A guide to phylogenetic metrics for conservation, community ecology and macroecology

Biological Reviews

Volumn 92, Issue 2, 2017, Pages 698-715

  Tucker, Caroline M ^a   Cadotte, Marc W ^b,c   Carvalho, Silvia B ^d   Jonathan Davies, T ^e,f   Ferrier, Simon ^g   Fritz, Susanne A ^h,i   Grenyer, Rich ^j   Helmus, Matthew R ^k,l   Jin, Lanna S ^b   Mooers, Arne O ^m   Pavoine, Sandrine ^n,o   Purschke, Oliver ^p,q   Redding, David W ^r   Rosauer, Dan F ^s   Winter, Marten ^p   Mazel, Florent ^t  

^a UNIVERSITY OF COLORADO   (United States)

^b UNIVERSITY OF TORONTO   (Canada)

^c SUN YAT SEN UNIVERSITY   (China)

^d CENTRO DE INVESTIGAÇÃO EM BIODIVERSIDADE E RECURSOS GENÉTICOS   (Portugal)

^e MCGILL UNIVERSITY   (Canada)

^f UNIVERSITY OF JOHANNESBURG   (South Africa)

^g CSIRO   (Australia)

^h SENCKENBERG DEUTSCHES ENTOMOLOGISCHES INSTITUT   (Germany)

ⁱ GOETHE UNIVERSITY   (Germany)

^j UNIVERSITY OF OXFORD   (United Kingdom)

^k VU UNIVERSITY AMSTERDAM   (Netherlands)

^l Temple University   (United States)

^m SIMON FRASER UNIVERSITY   (Canada)

ⁿ MUSÉUM NATIONAL D'HISTOIRE NATURELLE   (France)

^o UNIVERSITY OF OXFORD   (United Kingdom)

^p GERMAN CENTRE FOR INTEGRATIVE BIODIVERSITY RESEARCH IDIV HALLE JENA LEIPZIG   (Germany)

^q MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

^r UNIVERSITY COLLEGE LONDON   (United Kingdom)

^s AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^t UNIV GRENOBLE ALPES   (France)

more..

Author keywords

Biodiversity hotspots; Biogeography; Community assembly; Conservation; Diversity metrics; Evolutionary history; Phylogenetic diversity; Prioritization; Range size

Indexed keywords

BIODIVERSITY; ECOLOGY; ENVIRONMENTAL PROTECTION; EVOLUTION; PHYLOGENY; PROCEDURES;

BIODIVERSITY; BIOLOGICAL EVOLUTION; CONSERVATION OF NATURAL RESOURCES; ECOLOGY; PHYLOGENY;

EID: 85016126000     PISSN: 14647931     EISSN: 1469185X     Source Type: Journal    
DOI: 10.1111/brv.12252     Document Type: Article

References (108)

