Predicting loss of evolutionary history: Where are we?

Biological Reviews

Volumn 92, Issue 1, 2017, Pages 271-291

  Veron, Simon ^a   Davies, T Jonathan ^b,c   Cadotte, Marc W ^d   Clergeau, Philippe ^a   Pavoine, Sandrine ^a,e  

^a SORBONNE UNIVERSITÉ   (France)

^b MCGILL UNIVERSITY   (Canada)

^c UNIVERSITY OF JOHANNESBURG   (South Africa)

^d UNIVERSITY OF TORONTO   (Canada)

^e UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

biodiversity; conservation; evolutionary distinctiveness; phylogenetic diversity; predictions; species extinctions

Indexed keywords

ANIMAL; BIODIVERSITY; ENVIRONMENTAL PROTECTION; EVOLUTION; PHYLOGENY; SPECIES EXTINCTION;

ANIMALS; BIODIVERSITY; BIOLOGICAL EVOLUTION; CONSERVATION OF NATURAL RESOURCES; EXTINCTION, BIOLOGICAL; PHYLOGENY;

EID: 84951968123     PISSN: 14647931     EISSN: 1469185X     Source Type: Journal    
DOI: 10.1111/brv.12228     Document Type: Article

References (199)

1. Abellan, P., Sanchez-Fernandez, D., Picazo, F., Millán, A., Lobo, J. M. & Ribera, I. (2013). Preserving the evolutionary history of freshwater biota in Iberian National Parks. Biological Conservation 162, 116–226.
2. Agnarsson, I., Kuntner, M. & May-Collado, L. J. (2010). Dogs, cats, and kin: a molecular species level phylogeny of Carnivora. Molecular Phylogenetics and Evolution 54, 726–745.
3. Altschul, S. F. & Lipman, D. J. (1990). Equal animals. Nature 348, 493–494.
4. Angiosperm Phylogeny Group (2003). An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Botanical Journal of the Linnean Society 141, 399–436.
5. Arregoitia, L. D. V., Blomberg, S. P. & Fisher, D. O. (2013). Phylogenetic correlates of extinction risk in mammals: species in older lineages are not at greater risk. Proceedings of the Royal Society of London Series B: Biological Sciences 280, 20131092.
6. Avise, J. C. (2005). Phylogenetic units and currencies above and below the species level. In Phylogeny and Conservation (eds A. Purvis, J. L. Gittleman and T. Brooks), pp. 76–101. Cambridge University Press, Cambridge.
7. Baillie, J., Groombridge, B., Gärdenfors, U. L. F., Stattersfield, A. J. & Rabb, G. (1996). 1996 IUCN Red List of Threatened Animals. IUCN, Gland and Cambridge.
8. Baillie, J. E. M., Hilton-Taylor, C. & Stuart, S. N. (eds) (2004). 2004 IUCN Red List of Threatened Species. A Global Species Assessment. IUCN, Gland, Switzerland and Cambridge, UK, xxiv–191 pp.
9. 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.
10. Barnosky, A. D., Matzke, N., Tomiya, S., Wogan, G. O., Swartz, B., Quental, T. B., Marshall, C., Mcguire, J. L., Lindsey, E. L., Maguire, K. C., Mersey, B. & Ferrer, E. A. (2011). Has the earth's sixth mass extinction already arrived? Nature 471, 51–57.
11. Barraclough, T. G. & Nee, S. (2001). Phylogenetics and speciation. Trends in Ecology & Evolution 16, 391–399.
12. Batista, M. C., Gouveia, S. F., Silvano, D. L. & Rangel, T. F. (2013). Spatially explicit analyses highlight idiosyncrasies: species extinctions and the loss of evolutionary history. Diversity and Distributions 19, 1543–1552.
13. *Bennett, P. M. & Owens, I. P. F. (1997). Variation in extinction risk among birds: chance or evolutionarily predisposition? Proceedings of the Royal Society of London Series B: Biological Sciences 264, 401–408.
14. Billionnet, A. (2012). Solution of the generalized Noah's ark problem. Systematic Biology 62, 147–156.
15. Bininda-Emonds, O. R. (2004). The evolution of supertrees. Trends in Ecology & Evolution 6, 315–322.
16. Bininda-Emonds, O. R. (2009). The future of supertrees: bridging the gap with supermatrices. Palaeodiversity 3, 99–106.
17. Bininda-Emonds, O. R., Cardillo, M., Jones, K. E., Macphee, R. D., Beck, R. M., Grenyer, R., Price, S. A., Vos, R. A., Gittleman, J. L. & Purvis, A. (2007). The delayed rise of present-day mammals. Nature 446, 507–512.
18. Bininda-Emonds, O. R., Gittleman, J. L. & Purvis, A. (1999). Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia). Biological Reviews 74, 143–175.
19. Brooks, T. M., Cuttelod, A., Faith, D. P., Garcia-Moreno, J., Langhammer, P. & Pérez-Espona, S. (2015). Why and how might genetic and phylogenetic diversity be reflected in the identification of key biodiversity areas? Philosophical Transactions of the Royal Society, B: Biological Sciences 370, 20140019.
20. Cadotte, M. W., Cardinale, B. J. & Oakley, T. H. (2008). Evolutionary history and the effect of biodiversity on plant productivity. Proceedings of the National Academy of Sciences of the United States of America 105, 17012–17017.
