The future of evolutionary diversity in reef corals

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 370, Issue 1662, 2015, Pages 1-11

  Huang, Danwei ^a,b   Roy, Kaustuv ^c  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b UNIVERSITY OF IOWA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Coral reef; Ecoregions; Extinction risk; Phylogenetic diversity; Scleractinia; Tree shape

Indexed keywords

CONSERVATION GENETICS; CORAL REEF; ECOREGION; EVOLUTIONARY BIOLOGY; GENETIC VARIATION; GEOGRAPHICAL DISTRIBUTION; PHYLOGENETICS; REGIONAL PATTERN;

CORAL TRIANGLE; PACIFIC OCEAN;

ANTHOZOA; ERYTHRINA CORALLODENDRON; SCLERACTINIA;

ANIMAL; ANIMAL DISPERSAL; ANTHOZOA; BIOLOGICAL MODEL; CORAL REEF; ENVIRONMENTAL PROTECTION; EVOLUTION; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; PHYLOGENY; PROCEDURES; SPECIES DIFFERENCE; STATISTICAL MODEL; TRENDS;

ANIMAL DISTRIBUTION; ANIMALS; ANTHOZOA; BIOLOGICAL EVOLUTION; CONSERVATION OF NATURAL RESOURCES; CORAL REEFS; GENETIC VARIATION; GEOGRAPHY; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; SPECIES SPECIFICITY;

EID: 84920950199     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2014.0010     Document Type: Article

References (105)