1. Ackerly, D. (2009). Conservatism and diversification of plant functional traits: evolutionary rates versus phylogenetic signal. Proceedings of the National Academy of Sciences of the United States of America 106, 19699–19706.
2. Allen, B.L.,Kon, M.&Bar-Yam, Y.(2009). A new phylogenetic diversity measure generalizing the shanno index and its application to phyllostomid bats. American Naturalist 174, 236.
3. Barker, G. M. (2002). Phylogenetic diversity: a quantitative framework for measurement of priority and achievement in biodiversity conservation. Biological Journal of the Linnean Society 76, 165–194.
4. Beck, J.,Ballesteros-Mejia, L.,Buchmann, C.M.,Dengler, J.,Fritz, S.A., Gruber, B.,Hof, C.,Jansen, F., Knapp, S.&Kreft, H.(2012). What’s on the horizon for macroecology? Ecography 35, 673–683.
5. Bennett, J.R.,Elliott, G.,Mellish, B.,Joseph, L.N.,Tulloch, A.I.T., Probert, W.J.M.,Di Fonzo, M.M.I.,Monks, J.M.,Possingham, H.P. & Maloney, R.(2014). Balancing phylogenetic diversity and species numbers in conservation prioritization, using a case study of threatened species in New Zealand. Biological Conservation 174, 47–54.
6. Blomberg, S.P.,Garland,T.&Ives,A.R.(2003). Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57, 717–745.
7. Bryant, J.A.,Lamanna, C.,Morlon, H.,Kerkhoff, A.J.,Enquist, B.J.& Green,J.L.(2008). Microbes on mountainsides: contrasting elevational patterns of bacterial and plant diversity. Proceedings of the National Academy of Sciences of the United States of America 105, 11505–11511.
8. Cadotte, M. W. (2013). Experimental evidence that evolutionarily diverse assemblages result in higher productivity. Proceedings of the National Academy of Sciences of the United States of America 110, 8996–9000.
9. Cadotte, M.W.,Cavender-Bares, J.,Tilman, D.&Oakley, T.H.(2009). Using phylogenetic, functional and trait diversity to understand patterns of plant community productivity. PLoS One 4, e5695.
10. Cadotte, M.W.&Davies, T.J.(2010). Rarest of the rare: advances in combining evolutionary distinctiveness and scarcity to inform conservation at biogeographical scales. Diversity and Distributions 16, 376–384.
11. Cadotte, M.W.,Davies, T.J.,Regetz, J.,Kembel, S.W.,Cleland, E.& Oakley, T.H.(2010). Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history. Ecology Letters 13, 96–105.
12. Cavender-Bares, J.,Kozak, K.H.,Fine, P.V.A.&Kembel, S.W.(2009). The merging of community ecology and phylogenetic biology. Ecology Letters 12, 693–715.
13. Cavender-Bares,J.&Wilczek,A.(2003). Integrating micro-and macroevolution-ary processes in community ecology. Ecology 84, 592–597.
14. Chao, A.,Chiu, C.-H.&Jost, L.(2010). Phylogenetic diversity measures based on Hill numbers. Philosophical Transactions of the Royal Society, B: Biological Sciences 365, 3599–3609.
15. Chao, A.,Chiu, C.-H.&Jost, L.(2014). Unifying species diversity, phylogenetic diversity, functional diversity, and related similarity and differentiation measures through Hill numbers. Annual Review of Ecology, Evolution, and Systematics 45, 297–324.
16. Chen, J.,Bittinger, K.,Charlson, E.S.,Hoffmann, C.,Lewis, J.,Wu, G. D., Collman, R.G.,Bushman, F.D.&Li, H.(2012). Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics 28, 2106–2113.
17. Chiu, C.-H.,Jost, L.&Chao, A.(2014). Phylogenetic beta diversity, similarity, and differentiation measures based on Hill numbers. Ecological Monographs 84, 21–44.
18. Clarke, K.&Warwick, R.(1998). Quantifying structural redundancy in ecological communities. Oecologia 113, 278–289.
19. Clarke, K. & Warwick, R. (2001). A further biodiversity index applicable to species lists: variation in taxonomic distinctness. Marine Ecology Progress Series 216, 265–278.