21. Cadotte, M. W., Carscadden, K. & Mirotchnick, N. (2011). Beyond species: functional diversity and the maintenance of ecological processes and services. Journal of Applied Ecology 48, 1079–1087.
22. Cadotte, M. W. & Davies, J. T. (2010). Rarest of the rare: advances in combining evolutionary distinctiveness and scarcity to inform conservation at biogeographical scales. Diversity and Distributions 16, 376–385.
23. Cadotte, M. W., Davies, J. T., 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.
24. Cadotte, M. W., Dinnage, R. & Tilman, D. (2012). Phylogenetic diversity promotes ecosystem stability. Ecology 93, 223–233.
25. Cafaro, P. & Primack, R. (2014). Species extinction is a great moral wrong. Biological Conservation 170, 1–2.
26. Cardillo, M., Mace, G. M., Gittleman, J. L., Jones, K. E., Bielby, J. & Purvis, A. (2008). The predictability of extinction: biological and external correlates of decline in mammals. Proceedings of the Royal Society of London Series B: Biological Sciences 275, 1441–1448.
27. Cardillo, M., Mace, G. M., Gittleman, J. L. & Purvis, A. (2006). Latent extinction risk and the future battlegrounds of mammal conservation. Proceedings of the National Academy of Sciences of the United States of America 103, 4157–4161.
28. Carpenter, K. E., Abrar, M., Aeby, G., Aronson, R. B., Banks, S., Bruckner, A., Chiriboga, A., Cortés, J., Delbeek, J. C., Devantier, L., Edgar, G. J., Edwards, A. J., Fenner, D., Guzmán, H. M., Hoeksema, B. W., Hodgson, G., Johan, O., Licuanan, W. Y., Livingstone, S. R., Lovell, E. R., Moore, J. A., Obura, D. O., Ochavillo, D., Polidoro, B. A., Precht, W. F., Quibilan, M. C., Reboton, C., Richards, Z. T., Rogers, A. D., Sanciangco, J., Sheppard, A., Sheppard, C., Smith, J., Stuart, S., Turak, E., Veron, J. E. N., Wallace, C., Weil, C. & Wood, E. (2008). One-third of reef-building corals face elevated extinction risk from climate change and local impacts. Science 321, 560–563.
29. Ceballos, G. & Ehrlich, P. R. (2002). Mammal population losses and the extinction crisis. Science 296, 904–907.
30. Clements, G. R., Bradshaw, C. J., Brook, B. W. & Laurance, W. F. (2011). The safe index: using a threshold population target to measure relative species threat. Frontiers in Ecology and the Environment 9, 521–525.
31. Collen, B., Böhm, M., Kemp, R. & Baillie, J. E. M. (eds) (2012). Spineless: Status and Trends of the World's Invertebrates. Zoological Society of London, London.
32. 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.
33. Compagno, L. J. V. (2005). Global checklist of living chondrichthyan fishes. In Sharks, Rays and Chimaeras: The Status of Chondrichthyan Fishes (eds S. L. Fowler, R. D. Cavanagh, M. Camhi, G. H. Burgess, G. M. Cailliet, S. V. Fordham, C. A. Simpfendorfer and J. A. Musick), pp. 401–423. International Union for the Conservation of Nature, Gland.
34. Corey, S. J. & Waite, T. A. (2008). Phylogenetic autocorrelation of extinction threat in globally imperilled amphibians. Diversity and Distributions 14, 614–629.
35. Crawford, A. J., Lips, K. R. & Bermingham, E. (2010). Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of central panama. Proceedings of the National Academy of Sciences of the United States of America 107, 13777–13782.
36. Curnick, D. J., Head, C. E. I., Huang, D., Crabbe, M. J. C., Gollock, M., Hoeksema, B. W., Johnson, K. G., Jones, R., Koldewey, H. J., Obura, D. O., Rosen, B. R., Smith, D. J., Taylor, M. L., Turner, R., Wren, S. & Redding, D. W. (2015). Setting evolutionary-based conservation priorities for a phylogenetically data-poor taxonomic group (Scleractinia). Animal Conservation 18, 303–312.
37. D'agata, S., Mouillot, D., Kulbicki, M., Refouët, S., Bellwood, D. R., Cinner, J. E., Cowman, P. F., Kronen, M., Pinca, S. & Vigliola, L. (2014). Human-mediated loss of phylogenetic and functional diversity in coral reef fishes. Current Biology 24, 555–560.
38. Daru, B. H., Yessoufou, K., Mankga, L. T. & Davies, T. J. (2013). A global trend towards the loss of evolutionarily unique species in mangrove ecosystems. PLoS ONE 8, e66686.
39. *Davidson, A. D., Hamilton, M. J., Boyer, A. G., Brown, J. H. & Ceballos, G. (2009). Multiple ecological pathways to extinction in mammals. Proceedings of the National Academy of Sciences of the United States of America 106, 10702–10705.
40. Davies, T. J., Barraclough, T. G., Chase, M. W., Soltis, P. S., Soltis, D. E. & Savolainen, V. (2004). Darwin's abominable mystery: insights from a supertree of the angiosperms. Proceedings of the National Academy of Sciences of the United States of America 101, 1904–1909.
