Phylogenetic trees do not reliably predict feature diversity

Diversity and Distributions

Volumn 20, Issue 5, 2014, Pages 600-612

  Kelly, Steven ^a   Grenyer, Richard ^a   Scotland, Robert W ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Feature diversity; Homoplasy; Phenotype; Phylogeny; Predictivity; Traits

Indexed keywords

CONSERVATION; DATA SET; DIVERGENCE; EVOLUTIONARY BIOLOGY; GLOBAL PERSPECTIVE; LIFE HISTORY TRAIT; META-ANALYSIS; PHENOTYPIC PLASTICITY; PHYLOGENETICS; PHYLOGENY; SPECIES DIVERSITY; TAXONOMY;

EID: 84897963696     PISSN: 13669516     EISSN: 14724642     Source Type: Journal    
DOI: 10.1111/ddi.12188     Document Type: Article

References (85)

1. APG. (1998) An ordinal classification for the families of flowering plants. Annals of the Missouri Botanical Garden, 85, 531-553.
2. Archie, J.W. (1984) A new look at the predictive value of numerical classifications. Systematic Zoology, 33, 30-51.
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. Bottjer, P.D. (1980) Farris information content and phylogenetic versus evolutionary classification - The philosophical differences remain. Systematic Zoology, 29, 382-386.
5. Bremer, B., Bremer, K., Heidari, N., Erixon, P., Olmstead, R.G., Anderberg, A.A., Källersjö, M. & Barkhordarian, E. (2002) Phylogenetics of asterids based on 3 coding and 3 non-coding chloroplast DNA markers and the utility of non-coding DNA at higher taxonomic levels. Molecular Phylogenetics and Evolution, 24, 274-301.
6. Cadotte, M.W. & Davies, J. (2010) Rarest of the rare: advances in combining evolutionary distinctiveness and scarcity to inform conservation at biogeographical scales. Diversity and Distributions, 16, 376-385.
7. Cohen, J.I. (2011) A phylogenetic analysis of morphological and molecular characters of Lithospermum L. (Boraginaceae) and related taxa: evolutionary relationships and character evolution. Cladistics, 27, 559-580.
8. Collen, B., Turvey, S.T., Waterman, C., Meredith, H.M.R., Kuhn, T.S., Baillie, J.E.M. & Isaac, N.J.B. (2011) Investing in evolutionary history: implementing a phylogenetic approach for mammal conservation. Philosophical Transactions of the Royal Society B: Biological Sciences, 366, 2611-2622.
9. Colless, D.H. (1981) Predictivity and stability in classifications: some comments on recent studies. Systematic Zoology, 30, 325-331.
10. Cooper, N. & Purvis, A. (2010) Body size evolution in mammals: complexity in tempo and mode. The American Naturalist, 175, 727-738.
11. Correll, R.L. (1977) The application of maximal predictive classification to the Epacaridaceae. Taxon, 26, 65-67.
12. Cracraft, J. (2002) The seven great questions of systematic biology: an essential foundation for conservation and the sustainable use of biodiversity. Annals of the Missouri Botanical Garden, 89, 127-144.
13. Donoghue, M.J. & Ree, R.H. (2000) Homoplasy and developmental constraint: a model and an example from plants. American Zoologist, 40, 759-769.
14. Eberhard, W.G., Agnarsson, L. & Levi, H.W. (2008) Web forms and the phylogeny of theridiid spiders (Araneae:Theridiidae): chaos from order. Systematics and biodiversity, 6, 415-475.
15. Erwin, T.L. (1991) An evolutionary basis for conservation strategies. Science, 253, 750-752.
16. Faith, D.P. (1992a) Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10.
17. Faith, D.P. (1992b) Systematics and conservation- on predicting the feature diversity of subsets of taxa. Cladistics-the International Journal of the Willi Hennig Society, 8, 361-373.