20. Colless, D.(1982). Review of phylogenetics: the theory and practice of phylogenetic systematics. Systematic Zoology 31, 100–104.
21. Connolly, J.,Cadotte, M.W.,Brophy, C.,Dooley, Á., Finn, J.,Kirwan, L., Roscher, C.&Weigelt, A.(2011). Phylogenetically diverse grasslands are associated with pairwise interspecific processes that increase biomass. Ecology 92, 1385–1392.
22. Crozier,R.H.(1992). Genetic diversity and the agony of choice. Biological Conservation 61, 11–15.
23. Davies, T.J.&Buckley, L.B.(2011). Phylogenetic diversity as a window into the evolutionary and biogeographic histories of present-day richness gradients for mammals. Philosophical Transactions of the Royal Society, B: Biological Sciences 366, 2414–2425.
24. Davies, T.J.&Cadotte, M.W.(2011). Quantifying biodiversity–does it matter what we measure?. In Biodiversity Hotspots (eds F. E. Zachos and J. C. Habel), pp. 43–60. Springer, Heidelberg.
25. Dehling, D.,Fritz, S.A.,Topfer, T.&Packert, M.(2014). Functional and phylogenetic diversity and assemblage structure of frugivorous birds along an elevational gradient in the tropical Andes. Ecography 37, 1047–1055.
26. Dormann, C. F., Gruber, B.,Winter, M.&Herrmann, D.(2009). Evolution of climate niches in European mammals? Biology Letters 6, 229–232.
27. Faith, D.P.(1992). Conservation evaluation and phylogenetic diversity. Biological Conservation 61, 1–10.
28. Faith,D.P.(2008). Phylogenetic Diversity and Conservation. Oxford University Press, New York.
29. Forest, F., Grenyer, R.,Rouget, M.,Davies, T.J.,Cowling, R.M.,Faith, D. P., Balmford, A.,Manning, J.,Proches, S.,van der Bank, M.,Reeves, G., Hedderson, T.A.J.&Savolainen, V.(2007). Preserving the evolutionary potential of floras in biodiversity hotspots. Nature 445, 757–760.
30. Freckleton, R.P.,Harvey, P.H.&Pagel, M.(2002). Phylogenetic analysis and comparative data: a test and review of evidence. The American Naturalist 160, 712–726.
31. Fritz, S. A. & Rahbek, C. (2012). Global patterns of amphibian phylogenetic diversity. Journal of Biogeography 39, 1373–1382.
32. Gerhold, P., Cahill, J.F. Jr., Winter, M., Bartish, I. & Prinzing, A.(2015). Phylogenetic patterns are not proxies of community assembly mechanisms (they are far better). Functional Ecology 29, 600–614.
33. Gerhold, P.,Pärtel, M.,Tackenberg, O., Hennekens, S.M.,Bartish, I., Schaminée, J. H., Fergus, A. J., Ozinga, W. A. & Prinzing, A. (2011). Phylogenetically poor plant communities receive more alien species, which more easily coexist with natives. The American Naturalist 177, 668–680.
34. Hardy, O.J.&Jost, L.(2008). Interpreting and estimating measures of community phylogenetic structuring. Journal of Ecology 96, 849–852.
35. Hardy, O.J.&Senterre, B.(2007). Characterizing the phylogenetic structure of communities by an additive partitioning of phylogenetic diversity. Journal of Ecology 95, 493–506.
36. Harmon, L.J.,Weir, J.T.,Brock, C.,Glor, R.E.&Challenger, W.(2008). GEIGER: investigating evolutionary radiations. Bioinformatics 24, 129–131.
37. Harvey, P.H.&Pagel, M.(1991). The Comparative Method in Evolutionary Biology. Oxford University Press, Oxford.
38. Heard, S.B. & Cox, G.H.(2007). The shapes of phylogenetic trees of clades, faunas, and local assemblages: exploring spatial pattern in differential diversification. The American Naturalist 169, E107–E118.
39. Helmus, M.R.,Bland, T.J.,Williams, C.K.&Ives, A.R.(2007). Phylogenetic measures of biodiversity. The American Naturalist 169, E68–E83.
40. Helmus, M.R.,Keller, W.,Paterson, M.J.,Yan, N.D.,Cannon, C.H.& Rusak, J.A.(2010). Communities contain closely related species during ecosystem disturbance. Ecology Letters 13, 162–174.
41. Hill,M.O.(1973). Diversity and evenness: a unifying notation and its consequences. Ecology 54, 427–431.
42. Isaac, N.J.B.(2007). Mammals on the edge: conservation priorities based on threat and phylogeny. PLoS One 2, e296.
43. Ives, A.R.&Helmus, M.R.(2010). Phylogenetic metrics of community similarity. The American Naturalist 176, E128–E142.
44. Izsák, J.&Papp, L.(2000). A link between ecological diversity indices and measures of biodiversity. Ecological Modelling 130, 151–156.
45. Izsák, J.&Szeidl, L.(2002). Quadratic diversity: its maximization can reduce the richness of species. Environmental and Ecological Statistics 9, 423–430.
46. Jetz, W.,Thomas, G.,Joy, J.,Hartmann, K.&Mooers, A.(2012). The global diversity of birds in space and time. Nature 491, 444–448.
47. Jetz, W.,Thomas, G.,Joy, J.,Redding, D.W.,Hartmann, K.&Mooers, A. O. (2014). Global distribution and conservation of evolutionary distinctness in birds. Current Biology 24, 919–930.
48. Jin,L.S.,Cadotte,M.W.&Fortin,M.-J.(2015). Phylogenetic turnover implicates niche conservatism in montane plant species. Journal of Ecology 103, 742–749.
49. Jost, L.(2006). Entropy and diversity. Oikos 113, 363–375.
50. Jost, L.(2007). Partitioning diversity into independent alpha and beta components. Ecology 88, 2427–2439.
51. Kelly, S.,Grenyer, R.&Scotland, R.W.(2014). Phylogenetic trees do not reliably predict feature diversity. Diversity and Distributions 20, 600–612.
52. Kembel, S.W.,Cowan, P.D.,Helmus, M.R.,Cornwell, W.K.,Morlon, H., Ackerly, D.D.,Blomberg, S.P.&Webb, C.O.(2010). Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26, 1463–1464.
53. Kraft, N. J., Valencia, R. & Ackerly, D. D. (2008). Functional traits and niche-based tree community assembly in an Amazonian forest. Science 322, 580–582.
54. Leinster, T.&Cobbold, C.A.(2012). Measuring diversity: the importance of species similarity. Ecology 93, 477–489.
55. Lozupone,C.A.,Hamady,M.,Kelley,S.T.&Knight,R.W.(2007). Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Applied and Environmental Microbiology 73, 1576–1578.
56. Lozupone, C.A.&Knight, R.W.(2005). UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology 71, 8228–8235.
57. MacArthur,R.H.&Wilson,E.O.(1967). The Theory of Island Biogeography. Princeton University Press, Princeton.
58. Mace,G.M.,Gittleman,J.L.&Purvis,A.(2003). Preserving the tree of life. Science 300, 1707–1709.
59. Mayfield, M.M.&Levine, J.M.(2010). Opposing effects of competitive exclusion on the phylogenetic structure of communities. Ecology Letters 13, 1085–1093.
60. Miller,E.T.,Zanne,A.E.&Ricklefs,R.E.(2013). Niche conservatism constrains Australian honeyeater assemblages in stressful environments. Ecology Letters 16, 1186–1194.
61. Mouchet, M.A.&Mouillot, D.(2011). Decomposing phylogenetic entropy into α, β and γ components. Biology Letters 7, 205–209.
62. Mouillot, D., Mason, N.W., Dumany, O. & Wilson, J.B.(2005). Functional regularity: a neglected aspect of functional diversity. Oecologia 142, 353–359.
63. Mouquet, N., Devictor, V., Meynard, C. N., Munoz, F., Bersier, L. F., Chave, J.,Couteron, P.,Dalecky, A.,Fontaine, C.&Gravel, D.(2012). Ecophylogenetics: advances and perspectives. Biological Reviews 87, 769–785.
64. Narwani,A.,Alexandrou,M.A.,Oakley,T.H.,Carroll,I.T.&Cardinale, B. J. (2013). Experimental evidence that evolutionary relatedness does not affect the ecological mechanisms of coexistence in freshwater green algae. Ecology Letters 16, 1373–1381.
65. Nipperess, D. A., Faith, D. P. & Barton, K. (2010). Resemblance in phylogenetic diversity among ecological assemblages. Journal of Vegetation Science 21, 809–820.
66. *Paradis, E.,Claude, J.&Strimmer, K.(2004). APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289–290.
67. Pavoine, S.&Bonsall, M.(2011). Measuring biodiversity to explain community assembly: a unified approach. Biological Reviews 86, 792–812.