1. Barnosky AD et al. 2011 Has the Earth’s sixth mass extinction already arrived? Nature 470, 51-57. (doi:10.1038/nature09678)
2. Gaston KJ. 1996 Species richness: measure and measurement. In Biodiversity: a biology of numbers and difference (ed. KJ Gaston), pp. 77-113. Oxford, UK: Blackwell Science.
3. Vane-Wright RI, Humphries CJ, Williams PH. 1991 What to protect?—systematics and the agony of choice. Biol. Conserv. 55, 235-254. (doi:10.1016?0006-3207(91)90030-D)
4. Faith DP. 1992 Conservation evaluation and phylogenetic diversity. Biol. Conserv. 61, 1-10. (doi:10.1016/0006-3207(92)91201-3)
5. Mace GM, Gittleman JL, Purvis A. 2003 Preserving the tree of life. Science 300, 1707-1709. (doi:10.1126/science.1085510)
6. Rodrigues ASL, Gaston KJ. 2002 Maximising phylogenetic diversity in the selection of networks of conservation areas. Biol. Conserv. 105, 103-111. (doi:10.1016/S0006-3207(01)00208-7)
7. Mooers AØ, Heard SB, Chrostowski E. 2005 Evolutionary heritage as a metric for conservation. In Phylogeny and conservation (eds A Purvis, TM Brooks, JL Gittleman), pp. 120-138. Oxford, UK: Oxford University Press.
8. Forest F et al. 2007 Preserving the evolutionary potential of floras in biodiversity hotspots. Nature 445, 757-760. (doi:10.1038/nature05587)
9. Thuiller W, Lavergne S, Roquet C, Boulangeat I, Lafourcade B, Araújo MB. 2011 Consequences of climate change on the tree of life in Europe. Nature 470, 531-534. (doi:10.1038/nature09705)
10. Rosauer DF, Mooers AØ. 2013 Nurturing the use of evolutionary diversity in nature conservation. Trends Ecol. Evol. 28, 322-323. (doi:10.1016/j.tree.2013. 01.014)
11. Maherali H, Klironomos JN. 2007 Influence of phylogeny on fungal community assembly and ecosystem functioning. Science 316, 1746-1748. (doi:10.1126/science.1143082)
12. Cadotte MW, Cardinale BJ, Oakley TH. 2008 Evolutionary history and the effect of biodiversity on plant productivity. Proc. Natl Acad. Sci. USA 105, 17 012-17 017. (doi:10.1073/pnas.0805962105)
13. Cadotte MW, Cavender-Bares J, Tilman D, Oakley TH. 2009 Using phylogenetic, functional and trait diversity to understand patterns of plant community productivity. PLoS ONE 4, e5695. (doi:10.1371?journal.pone.0005695)
14. Flynn DFB, Mirotchnick N, Jain M, Palmer MI, Naeem S. 2011 Functional and phylogenetic diversity as predictors of biodiversity-ecosystemfunction relationships. Ecology 92, 1573-1581. (doi:10.1890/10-1245.1)
15. Cadotte MW. 2013 Experimental evidence that evolutionarily diverse assemblages result in higher productivity. Proc. Natl Acad. Sci. USA 110, 8996-9000. (doi:10.1073/pnas. 1301685110)
16. Cadotte MW, Davies TJ, Regetz J, Kembel SW, Cleland EE, Oakley TH. 2010 Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history. Ecol. Lett. 13, 96-105. (doi:10.1111/j.1461-0248.2009.01405.x)
17. Collen B, Turvey ST, Waterman C, Meredith HMR, Kuhn TS, Baillie JEM, Isaac NJB. 2011 Investing in evolutionary history: implementing a phylogenetic approach for mammal conservation. Phil. Trans. R. Soc. B 366, 2611-2622. (doi:10.1098/rstb. 2011.0109)
18. Schweiger O, Klotz S, Durka W, Kühn I. 2008 A comparative test of phylogenetic diversity indices. Oecologia 157, 485-495. (doi:10.1007/s00442-008-1082-2)
19. Winter M, Devictor V, Schweiger O. 2013 Phylogenetic diversity and nature conservation: where are we? Trends Ecol. Evol. 28, 199-204. (doi:10.1016/j.tree.2012.10.015)
20. Carpenter KE et al. 2008 One-third of reef-building corals face elevated extinction risk from climate change and local impacts. Science 321, 560-563. (doi:10.1126/science.1159196)
21. Knowlton N. 2001 The future of coral reefs. Proc. Natl Acad. Sci. USA 98, 5419-5425. (doi:10.1073?pnas.091092998)
22. Hughes TP et al. 2003 Climate change, human impacts, and the resilience of coral reefs. Science 301, 929-933. (doi:10.1126/science.1085046)
23. Pandolfi JM et al. 2003 Global trajectories of the long-term decline of coral reef ecosystems. Science 301, 955-958. (doi:10.1126/science.1085706)
24. Bellwood DR, Hughes TP, Folke C, Nyström M. 2004 Confronting the coral reef crisis. Nature 429, 827-833. (doi:10.1038/nature02691)
25. Hoegh-Guldberg O et al. 2007 Coral reefs under rapid climate change and ocean acidification. Science 318, 1737-1742. (doi:10.1126/science. 1152509)
26. Hoegh-Guldberg O. 1999 Climate change, coral bleaching and the future of the world’s coral reefs. Mar. Freshw. Res. 50, 839-866. (doi:10.1071?MF99078)
27. Bruno JF, Selig ER, Casey KS, Page CA, Willis BL, Harvell CD, Sweatman HPA, Melendy AM. 2007 Thermal stress and coral cover as drivers of coral disease outbreaks. PLoS Biol. 5, e124. (doi:10.1371?journal.pbio.0050124)
28. Brandt ME, McManus JW. 2009 Disease incidence is related to bleaching extent in reef-building corals. Ecology 90, 2859-2867. (doi:10.1890/08-0445.1)
29. Miller J, Muller E, Rogers CS, Waara R, Atkinson A, Whelan KRT, Patterson MR, Witcher B. 2009 Coral disease following massive bleaching in 2005 causes 60% decline in coral cover on reefs in the US Virgin Islands. Coral Reefs 28, 925-937. (doi:10.1007?s00338-009-0531-7)