41. Davies, T. J., Fritz, S. A., Grenyer, R., Orme, C. D. L., Bielby, J., Bininda-Emonds, O. R., Cardillo, M., Jones, K. E., Gittleman, J. L. & Mace, G. M. (2008). Phylogenetic trees and the future of mammalian biodiversity. Proceedings of the National Academy of Sciences of the United States of America 105, 11556–11563.
42. Davies, T. J., Smith, G. F., Bellstedt, D. U., Boatwright, J. S., Bytebier, B., Cowling, R. M., Forest, F., Harmon, L. J., Muasya, A. M., Schrire, B. D., Steenkamp, Y., Van Der Bank, M. & Savolainen, V. (2011). Extinction risk and diversification are linked in a plant biodiversity hotspot. PLoS Biology 9, e1000620.
43. Davies, T. J. & Yessoufou, K. (2013). Revisiting the impacts of non-random extinction on the tree-of-life. Biology Letters 9, 20130343.
44. Del Hoyo, J., Elliott, A., Sargatal, J. & Christie, D. A. (eds) (1992–2011). Handbook of the Birds of the World. Lynx Editions, Barcelona.
45. Diniz-Filho, J. A. F. (2004). Phylogenetic autocorrelation analysis of extinction risks and the loss of evolutionary history in felidae (Carnivora: Mammalia). Evolutionary Ecology 18, 273–282.
46. Diniz-Filho, J. A. F. & Bini, L. M. (2005). Modelling geographical patterns in species richness using eigenvector-based spatial filters. Global Ecology and Biogeography 14, 177–185.
47. Diniz-Filho, J. A. F., de Sant'Ana, C. E. R. & Bini, L. M. (1998). An eigenvector method for estimating phylogenetic inertia. Evolution 52, 1247–1262.
48. Dirzo, R. & Raven, P. H. (2003). Global state of biodiversity and loss. Annual Review of Environment and Resources 28, 137–167.
49. Dunn, R. R., Harris, N. C., Colwell, R. K., Koh, L. P. & Sodhi, N. S. (2009). The sixth mass coextinction: are most endangered species parasites and mutualists? Proceedings of the Royal Society of London Series B: Biological Sciences 276, 3037–3045.
50. Edge (2014). The EDGE of existence program, version 2014. http://www.edgeofexistence.org/ Accessed 09.9.2014.
51. Edge (2015). The EDGE of existence program, version 2015. http://www.edgeofexistence.org/about/future_edge.php Accessed 20.02.2015
52. Erwin, D. H. (2008). Extinction as the loss of evolutionary history. Proceedings of the National Academy of Sciences of the United States of America 105, 11520–11527.
53. von Euler, F. (2001). Selective extinction and rapid loss of evolutionary history in the bird fauna. Proceedings of the Royal Society of London Series B: Biological Sciences 268, 127–130.
54. Faith, D. P. (1992). Conservation evaluation and phylogenetic diversity. Biological Conservation 61, 1–10.
55. Faith, D. P. (2008). Threatened species and the potential loss of phylogenetic diversity: Conservation scenarios based on estimated extinction probabilities and phylogenetic risk analysis. Conservation Biology 22, 1461–1470.
56. 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.
57. Faith, D. P. & Baker, A. M. (2006). Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges. Evolutionary Bioinformatics Online 2, 121–128.
58. Faith, D. P., Magallón, S., Hendry, A. P., Conti, E., Yahara, T. & Donoghue, M. J. (2010). Evosystem services: an evolutionary perspective on the links between biodiversity and human well-being. Current Opinion in Environmental Sustainability 2, 66–74.
59. Faith, D. P. & Pollock, L. J. (2014). Phylogenetic diversity and the sustainable use of biodiversity. In Applied Ecology and Human Dimensions in Biological Conservation (eds M. C. Lyra-Jorge and L. M. Verdade), pp. 35–52. Springer, Berlin.
60. Faith, D. P. & Richards, Z. T. (2012). Climate change impacts on the tree of life: changes in phylogenetic diversity illustrated for Acropora corals. Biology 1, 906–932.
61. FAO (2007). The World's Mangroves 1980–2005. Forest Resources Division, FAO.
62. Fay, J. J. & Thomas, W. (1983). Endangered and threatened species listing and recovery priority guidelines. Federal Register 48, 43098–43105.
63. Forest, F., Crandall, K. A., Chase, M. W. & Faith, D. (2015). Phylogeny, extinction & conservation: embracing uncertainties in a time of urgency. Philosophical Transactions of the Royal Society, B: Biological Sciences 370, 20140002.
64. 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.
65. Fritz, S. A., Bininda-Emonds, O. R. P. & Purvis, A. (2009). Geographical variation in predictors of mammalian extinction risk: big is bad, but only in the tropics. Ecology Letters 12, 538–549.
66. Fritz, S. A. & Purvis, A. (2010a). Phylogenetic diversity does not capture body size variation at risk in the world's mammals. Proceedings of the Royal Society of London Series B: Biological Sciences 277, 2435–2441.
67. Fritz, S. A. & Purvis, A. (2010b). Selectivity in mammalian extinction risk and threat types: a new measure of phylogenetic signal strength in binary traits. Conservation Biology 24, 1042–1051.
68. Fritz, S. A. & Rahbek, C. (2012). Global patterns of amphibian phylogenetic diversity. Journal of Biogeography 39, 1373–1382.
69. Frost, D. R. (2007). Amphibian Species of the World: An Online Reference, Version 5. American Museum of Natural History, New York.
70. Frost, D. R. (2009). Amphibian Species of the World: An Online Reference, Version 5.3. American Museum of Natural History, New York.
71. Gaston, K. J. (1994). Rarity. Chapman and Hall, London.
72. *Gaston, K. J. & Blackburn, T. M. (1995). Birds, body size and the threat of extinction. Philosophical Transactions of the Royal Society of London B 347, 205–212.
73. Gatesy, J. & Springer, M. S. (2004). A critique of matrix representation with parsimony supertrees. In Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life (ed. O. R. P. Bininda-Emonds), pp. 369–388. Kluwer Academic Publishers, Dordrecht.
74. Gittenberg, A., Reijinen, B. T. & Hoeksema, B. W. (2011). A molecularly based phylogeny reconstruction of mushroom corals (Scleractinia: Fungiidae) with taxonomic consequences and evolutionary implications for life history traits. Contributions to Zoology 80, 107–132.
75. Gittleman, J. L., Jones, K. E. & Price, S. A. (2004). Supertrees: using complete phylogenies in comparative biology. In Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life (ed. O. R. P. Bininda-Emonds), pp. 439–460. Kluwer Academic Publishers, Dordrecht.
76. Gribaldo, S. & Philippe, H. (2002). Ancient phylogenetic relationships. Theoretical Population Biology 61, 391–408.
77. Gudde, R. M., Joy, J. B. & Mooers, A. O. (2013). Imperilled phylogenetic endemism of Malagasy lemuriformes. Diversity and Distributions 19, 664–675.
78. Heard, S. B. & Mooers, A. O. (2000). Phylogenetically patterned speciation rates and extinction risks change the loss of evolutionary history during extinctions. Proceedings of the Royal Society of London Series B: Biological Sciences 267, 613–620.
79. Heinicke, M. P., Naylor, G. J. P. & Hedges, S. B. (2009). Cartilaginous fishes (Chondrichthyes). In The Timetree of Life (eds S. B. Hedges and S. Kumar), pp. 320–327. Oxford University Press, New York.
80. Helmus, M. R., Savage, K., Diebel, M. W., Maxted, J. T. & Ives, A. R. (2007). Separating the determinants of phylogenetic community structure. Ecology Letters 10, 917–925.
81. Hoffmann, M., Hilton-Taylor, C., Angulo, A., Böhm, M., Brooks, T. M., Butchart, S. H., Carpenter, K. E., Chanson, J., Collen, B., Cox, N. A., Darwall, W. R. T., Dulvy, N. K., Harrison, L. R., Katariya, V., Pollock, C. M., et al. (2010). The impact of conservation on the status of the world's vertebrates. Science 330, 1503–1509.
82. Holman, E. W. (2005). Nodes in phylogenetic trees: the relation between imbalance and number of descendent species. Systematic Biology 54, 895–899.
83. Howard, S. D. & Bickford, D. P. (2014). Amphibians over the edge: silent extinction risk of Data Deficient species. Diversity and Distributions 20, 837–846.
84. Huang, D. (2012). Threatened reef corals of the world. PLoS ONE 7, e34459.
85. Huang, D., Licuanan, W. Y., Hoeksema, B. W., Chen, C. A., Ang, P. O., Huang, H., Lane, D. J. W., Vo, S. T., Waheed, Z., Affendi, Y. A., Yeemin, T. & Chou, L. M. (2014). Extraordinary diversity of reef corals in the South China Sea. Marine Biodiversity 1, 1–14.
86. Huang, D. & Roy, K. (2013). Anthropogenic extinction threats and future loss of evolutionary history in reef corals. Ecology and Evolution 3, 1184–1193.
87. Huang, D. & Roy, K. (2015). The future of evolutionary diversity in reef corals. Philosophical Transactions of the Royal Society, B: Biological Sciences 370, 20140010.
88. Huang, J., Chen, B., Liu, C., Lai, J., Zhang, J. & Ma, K. (2012a). Identifying hotspots of endemic woody seed plant diversity in China. Diversity and Distributions 18, 673–688.
89. Huang, S., Stephens, P. R. & Gittleman, J. L. (2012b). Traits, trees and taxa: global dimensions of biodiversity in mammals. Proceedings of the Royal Society of London Series B: Biological Sciences 279, 4997–5003.
90. Huang, S., Davies, T. J. & Gittleman, J. L. (2011). How global extinctions impact regional biodiversity in mammals. Biology Letters 8, 222–225.
91. Isaac, N. J. & Purvis, A. (2004). The “species problem” and testing macroevolutionary hypotheses. Diversity and Distributions 10, 275–281.