68. Pavoine,S.,Gasc,A.,Bonsall,M.&Mason,N.W.(2013). Correlations between phylogenetic and functional diversity: mathematical artefacts or true ecological and evolutionary processes. Journal of Vegetation Science 24, 781–793.
69. *Pavoine, S.&Izsák, J.(2014). New biodiversity measure that includes consistent interspecific and intraspecific components. Methods in Ecology and Evolution 5, 165–172.
70. Pavoine, S., Love, M. S. & Bonsall, M. B. (2009). Hierarchical partitioning of evolutionary and ecological patterns in the organization of phylogenetically-structured species assemblages: application to rockfish (genus: Sebastes) in the Southern California Bight. Ecology Letters 12, 898–908.
71. Pavoine, S., Ollier, S. & Pontier, D. (2005). Measuring diversity from dissimilarities with Rao’s quadratic entropy: are any dissimilarities suitable? Theoretical Population Biology 67, 231–239.
72. Pavoine, S.&Ricotta, C.(2014). Functional and phylogenetic similarity among communities. Methods in Ecology and Evolution 5, 666–675.
73. Pearse, W.D.,Cadotte, M.W.,Cavender-Bares, J.,Ives, A.R.,Tucker, C. M., Walker, S. & Helmus, M. R. (2015). pez: phylogenetics for the environmental sciences. Bioinformatics, btv277.
74. Pearse, W.D.,Cavender-Bares, J.,Purvis, A.&Helmus, M.R.(2014). Metrics and models of community phylogenetics. In Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology (edL.Z.Garamszegi), pp. 451–454. Springer-Verlag, Berlin.
75. Pigot, A.L.&Etienne, R.S.(2015). A dynamic null model for phylogenetic community structure. Ecology Letters 18, 153–163.
76. Purschke, O., Schmid,B.,Sykes,M.T.,Poschlod,P.,Michalski,S.G.,Durka, W., Kuhn, I.,Winter, M.&Prentice, H.C.(2013). Contrasting changes in taxonomic, phylogenetic and functional diversity during a long-term succession: insights into assembly processes. Journal of Ecology 101, 857–866.
77. Purvis,A.(2008). Phylogenetic approaches to the study of extinction. Annual Review of Ecology, Evolution, and Systematics 39, 301–319.
78. Purvis, A.,Agapow, P.M.,Gittleman, J.L.&Mace, G.M.(2000). Nonrandom extinction and the loss of evolutionary history. Science 288, 328–330.
79. Purvis, A.,Fritz, S.A.,Rodríguez, J.,Harvey, P.H.&Grenyer, R.(2011). The shape of mammalian phylogeny: patterns, processes and scales. Philosophical Transactions of the Royal Society, B: Biological Sciences 366, 2462–2477.
80. Pybus, O. & Harvey, P. H. (2000). Testing macro-evolutionary models using incomplete molecular phylogenies. Proceedings of the Royal Society B: Biological Sciences 267, 2267–2272.
81. Rao,R.C.(1982). Diversity and dissimilarity coefficients: a unified approach. Theoretical Population Biology 21, 24–43.
82. Redding, D.W.(2003). Incorporating genetic distinctness and reserve occupancy into a conservation prioritisation approach. Masters Thesis: University of East Anglia, Norwich.
83. Ricotta,C.(2007). A semantic taxonomy for diversity measures. Acta Biotheoretica 55, 23–33.
84. Rodrigues, A.S.L., Brooks, T.M. & Gaston, K.J.(2005). Integrating phylogenetic diversity in the selection of priority areas for conservation: does it make a difference?. In Phylogeny and Conservation (eds A. Purvis, J.L.Gittleman and T. M. Brooks), pp. 101–199. Cambridge University Press, Cambridge.
85. Rodrigues, A. S. L., Grenyer, R., Baillie, J. E. M., Bininda-Emonds, O. R. P., Gittleman, J.L.,Hoffmann, M.,Safi, K.,Schipper, J.,Stuart, S. N. & Brooks, T.M.(2011). Complete, accurate, mammalian phylogenies aid conservation planning, but not much. Philosophical Transactions of the Royal Society of London B 1579, 2652–2660.
86. Rosauer,D.,Laffan,S.W.,Crisp,M.D.,Donnellan,S.C.&Cook,L.G.(2009). Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history. Molecular Ecology 18, 4061–4072.