30. Dulvy NK, Freckleton RP, Polunin NVC. 2004 Coral reef cascades and the indirect effects of predator removal by exploitation. Ecol. Lett. 7, 410-416. (doi:10.1111/j.1461-0248.2004.00593.x)
31. Sweatman HPA. 2008 No-take reserves protect coral reefs from predatory starfish. Curr. Biol. 18, R598-R599.(doi:10.1016/j.cub.2008.05.033)
32. Fabricius KE, Okaji K, De’ath G. 2010 Three lines of evidence to link outbreaks of the crown-of-thorns seastar Acanthaster planci to the release of larval food limitation. Coral Reefs 29, 593-605. (doi:10. 1007/s00338-010-0628-z)
33. Baird AH, Pratchett MS, Hoey AS, Herdiana Y, Campbell SJ. 2013 Acanthaster planci is a major cause of coral mortality in Indonesia. Coral Reefs 32, 803-812. (doi:10.1007/s00338-013-1025-1)
34. Huang D. 2012 Threatened reef corals of the world. PLoS ONE 7, e34459. (doi:10.1371/journal.pone.0034459)
35. Faith DP, Richards ZT. 2012 Climate change impacts on the tree of life: changes in phylogenetic diversity illustrated for Acropora corals. Biology 1, 906-932.(doi:10.3390/biology1030906)
36. Huang D, Roy K. 2013 Anthropogenic extinction threats and future loss of evolutionary history in reef corals. Ecol. Evol. 3, 1184-1193. (doi:10.1002?ece3.527)
37. Gubbay S. 1995 Marine protected areas—past, present and future. In Marine protected areas: principles and techniques for management (ed. S Gubbay), pp. 1-14. London, UK: Chapman & Hall.
38. Christie P, White AT. 2007 Best practices for improved governance of coral reef marine protected areas. Coral Reefs 26, 1047-1056. (doi:10.1007?s00338-007-0235-9)
39. Helmus MR, Bland TJ, Williams CK, Ives AR. 2007 Phylogenetic measures of biodiversity. Am. Nat. 169, E68-E83. (doi:10.1086/511334)
40. Tucker CM, Cadotte MW. 2013 Unifying measures of biodiversity: understanding when richness and phylogenetic diversity should be congruent. Divers. Distrib. 19, 845-854. (doi:10.1111?ddi.12087)
41. Helmus MR, Savage K, Diebel MW, Maxted JT, Ives AR. 2007 Separating the determinants of phylogenetic community structure. Ecol. Lett. 10, 917-925. (doi:10.1111/j.1461-0248.2007.01083.x)
42. Pavoine S, Bonsall MB. 2011 Measuring biodiversity to explain community assembly: a unified approach. Biol. Rev. 86, 792-812. (doi:10.1111/j.1469-185X. 2010.00171.x)
43. Sechrest W, Brooks TM, da Fonseca GAB, Konstant WR, Mittermeier RA, Purvis A, Rylands AB, Gittleman JL. 2002 Hotspots and the conservation of evolutionary history. Proc. Natl Acad. Sci. USA 99, 2067-2071. (doi:10.1073/pnas.251680798)
44. Fritz SA, Purvis A. 2010 Phylogenetic diversity does not capture body size variation at risk in the world’s mammals. Proc. R. Soc. B 277, 2435-2441. (doi:10. 1098/rspb.2010.0030)
45. Devictor V, Mouillot D, Meynard C, Jiguet F, Thuiller W, Mouquet N. 2010 Spatial mismatch and congruence between taxonomic, phylogenetic and functional diversity: the need for integrative conservation strategies in a changing world. Ecol. Lett. 3, 1030-1040. (doi:10.1111/j.1461-0248.2010. 01493.x)
46. Hughes TP, Graham NAJ, Jackson JBC, Mumby PJ, Steneck RS. 2010 Rising to the challenge of sustaining coral reef resilience. Trends Ecol. Evol. 25, 633-642. (doi:10.1016/j.tree.2010.07.011)
47. D’agata S et al. 2014 Human-mediated loss of phylogenetic and functional diversity in coral reef fishes. Curr. Biol. 24, 555-560. (doi:10.1016/j.cub. 2014.01.049)
48. Gravel D, Bell T, Barbera C, Combe M, Pommier T, Mouquet N. 2012 Phylogenetic constraints on ecosystem functioning. Nat. Commun. 3, 1117. (doi:10.1038/ncomms2123)
49. Best RJ, Caulk NC, Stachowicz JJ. 2013 Trait vs. phylogenetic diversity as predictors of competition and community composition in herbivorous marine amphipods. Ecol. Lett. 16, 72-80. (doi:10.1111?ele.12016)
50. Cairns SD. 2009 Phylogenetic list of 722 valid recent azooxanthellate scleractinian species, with their junior synonyms and depth ranges. In Cold-water corals: the biology and geology of deep-sea coral habitats (eds JM Roberts, A Wheeler, A Freiwald, SD Cairns), online appendix. Cambridge, UK: Cambridge University Press.
51. Swenson MS, Suri R, Linder CR, Warnow T. 2012 SuperFine: fast and accurate supertree estimation. Syst. Biol. 61, 214-227. (doi:10.1093/sysbio?syr092)
52. Swofford DL. 2003 PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version4. Sunderland, MA: Sinauer Associates.
53. Nguyen N, Mirarab S, Warnow T. 2012 MRL and SuperFineþMRL: new supertree methods. Algorithms Mol. Biol. 7, 3. (doi:10.1186/1748-7188-7-3)
54. Stamatakis A. 2006 RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690. (doi:10.1093/bioinformatics/btl446)
55. Miller MA, Pfeiffer W, Schwartz T. 2010 Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In Gateway Computing Environments Workshop, New Orleans, LA, USA, 14 November 2010, pp. 1-7. (doi:10.1109/GCE. 2010.5676129)
56. Drummond AJ, Rambaut A. 2007 BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214. (doi:10.1186/1471-2148-7-214)
57. Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012 Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969-1973. (doi:10.1093/molbev/mss075)
58. Stolarski J, Kitahara MV, Miller DJ, Cairns SD, