankfurt, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Grenyer</LastName><ForeName>Rich</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>School of Geography and the Environment, University of Oxford, Oxford, OX1 3QY, U.K.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Helmus</LastName><ForeName>Matthew R</ForeName><Initials>MR</Initials><AffiliationInfo><Affiliation>Department of Ecological Sciences - Animal Ecology, Vrije Universiteit, Amsterdam, Netherlands.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Biodiversity, Department of Biology, Temple University, Suite 502, Philadelphia, PA, 19122, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jin</LastName><ForeName>Lanna S</ForeName><Initials>LS</Initials><AffiliationInfo><Affiliation>Ecology & Evolutionary Biology, University of Toronto, Room 3055, Toronto, M5S 3B2, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mooers</LastName><ForeName>Arne O</ForeName><Initials>AO</Initials><AffiliationInfo><Affiliation>Department of Biology, Simon Fraser University, Burnaby, V5A 1S6, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pavoine</LastName><ForeName>Sandrine</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Centre of Ecology and Conservation Sciences (UMR 7204 CESCO), Museum National d'Histoire Naturelle, Paris, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Zoology, University of Oxford, Oxford, OX1 3QY, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Purschke</LastName><ForeName>Oliver</ForeName><Initials>O</Initials><AffiliationInfo><Affiliation>German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, DE-04103, Leipzig, Germany.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Geobotany and Botanical Garden, Institute of Biology, Martin Luther University, Halle-Wittenberg, DE-06108, Halle (Saale), Germany.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Computer Science, Martin-Luther-University, Halle-Wittenberg, DE-06120, Halle (Saale), Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Redding</LastName><ForeName>David W</ForeName><Initials>DW</Initials><AffiliationInfo><Affiliation>Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, U.K.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rosauer</LastName><ForeName>Dan F</ForeName><Initials>DF</Initials><AffiliationInfo><Affiliation>Research School of Biology, Australian National University, Acton, 2601, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Winter</LastName><ForeName>Marten</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, DE-04103, Leipzig, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mazel</LastName><ForeName>Florent</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Laboratoire d'Ecologie Alpine (LECA), CNRS - Université Grenoble Alpes (UMR 5553), BP 53, 38041, Grenoble Cedex 9, France.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>281422</GrantID><Agency>European Research 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history</Keyword><Keyword MajorTopicYN="N">phylogenetic diversity</Keyword><Keyword MajorTopicYN="N">prioritization</Keyword><Keyword MajorTopicYN="N">range size</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>05</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2015</Year><Month>12</Month><Day>01</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>12</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>1</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>1</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>1</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26785932</ArticleId><ArticleId IdType="doi">10.1111/brv.12252</ArticleId><ArticleId IdType="pmc">PMC5096690</ArticleId><ArticleId IdType="mid">EMS66864</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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