92. Isaac, N. J., Redding, D. W., Meredith, H. M. & Safi, K. (2012). Phylogenetically informed priorities for amphibian conservation. PLoS ONE 7, e43912.
93. 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.
94. IUCN (2008). The IUCN Red List of Threatened Species. Amphibian, update 2008. http://www.iucnredlist.org/initiatives/amphibians/analysis/2008-update Accessed 09.9.2014.
95. IUCN (2014). The IUCN Red List of Threatened Species. Version 2014.2. http://www.iucnredlist.org Accessed 09.9.2014.
96. Jablonski, D. & Chaloner, W. G. (1994). Extinctions in the fossil record [and Discussion]. Philosophical Transactions of the Royal Society, B: Biological Sciences 344, 11–17.
97. Jetz, W. & Freckleton, R. P. (2015). Towards a general framework for predicting threat status of data-deficient species from phylogenetic, spatial and environmental information. Philosophical Transactions of the Royal Society, B: Biological Sciences 370, 20140016.
98. Jetz, W., Thomas, G., Joy, J., Hartmann, K. & Mooers, A. (2012). The global diversity of birds in space and time. Nature 491, 444–448.
99. Jetz, W., Thomas, G. H., Joy, J. B., Redding, D. W., Hartmann, K. & Mooers, A. O. (2014). Global distribution and conservation of evolutionary distinctness in birds. Current Biology 24, 919–930.
100. Jono, C. M. A. & Pavoine, S. (2012). Threat diversity will erode mammalian phylogenetic diversity in the near future. PLoS ONE 7, e46235.
101. Kelly, S., Grenyer, R. & Scotland, R. W. (2014). Phylogenetic trees do not reliably predict feature diversity. Diversity and Distributions 20, 600–612.
102. Kuhn, T. S., Mooers, A. Ø. & Thomas, G. H. (2011). A simple polytomy resolver for dated phylogenies. Methods in Ecology and Evolution 2, 427–436.
103. Kuntner, M., May-Collado, L. J. & Agnarsson, I. (2011). Phylogeny and conservation priorities of afrotherian mammals (Afrotheria, Mammalia). Zoologica Scripta 40, 1–15.
104. Lasram, F. B. & Mouillot, D. (2009). Increasing southern invasion enhances congruence between endemic and exotic Mediterranean fish fauna. Biological Invasions 11, 697–711.
105. Lee, T. M. & Jetz, W. (2010). Unravelling the structure of species extinction risk for predictive conservation science. Proceedings of the Royal Society of London Series B: Biological Sciences 278, 1329–1338.
106. Losos, J. B. (2008). Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecology Letters 11, 995–1007.
107. Lozano, F. D. & Schwartz, M. W. (2005). Patterns of rarity and taxonomic group size in plants. Biological Conservation 126, 146–154.
108. Mace, G. M., Collar, N. J., Gaston, K. J., Hilton-Taylor, C., Akçakaya, H. R., Leader-Williams, N., Milner-Gulland, E. & Stuart, S. N. (2008). Quantification of extinction risk: IUCN's system for classifying threatened species. Conservation Biology 22, 1424–1442.
109. Mace, G. M., Gittleman, J. L. & Purvis, A. (2003). Preserving the tree of life. Science 300, 1707–1709.
110. Machado, N. & Loyola, R. D. (2013). A comprehensive quantitative assessment of bird extinction risk in Brazil. PLoS ONE 8, e72283.
111. Mackee, J., Chambers, E. & Guseman, J. (2013). Human population density and growth validated as extinction threats to mammal and bird species. Human Ecology 41, 773–778.
112. MacLaughlin, J. F., Hellmann, J. J., Boggs, C. L. & Ehrlich, P. R. (2002). Climate change hastens population extinctions. Proceedings of the National Academy of Sciences of the United States of America 99, 6070–6074.
113. Maddison, W. P. & Maddison, D. R. (2007). Mesquite: a modular system for evolutionary analysis, Version 2.01. Available at http://mesquiteproject.org Accessed 09.9.2014.
114. Magnuson-Ford, K., Ingram, T., Redding, D. W. & Mooers, A. (2009). Rockfish (Sebastes) that are evolutionarily isolated are also large, morphologically distinctive and vulnerable to overfishing. Biological Conservation 142, 1787–1796.
115. Martyn, I., Kuhn, T. S., Mooers, A. O., Moulton, V. & Spillner, A. (2012). Computing evolutionary distinctiveness indices in large scale analysis. Algorithms for Molecular Biology 7, 6.
116. Marvier, M. & Kareiva, P. (2014). Extinction is a moral wrong but conservation is complicated. Biological Conservation 176, 281–282.
117. May, R. M. (1990). Taxonomy as destiny. Nature 347, 129–130.
118. May-Collado, L. J. & Agnarsson, I. (2011). Phylogenetic analysis of conservation priorities for aquatic mammals and their terrestrial relatives, with a comparison of methods. PLoS ONE 6, e22562.
119. Meynard, C. N., Mouillot, D., Mouquet, N. & Douzery, E. J. (2012). A phylogenetic perspective on the evolution of mediterranean teleost fishes. PLoS ONE 7, e36443.