18. Faith, D.P. (2013) Biodiversity and evolutionary history: useful extensions of the PD phylogenetic diversity assessment framework. Annals of the New York Academy of Sciences, 1289, 69-89.
19. Farris, J.S. (1979) The information content of the phylogenetic system. Systematic Zoology, 28, 483-519.
20. Farris, J.S. (1982) Simplicity and Informativeness in systematics and phylogeny. Systematic Zoology, 31, 413-444.
21. Felsenstein, J. (1978) Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology, 27, 401-410.
22. Felsenstein, J. (1985) Phylogenies and the comparative method. The American Naturalist, 125, 1-15.
23. Felsenstein, J. (1988) Phylogenies and quantitative characters. Annual Review of Ecology & Systematics, 19, 445-471.
24. Felsenstein, J. (2004) Inferring phylogenies. Sinauer Associates, Sunderland, MA.
25. Forest, F., Grenyer, R., Rouget, M., Davies, T.J., Cowling, R.M., Faith, D.P., Balmford, A., Manning, J.C., 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.
26. Goodman, G. & Walsh, V. (2001) The story of taxol. Cambridge University Press, Cambridge.
27. Gower, J.C. (1974) Maximal predictive classification. Biometrics, 30, 643-654.
28. Graham, C.H., Parra, J.L., Tinoco, B.A., Stiles, F.G. & McGuire, J.A. (2012) Untangling the influence of ecological and evolutionary factors on trait variation across hummingbird assemblages. Ecology, 39, S99-S111.
29. Harmon, L.J., Losos, J.B., Davies, T.J., Gillespie, R.G., Gittleman, J.L., Jennings, B.W., Kozak, K.H., McPeek, M.A., Moreno-Roark, F., Near, T.J., Purvis, A., Ricklefs, R.E., Schluter, D., Schulte, J.A. II, Seehausen, O., Sidlauskas, B.L., Torres-Carvajal, O. & Weir, J.T. (2010) Early bursts of body size and shape evolution are rare in comparative data. Evolution, 64, 2385-2396.
30. Harvey, P.H. & Pagel, M.D. (1991) The comparative method in evolutionary biology. Oxford University Press, Oxford.
31. Hennig, W. (1966) Phylogenetic Systematics. University of Ilinois Press, Urbana.
32. Hillis, D.M. (1987) Molecular versus morphological approaches to systematics. Annual Review of Ecology and Systematics, 18, 23-42.
33. Hillis, D.M. (1995) Approaches for assessing phylogenetic accuracy. Systematic Biology, 44, 3-16.
34. Hillis, D.M., Huelsenbeck, J.P. & Cunningham, C.W. (1994) Application and accuracy of molecular phylogenies. Science, 264, 671-677.
35. Huelsenbeck, J.P. & Crandall, K.A. (1997) Maximum likelihood in phylogenetics. Annual Review of Ecology and Systematics, 28, 437-466.
36. Huelsenbeck, J.P., Bull, J.J. & Cunningham, C.W. (1996) Combining data in phylogenteic analyses. Trends in Ecology and Evolution, 11, 152-158.
37. Ingram, T., Harmon, L.J. & Shurin, J.B. (2012) When should we expect early bursts of trait evolution in comparative data? Predictions from an evolutionary food web model. Journal of Evolutionary Biology, 25, 1902-1910.
38. Isaac, N.J., Turvey, S.T., Collen, B., Waterman, C. & Baillie, J.E. (2007) Mammals on the EDGE: conservation priorities based on threat and phylogeny. PLoS ONE, 2, e296.
39. Jansky, S.H., Simon, R. & Spooner, D.M. (2006) A test of taxonomic predictivity: resistance to white mold in wild relatives of cultivated potato. Crop Science, 46, 2561-2570.
40. Judd, W.S., Campbell, C.S., Kellog, E.A. & Stevens, P.F. (1999) Plant Systematics: a phylogenetic approach. Sinauer, Sunderland, MA.
41. Kluge, A.G. & Wolfe, A.J. (1993) Cladistics: whats in a word? Cladistics, 9, 183-200.
42. Kraft, N.J.B., Cornwell, W.K., Webb, C.O. & Ackerly, D.D. (2007) Trait evolution, community assembly, and the phylogenetic structure of ecological communities. The American Naturalist, 170, 271-283.
