A guide to phylogenetic metrics for conservation, community ecology and macroecology.
Identifieur interne : 001293 ( Main/Exploration ); précédent : 001292; suivant : 001294A 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
Affiliations:
- Allemagne, Australie, Canada, France, Pays-Bas, Portugal, Royaume-Uni, États-Unis
- Angleterre, District de Darmstadt, District de Leipzig, Grand Londres, Hesse (Land), Hollande-Septentrionale, Ontario, Oxfordshire, Québec, Saxe (Land), Île-de-France
- Amsterdam, Francfort-sur-le-Main, Leipzig, Londres, Montréal, Oxford, Paris, Toronto
- University College de Londres, Université McGill, Université d'Oxford, Université de Toronto
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Le document en format XML
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<region type="district" nuts="2">District de Leipzig</region>
<settlement type="city">Leipzig</settlement>
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</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>
<wicri:noRegion>38041, Grenoble Cedex 9</wicri:noRegion>
<wicri:noRegion>38041, Grenoble Cedex 9</wicri:noRegion>
</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>
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<profileDesc><textClass></textClass>
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<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>
<affiliations><list><country><li>Allemagne</li>
<li>Australie</li>
<li>Canada</li>
<li>France</li>
<li>Pays-Bas</li>
<li>Portugal</li>
<li>Royaume-Uni</li>
<li>États-Unis</li>
</country>
<region><li>Angleterre</li>
<li>District de Darmstadt</li>
<li>District de Leipzig</li>
<li>Grand Londres</li>
<li>Hesse (Land)</li>
<li>Hollande-Septentrionale</li>
<li>Ontario</li>
<li>Oxfordshire</li>
<li>Québec</li>
<li>Saxe (Land)</li>
<li>Île-de-France</li>
</region>
<settlement><li>Amsterdam</li>
<li>Francfort-sur-le-Main</li>
<li>Leipzig</li>
<li>Londres</li>
<li>Montréal</li>
<li>Oxford</li>
<li>Paris</li>
<li>Toronto</li>
</settlement>
<orgName><li>University College de Londres</li>
<li>Université McGill</li>
<li>Université d'Oxford</li>
<li>Université de Toronto</li>
</orgName>
</list>
<tree><country name="États-Unis"><noRegion><name sortKey="Tucker, Caroline M" sort="Tucker, Caroline M" uniqKey="Tucker C" first="Caroline M" last="Tucker">Caroline M. Tucker</name>
</noRegion>
</country>
<country name="Canada"><noRegion><name sortKey="Cadotte, Marc W" sort="Cadotte, Marc W" uniqKey="Cadotte M" first="Marc W" last="Cadotte">Marc W. Cadotte</name>
</noRegion>
<name sortKey="Davies, T Jonathan" sort="Davies, T Jonathan" uniqKey="Davies T" first="T Jonathan" last="Davies">T Jonathan Davies</name>
<name sortKey="Jin, Lanna S" sort="Jin, Lanna S" uniqKey="Jin L" first="Lanna S" last="Jin">Lanna S. Jin</name>
<name sortKey="Mooers, Arne O" sort="Mooers, Arne O" uniqKey="Mooers A" first="Arne O" last="Mooers">Arne O. Mooers</name>
</country>
<country name="Portugal"><noRegion><name sortKey="Carvalho, Silvia B" sort="Carvalho, Silvia B" uniqKey="Carvalho S" first="Silvia B" last="Carvalho">Silvia B. Carvalho</name>
</noRegion>
</country>
<country name="Australie"><noRegion><name sortKey="Ferrier, Simon" sort="Ferrier, Simon" uniqKey="Ferrier S" first="Simon" last="Ferrier">Simon Ferrier</name>
</noRegion>
<name sortKey="Rosauer, Dan F" sort="Rosauer, Dan F" uniqKey="Rosauer D" first="Dan F" last="Rosauer">Dan F. Rosauer</name>
</country>
<country name="Allemagne"><region name="Hesse (Land)"><name sortKey="Fritz, Susanne A" sort="Fritz, Susanne A" uniqKey="Fritz S" first="Susanne A" last="Fritz">Susanne A. Fritz</name>
</region>
<name sortKey="Purschke, Oliver" sort="Purschke, Oliver" uniqKey="Purschke O" first="Oliver" last="Purschke">Oliver Purschke</name>
<name sortKey="Winter, Marten" sort="Winter, Marten" uniqKey="Winter M" first="Marten" last="Winter">Marten Winter</name>
</country>
<country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Grenyer, Rich" sort="Grenyer, Rich" uniqKey="Grenyer R" first="Rich" last="Grenyer">Rich Grenyer</name>
</region>
<name sortKey="Redding, David W" sort="Redding, David W" uniqKey="Redding D" first="David W" last="Redding">David W. Redding</name>
</country>
<country name="Pays-Bas"><region name="Hollande-Septentrionale"><name sortKey="Helmus, Matthew R" sort="Helmus, Matthew R" uniqKey="Helmus M" first="Matthew R" last="Helmus">Matthew R. Helmus</name>
</region>
</country>
<country name="France"><region name="Île-de-France"><name sortKey="Pavoine, Sandrine" sort="Pavoine, Sandrine" uniqKey="Pavoine S" first="Sandrine" last="Pavoine">Sandrine Pavoine</name>
</region>
<name sortKey="Mazel, Florent" sort="Mazel, Florent" uniqKey="Mazel F" first="Florent" last="Mazel">Florent Mazel</name>
</country>
</tree>
</affiliations>
</record>
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