87. Rosauer, D.F.&Mooers, A.O.(2013). Nurturing the use of evolutionary diversity in nature conservation. Trends in Ecology & Evolution 28, 322–323.
88. Safi, K.,Armour-Marshall, K.,Baillie, J.E.M.&Isaac, N.J.B.(2013). Global patterns of evolutionary distinct and globally endangered amphibians and mammals. PLoS One 8, e63582.
89. Scheiner,S.M.(2012). A metric of biodiversity that integrates abundance, phylogeny, and function. Oikos 121, 1191–1202.
90. Schweiger, O., Klotz, S.,Durka, W.&Kuhn, I.(2008). A comparative test of phylogenetic diversity indices. Oecologia 157, 485–495.
91. Srivastava,D.S.,Cadotte,M.W.,MacDonald,A.A.M.,Marushia,R.G.& Mirotchnick,N.(2012). Phylogenetic diversity and the functioning of ecosystems. Ecology Letters 15, 637–648.
92. Swenson, N.G.(2011). Phylogenetic beta diversity metrics, trait evolution and inferring the functional beta diversity of communities. PLoS One 6, e21264.
93. Thuiller, W.,Lavergne, S.,Roquet, C.,Boulangeat, I.,Lafourcade, B.& Araujo,M.B.(2011). Consequences of climate change on the tree of life in Europe. Nature 470, 531–534.
94. Tucker, C.M.&Cadotte, M.W.(2013). Unifying measures of biodiversity: understanding when richness and phylogenetic diversity should be congruent. Diversity and Distributions 19, 845–854.
95. Tucker, C.M.,Cadotte, M.W.,Davies, T.J.&Rebelo, A.G.(2012). The distribution of biodiversity: linking richness to geographical and evolutionary rarity in a biodiversity hotspot. Conservation Biology 25, 593–601.
96. Underwood, A. J. (1997). Experiments in Ecology. Cambridge University Press, Cambridge.
97. Vane-Wright, R. I., Humphries, C. J. & Williams, P. H. (1991). What to protect?–Systematics and the agony of choice. Biological Conservation 55, 235–254.
98. Vellend, M., Cornwell, W.K., Magnuson-Ford, K. & Mooers, A.Ø.(2010). Measuring phylogenetic biodiversity. In Biological Diversity: Frontiers in Measurement and Assessment (eds A. E. Magurran and B. J. McGill), pp. 194–207. Oxford University Press, Oxford.
99. Villéger, S., Mason, N. W. & Mouillot, D. (2008). New multidimensional functional diversity indices for a multifaceted framework in functional ecology. Ecology 89, 2290–2301.
100. Violle, C., Nemergut, D.R., Pu, Z. & Jiang, L.(2011). Phylogenetic limiting similarity and competitive exclusion. Ecology Letters 14, 782–787.
101. Webb, C.O.(2000). Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. The American Naturalist 156, 145–155.
102. Webb, C. O., Ackerly, D.D.&Kembel, S.W.(2008). Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 24, 2098–2100.
103. Webb, C. O., Ackerly, D. D., McPeek, M. A. & Donoghue, M. J. (2002). Phylogenies and community ecology. Annual Review of Ecology, Evolution, and Systematics 33, 475–505.
104. Weiher, E.&Keddy, P.A.(1995). Assembly rules, null models, and trait dispersion: new questions from old patterns. Oikos 74, 159–164.
105. Weir,J.T.&Schluter,D.(2007). The latitudinal gradient in recent speciation and extinction rates of birds and mammals. Science 315, 1574–1576.
106. Wiens,J.J.&Donoghue,M.J.(2004). Historical biogeography, ecology and species richness. Trends in Ecology & Evolution 19, 639–644.
107. Winter, M.,Devictor, V.&Schweiger, O.(2013). Phylogenetic diversity and nature conservation: where are we? Trends in Ecology & Evolution 28, 199–204.
108. Winter, M., Schweiger, O., Klotz, S., Nentwig, W., Andriopoulos, P., Arianoutsou, M., Basnou, C., Delipetrou, P., Didžiulis, V., Hejda, M., Hulme, P.E., Lambdon, P.W., Pergl, J., Pysek, P., Roy, D.P. & Kuhn, I. (2009). Plant extinctions and introductions lead to phylogenetic and taxonomic homogenization of the European flora. Proceedings of the National Academy of Sciences of the United States of America 106, 21721–21725.