43. Krajewski, C. (1994) Phylogenetic measures of biodiversity: a comparison and critique. Biological Conservation, 69, 33-39.
44. Lankester, E.R. (1870) On the use of the term homology in modern zoology, and the distinction between homogenetic and homoplastic agreements. Annals and Magazine of Natural History, 6, 34-43.
45. Lewis, P.O. (2001) A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology, 50, 913-925.
46. Losos, J.B. (2008) Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecology Letters, 11, 995-1003.
47. Maddison, D.R. & Schulz, K.S. (2007) The tree of life web project. Available at: http://tolweb.org (accessed 1 July 2011).
48. May, R.M. (1990) Taxonomy is destiny. Nature, 347, 129-130.
49. Minh, B.Q., Klaere, S. & Haeseler, A.v. (2006) Phylogenetic diversity within seconds. Systematic Biology, 55, 769-773.
50. Mishler, B.D. (2009) Three centuries of paradigm changes in biological classification: is the end in sight? Taxon, 58, 61-67.
51. Mouquet, N., Devictor, V., Meynard, C.N. et al. (2012) Ecophylogenetics: advances and perspectives. Biological Reviews, 87, 769-785.
52. Nixon, K.C. & Carpenter, J.M. (1996) On simultaneous analysis. Cladistics, 12, 221-241.
53. Olmstead, R.G., dePamphilis, C.W., Wolfe, A.D., Young, N.D., Elisons, W.J. & Reeves, P.A. (2001) Disintegration of the Scrophulariaceae. American Journal of Botany, 88, 348-361.
54. Pagel, M. (1994) Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proceedings of the Royal Society B: Biological Sciences, 255, 37-45.
55. Pagel, M. & Meade, A. (2006) Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo. The American Naturalist, 167, 808-825.
56. Patterson, C., Williams, D.M. & Humpries, C.J. (1993) Congruence between molecular and morphological phylogenies. Annual Review of Ecology and Systematics, 24, 153-188.
57. Piel, W.H., Auman, J., Chan, L., Dominus, M.J., Grapeyev, V., Gujral, M., Guo, Y., Lapp, H., Ruan, J., Shyket, H., Vos, R.A. & Tannen, V.. (2010) A database of phylogenetic knowledge. Available at: http://treebase.org (accessed 1 July 2011).
58. Posada, D. & Crandall, K.A. (1998) MODELTEST: testing the model of dna substitution. Bioinformatics, 14, 817-818.
59. 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? Phylogeny and conservation (ed. by A. Purvis, J.L. Gittleman and T.M. Brooks ), pp. 101-119. Cambridge University Press, Cambridge.
60. Rodrigues, A.S.L., Grenyer, R., Baillie, J.E.M., Bininda-Emonds, O.R.P., Gittlemann, J.L., Hoffman, N.M., Safi, K., Schipper, J., Stuart, S.N. & Brooks, T. (2011) Complete, accurate, mammalian phylogenies aid conservation planning, but not much. Philosophical Transactions of the Royal Society B: Biological Sciences, 366, 2652-2660.
61. Ronquist, F. & Huelsenbeck, J.P. (2003) MrBayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-4.
62. Ronsted, N., Symonds, M.R., Birkholm, T., Christensen, S., Meerow, A., Molander, M., Molgaard, P., Petersen, G., Rasmussen, N., van Staden, J., Stafford, G. & Jager, A. (2012) Can phylogeny predict chemical diversity and potential medicinal activity of plants? A case study of amaryllidaceae. BMC Evolutionary Biology, 12, 182.
63. Sanderson, M.J. & Donoghue, M.J. (1996) The relationship between homoplasy and confidence in a phylogenetic tree. Homoplasy: the recurrence of similarity in evolution (ed. by M.J. Sanderson and L. Hufford ), pp. 67-89. Academic Press, San Diego.
