title: A guide to phylogenetic metrics for conservation, community ecology and macroecology.
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.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Colorado, Box 334, Boulder, CO, 80309-0334, U.S.A.
authors.forename: Caroline M
authors.initials: CM
authors.lastname: Tucker
authors.affiliation: Biological Sciences, University of Toronto-Scarborough, Scarborough, M1C 1A4, Canada.|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.
authors.forename: Marc W
authors.initials: MW
authors.lastname: Cadotte
authors.affiliation: CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, 4485-661, Vairão, Portugal.
authors.forename: Silvia B
authors.initials: SB
authors.lastname: Carvalho
authors.affiliation: Department of Biology, McGill University, Montréal, H3A 1B1, Canada.|African Centre for DNA Barcoding, University of Johannesburg, PO Box 524, Johannesburg, 2006, South Africa.
authors.forename: T Jonathan
authors.initials: TJ
authors.lastname: Davies
authors.affiliation: CSIRO Ecosystem Sciences, Climate Adaptation Flagship, GPO BOX 1600, Canberra, 2601, Australia.
authors.forename: Simon
authors.initials: S
authors.lastname: Ferrier
authors.affiliation: Biodiversity & Climate Research Centre (BiK-F) and Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt am Main, Germany.|Institute of Ecology, Evolution and Diversity, Goethe University, 60438, Frankfurt, Germany.
authors.forename: Susanne A
authors.initials: SA
authors.lastname: Fritz
authors.affiliation: School of Geography and the Environment, University of Oxford, Oxford, OX1 3QY, U.K.
authors.forename: Rich
authors.initials: R
authors.lastname: Grenyer
authors.affiliation: Department of Ecological Sciences - Animal Ecology, Vrije Universiteit, Amsterdam, Netherlands.|Center for Biodiversity, Department of Biology, Temple University, Suite 502, Philadelphia, PA, 19122, U.S.A.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Helmus
authors.affiliation: Ecology & Evolutionary Biology, University of Toronto, Room 3055, Toronto, M5S 3B2, Canada.
authors.forename: Lanna S
authors.initials: LS
authors.lastname: Jin
authors.affiliation: Department of Biology, Simon Fraser University, Burnaby, V5A 1S6, Canada.
authors.forename: Arne O
authors.initials: AO
authors.lastname: Mooers
authors.affiliation: Centre of Ecology and Conservation Sciences (UMR 7204 CESCO), Museum National d'Histoire Naturelle, Paris, France.|Department of Zoology, University of Oxford, Oxford, OX1 3QY, UK.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Pavoine
authors.affiliation: German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, DE-04103, Leipzig, Germany.|Geobotany and Botanical Garden, Institute of Biology, Martin Luther University, Halle-Wittenberg, DE-06108, Halle (Saale), Germany.|Department of Computer Science, Martin-Luther-University, Halle-Wittenberg, DE-06120, Halle (Saale), Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Purschke
authors.affiliation: Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, U.K.
authors.forename: David W
authors.initials: DW
authors.lastname: Redding
authors.affiliation: Research School of Biology, Australian National University, Acton, 2601, Australia.
authors.forename: Dan F
authors.initials: DF
authors.lastname: Rosauer
authors.affiliation: German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, DE-04103, Leipzig, Germany.
authors.forename: Marten
authors.initials: M
authors.lastname: Winter
authors.affiliation: Laboratoire d'Ecologie Alpine (LECA), CNRS - Université Grenoble Alpes (UMR 5553), BP 53, 38041, Grenoble Cedex 9, France.
authors.forename: Florent
authors.initials: F
authors.lastname: Mazel
mesh_terms: D044822:Biodiversity; D005075:Biological Evolution; D003247:Conservation of Natural Resources / Q000379:methods*; D004463:Ecology / Q000379:methods*; D010802:Phylogeny
keywords: biodiversity hotspots; biogeography; community assembly; conservation; diversity metrics; evolutionary history; phylogenetic diversity; prioritization; range size