120. Minh, B. Q., Klaere, S. & Von Haeseler, A. (2009a). Taxon selection under split diversity. Systematic Biology 58, 586–594.
121. Minh, B. Q., Pardi, F., Klaere, S. & Von Haeseler, A. (2009b). Budgeted phylogenetic diversity on circular split systems. Computational Biology and Bioinformatics 6, 22–29.
122. Mooers, A. & Atkins, R. (2003). Indonesia's threatened birds: over 500 million years of evolutionary heritage at risk. Animal Conservation 6, 183–188.
123. Mooers, A., Faith, D. P. & Maddison, W. P. (2008). Converting endangered species categories to probabilities of extinction for phylogenetic conservation prioritization. PLoS ONE 3, e3700.
124. Mooers, A., Gascuel, O., Stadler, T., Li, H. & Steel, M. (2011). Branch lengths on birth-death trees and the expected loss of phylogenetic diversity. Systematic Biology 61, 195–203.
125. Morlon, H., Schwilk, D. W., Bryant, J. A., Marquet, P. A., Rebelo, A. G., Tauss, C., Bohannan, B. J. & Green, J. L. (2011). Spatial patterns of phylogenetic diversity. Ecology Letters 14, 141–149.
126. Moritz, C. (1994). Defining evolutionarily significant units for conservation. Trends in Ecology & Evolution 9, 373–375.
127. Mouquet, N., Devictor, V., Meynard, C. N., Munoz, F., Bersier, L. F., Chave, J., Couteron, P., Dalecky, A., Fontaine, C., Gravel, D., Hardy, O. J., Jabot, F., Lavergne, S., Leibold, M., Mouillot, D., Münkemüller, T., Pavoine, S., Prinzing, A., Rodrigues, A. S., Rohr, R. P., Thebault, E. & Thuiller, W. (2012). Ecophylogenetics: advances and perspectives. Biological Reviews 87, 769–785.
128. Musters, C. J. M., Kalkman, V. & van Strien, A. (2013). Predicting rarity and decline in animals, plants, and mushrooms based on species attributes and indicator groups. Ecology and Evolution 3, 3401–3414.
129. Naylor, G. J., Caira, J. N., Jensen, K., Rosana, K. A., Straube, N. & Lakner, C. (2012). Elasmobranch phylogeny: a mitochondrial estimate based on 595 species. In The Biology of Sharks and their Relatives (eds J. C. Carrier, J. A. Musick and M. R. Heithaus), pp. 31–56. CRC Press, Taylor & Francis Group, London.
130. Nee, S. (2005). Phylogenetic futures after the latest mass extinction. In Phylogeny and Conservation (eds A. Purvis, J. L. Gittleman and T. Brooks), pp. 76–101. Cambridge University Press, Cambridge.
131. Nee, S. & May, R. (1997). Extinction and the loss of evolutionary history. Science 278, 692–694.
132. Nixon, K. C. & Wheeler, Q. D. (1992). Measures of phylogenetic diversity. In Extinction and Phylogeny (eds M. J. Novacek and Q. D. Wheeler), pp. 216–234. Columbia University Press, New York.
133. Nyakatura, K. & Bininda-Emonds, O. R. (2012). Updating the evolutionary history of carnivore (Mammalia): a new species-level supertree complete with divergence time estimates. BMC Biology 10, 12.
134. Parhar, R. K. & Mooers, A. (2011). Phylogenetically clustered extinction risks do not substantially prune the tree of life. PLoS ONE 6, e23528.
135. Pavoine, S. & Bonsall, M. B. (2011). Measuring biodiversity to explain community assembly: a unified approach. Biological Reviews 86, 792–812.
136. Pavoine, S., Gasc, A., Bonsall, M. B. & 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.
137. Pavoine, S., Ollier, S. & Dufour, A. B. (2005). Is the originality of a species measurable? Ecology Letters 8, 579–586.
138. Pereira, H. M., Leadley, P. W., Proença, V., Alkemade, R., Scharlemann, J. P., Fernandez-Manjarrés, J. F., Araújo, M. B., Balvanera, P., Biggs, R., Cheung, W. W., Chini, L., Cooper, H. D., Gilman, E. L., Guenette, S., Hurtt, G. C., Huntington, P., Mace, G. M., Oberdorff, T., Revenga, C., Rodrigues, P., Scholes, R. J., Sumaila, U. R. & Walpole, M. (2010). Scenarios for global biodiversity in the 21st century. Science 330, 1496–1501.
139. Pisani, D. & Wilkinson, M. (2002). Matrix representation with parsimony, taxonomic congruence, and total evidence. Systematic Biology 51(1), 151–155.
140. Possingham, H. P., Andelman, S. J., Burgman, M. A., Medellín, R. A., Master, L. L. & Keith, D. A. (2002). Limits to the use of threatened species lists. Trends in Ecology & Evolution 17, 503–507.
141. Purvis, A. (2008). Phylogenetic approaches to the study of extinction. Annual Review of Ecology, Evolution, and Systematics 39, 301–319.
142. Purvis, A., Agapow, P. M., Gittleman, J. L. & Mace, G. M. (2000a). Non-random extinction and the loss of evolutionary history. Science 288, 328–330.