64. Saslis-Lagoudakis, C.H., Klitgaard, B.B., Forest, F., Francis, L., Savolainen, V., Williamson, E.M. & Hawkins, J.A. (2011) The use of phylogeny to interpret cross-cultural patterns in plant use and guide medicinal plant discovery: an example from Pterocarpus (Leguminosae). PLoS ONE, 6, e22275.
65. Saslis-Lagoudakis, C.H., Savolainen, V., Williamson, E.M., Forest, F., Wagstaff, S.J., Baral, S.R., Watson, M.F., Pendry, C.A. & Hawkins, J.A. (2012) Phylogenies reveal predictive power of traditional medicine in bioprospecting. Proceedings of the National Academy of Sciences USA, 109, 15835-15840.
66. Scotland, R.W., Olmstead, R.G. & Bennett, J.R. (2003) Phylogeny reconstruction: the role of morphology. Systematic Biology, 52(4), 539-548.
67. Simpson, G.G. (1953) The major features of evolution. Columbia University Press, New York.
68. Simpson, M.G. (2006) Plant systematics. Elsevier, Burlington, MA.
69. Smith, W.L. & Wheeler, W.C. (2006) Venom evolution widespread in fishes: a phylogenetic road map for the bioprospecting of piscinevenoms. Journal of Heredity, 97, 206-217.
70. Sneath, P.H.A. (1989) Predictivity in taxonomy and the probability of a tree. Plant Systematics and Evolution, 167, 43-57.
71. Sneath, P.H.A. & Hansell, R.I.C. (1985) Naturalness and predictivity of classifications. Biological Journal of the Linnean Society, 24, 217-231.
72. Sober, E. & Steel, M. (2002) Testing the hypothesis of common ancestry. Journal of Theoretical Biology, 218, 395-408.
73. Soutullo, A., Dodsworth, S., Heard, S.B. & Mooers, A.O. (2005) Distribution and correlates of carnivore phylogenetic diversity across the Americas. Animal Conservation, 8, 249-258.
74. Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22, 2688-2690.
75. Systematics Agenda 2000. (1994) Charting the biosphere. New York: Society of Systematic Biologists, American Society of Plant Taxonomists, Willi Hennig Society, Association of Systematics Collections.
76. Tenaillon, O., Rodríguez-Verdugo, A., Gaut, R.L., McDonald, P., Bennett, A.F., Long, A.D. & Gaut, B.S. (2012) The molecular diversity of adaptive convergence Science, 335, 457-461.
77. Vander Velde, D.G., Georg, G.I., Gollapudi, S.R., Jampani, H.B., Liang, X.Z., Mitscher, L.A. & Ye, Q.M. (1994) Wallifoliol, a taxol congener with a novel carbon skeleton, from Himalayan Taxus wallichiana. Journal of Natural Products, 57, 862-7.
78. 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.
79. Wagner, W.H. (1961) Problems in the classification of ferns. Recent Advances in Botany, 1, 841-844.
80. Wake, D.B., Wake, M.H. & Specht, C.D. (2011) Homoplasy: from detecting pattern to determining process and mechanism of evolution. Science, 331, 1032-1035.
81. Webb, C.O. (2000) Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. The American Naturalist, 156, 145-155.
82. Wiens, J.J. (2004) The role of morphological data in phylogeny reconstruction. Systematic Biology, 53, 653-661.
83. Winter, M., Devictor, V. & Schweiger, O. (2013) Phylogenetic diversity and nature conservation: where are we? Trends in Ecology & Evolution, 28, 199-204.
84. Wortley, A.H., Rudall, P.J., Harris, D.J. & Scotland, R.W. (2005) How much data are needed to resolve a difficult phylogeny? Systematic Biology, 54, 697-709.
85. Yoder, J.B., Clancey, E., Des Roches, S., Eastman, J.M., Gentry, L., Godsoe, W., Hagey, T.J., Jochimsen, D., Oswald, B.P., Robertson, J., Sarver, B.A.J., Schenks, J.J., Spear, S.F. & Harmon, L.J. (2010) Ecological opportunity and the origin of adaptive radiations. Journal of Evolutionary Biology, 23, 1581-1596.