143. Purvis, A., Gittleman, J. L., Cowlishaw, G. & Mace, G. M. (2000b). Predicting extinction risk in declining species. Proceedings of the Royal Society of London Series B: Biological Sciences 267, 1947–1952.
144. Pybus, O. G. & Harvey, P. H. (2000). Testing macro-evolutionary models using incomplete molecular phylogenies. Proceedings of the Royal Society of London Series B: Biological Sciences 267, 2267–2272.
145. Pyron, R. A. & Burbrink, F. T. (2014). Early origin of viviparity and multiple reversions to oviparity in squamate reptiles. Ecology Letters 17, 13–21.
146. Pyron, A. R. & Wien, J. J. (2011). A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians. Molecular Phylogenetics and Evolution 61, 543–583.
147. Raup, D. M. & Sepkoski, J. J. (1982). Mass extinctions in the marine fossil record. Science 215, 1501–1503.
148. Redding, D. (2003). Incorporating genetic distinctness and reserve occupancy into a conservation priorisation approach. Master thesis: University of East Anglia, Norwich.
149. Redding, D. W., Dewolff, C. V. & Mooers, A. (2010). Evolutionary distinctiveness, threat status, and ecological oddity in primates. Conservation Biology 24, 1052–1058.
150. Redding, D. W., Hartmann, K., Mimoto, A., Bokal, D., Devos, M. & Mooers, A. (2008). Evolutionarily distinctive species often capture more phylogenetic diversity than expected. Journal of Theoretical Biology 251, 606–615.
151. Redding, D. W. & Mooers, A. (2006). Incorporating evolutionary measures into conservation prioritization. Conservation Biology 20, 1670–1678.
152. Ren, D., Chin, K. R. & French, J. A. (2014). Molecular variation in AVP and AVPR1 in New World Monkeys (Primates, Platyrrhini): Evolution and implication for social monogamy. PLoS ONE 9, e111638.
153. Rezende, E. L., Lavabre, J. E., Guimaraes, P. R., Jordano, P. & Bascompte, J. (2007). Non-random coextinctions in phylogenetically structured mutualistic networks. Nature 448, 925–928.
154. Rodrigues, A. S., 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. Brooks), pp. 101–119. Cambridge University Press, Cambridge.
155. Rodrigues, A. S. & Gaston, K. J. (2002). Maximising phylogenetic diversity in the selection of networks of conservation areas. Biological Conservation 105, 103–111.
156. Rodrigues, A. S., Grenyer, R., Baillie, J. E. M., Bininda-Emonds, O. R. P., Gittlemann, J. L., Hoffmann, 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.
157. Roquet, C., Thuiller, W. & Lavergne, S. (2013). Building megaphylogenies for macroecology: taking-up the challenge. Ecography 36, 13–26.
158. Rosauer, D. F. & Jetz, W. (2015). Phylogenetic endemism in terrestrial mammals. Global Ecology and Biogeography 24, 168–179.
159. Rosauer, D. F., 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.
160. Rosauer, D. F. & Mooers, A. O. (2013). Nurturing the use of evolutionary diversity in nature conservation. Trends in Ecology & Evolution 28, 322–323.
161. Ryder, O. A. (1986). Species conservation and systematics: the dilemma of subspecies. Trends in Ecology & Evolution 1, 9–10.
162. 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.
163. Safi, K. & Pettorelli, N. (2010). Phylogenetic, spatial and environmental components of extinction risk in carnivores: decomposing extinction risk. Global Ecology and Biogeography 19, 352–362.
164. Sanderson, M. J., Purvis, A. & Henze, C. (1998). Phylogenetic supertrees: assembling the trees of life. Trends in Ecology & Evolution 13, 105–109.
165. Sanderson, M. J. & Shaffer, H. B. (2002). Troubleshooting molecular phylogenetic analyses. Annual Review of Ecology and Systematics 33, 49–72.
166. Santamaría, L. & Mendez, P. F. (2012). Evolution in biodiversity policy current gaps and future needs. Evolutionary Applications 5, 202–218.
167. Schwartz, M. W. & Simberloff, D. (2001). Taxon size predicts rates of rarity in vascular plants. Ecology Letters 4, 464–469.
168. Sibley, C. G. & Monroe, B. L. Jr. (1990). Distribution and Taxonomy of Birds of the World. Yale University Press, New Haven.
169. Sibley, C. G. & Monroe, B. L. Jr. (1993). A Supplement to Distribution and Taxonomy of Birds of the World. Yale University Press, New Haven.
170. Sitas, N., Baillie, J. & Isaac, N. (2009). What are we saving? Developing a standardized approach for conservation action. Animal Conservation 12, 231–237.
171. Sobral, F. L., Jardim, L., Lemes, P., Machado, N., Loyola, R. & Cianciaruso, M. V. (2014). Spatial conservation priorities for top predators reveal mismatches among taxonomic, phylogenetic and functional diversity. Natureza & Consevação 12, 150–155.
172. 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.
173. Stamatakis, A., Hoover, P. & Rougemont, J. (2008). A rapid bootstrap algorithm for the RAxML Web servers. Systematic Biology 57, 758–771.
174. Steel, M., Mimoto, A. & Mooers, A. (2007). Hedging our bets: the expected contribution of species to future phylogenetic diversity. Evolutionary Bioinformatics Online 3, 237–244.
175. Swenson, N. G. (2009). Phylogenetic resolution and quantifying the phylogenetic diversity and dispersion of communities. PLoS ONE 4, e4390.
176. Szabo, J. K., Khwaja, N., Garnett, S. T. & Butchart, S. H. (2012). Global patterns and drivers of avian extinctions at the species and subspecies level. PLoS ONE 7, e47080.
177. 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.
178. Thuiller, W., Maiorano, L., Mazel, F., Guilhaumon, F., Ficetola, F. G., Lavergne, S., Renaud, J., Roquet, C. & Mouillot, D. (2015). Conserving the functional and phylogenetic trees of life of European tetrapods. Philosophical Transactions of the Royal Society, B: Biological Sciences 370, 20140005.
179. 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.
180. Tucker, C. M., Cadotte, M. W., Davies, T. J. & Rebelo, T. G. (2012). Incorporating geographical and evolutionary rarity into conservation prioritization. Conservation Biology 26, 593–601.
181. Vamosi, J. C. & Wilson, J. R. U. (2008). Non-random extinction leads to elevated loss of angiosperm evolutionary history. Ecology Letters 11, 1047–1053.
182. 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.
183. Vélez-Zuazo, X. & Agnarsson, I. (2011). Shark tales: a molecular species-level phylogeny of sharks (selachimorpha, chondrichthyes). Molecular Phylogenetics and Evolution 58, 207–217.
184. Vellend, M., Cornwell, W. K., Magnuson-Ford, K. & Mooers, A. (2011). Measuring phylogenetic biodiversity. In Biological Diversity: Frontiers in Measurement and Assessment, pp. 194–207. Oxford University Press, Oxford.
185. Veron, J. E. N. (2000). Corals of the World. Australian Institute of Marine Science, Townsville.
186. Vié, J. C., Hilton-Taylor, C. & Stuart, S. N. (eds) (2008). Wildlife in a Changing World – An Analysis of the 2008 IUCN Red List of Threatened Species. International Union for the Conservation of Nature, Gland.
187. Volkmann, L., Martyn, I., Moulton, V., Spillner, A. & Mooers, A. O. (2014). Prioritizing populations for conservation using phylogenetic networks. PLoS ONE 9, e88945.
188. Wallace, C. C. (1999). Staghorn Corals of the World: A Revision of the Coral Genus Acropora. CSIRO Publishing, Collingwood.
189. Webb, C. O. (2000). Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. The American Naturalist 156, 145–155.
190. Waples, R. S. (1991). Pacific salmon, Oncorhynchus spp., and the definition of species under the Endangered Species Act. Marine Fisheries Review 53, 11–22.
191. Whittaker, K., Michelle, K. S., David, W. B. & Vance, V. T. (2013). Global declines of amphibians. In Encyclopedia of Biodiversity. Second (Volume 3, Edition (, ed. S. A. Levin), pp. 691–699. Academic Press, Waltham.
192. Wilson, D. & Reeder, D. M. (eds) (1993). Mammal Species of the World: A Taxonomic and Geographic Reference. Smithsonian Institution, Washington.
193. Wilson, D. E. & Reeder, D. M. (eds) (2005). Mammal Species of the World: A Taxonomic and Geographic Reference. Smithsonian Institution, Washington.
194. Winter, M., Devictor, V. & Schweiger, O. (2012). Phylogenetic diversity and nature conservation: where are we? Trends in Ecology & Evolution 28, 199–204.
195. Winter, M., Devictor, V. & Schweiger, O. (2013). Conquering current obstacles for avoiding the misuse of evolutionary diversity in nature conservation: a reply to Rosauer and Mooers. Trends in Ecology & Evolution 28, 323–324.
196. Witting, L., Tomiuk, J. & Loeschcke, V. (2000). Modelling the optimal conservation of interacting species. Ecological Modelling 125, 123–144.
197. Wozencraft, W. C. (1993). Order Carnivora. In Mammal Species of the World: A Taxonomic and Geographic Reference. Second Edition (eds D. E. Wilson and D. A. Reeder), pp. 279–348. Smithsonian Institution Press, Washington.
198. Wozencraft, W. C. (2005). Order Carnivora. In Mammal Species of the World: A Taxonomic & Geographic Reference. Third Edition (, eds D. E. Wilson and D. A. Reeder), pp. 532–628. Johns Hopkins University Press, Baltimore.
199. Zupan, L., Cabeza, M., Maiorano, L., Roquet, C., Devictor, V., Lavergne, S., Mouillot, D., Mouquet, N., Renaud, J. & Thuiller, W. (2014). Spatial mismatch of phylogenetic diversity across three vertebrate groups and protected areas in Europe. Diversity and Distributions 20, 674–685.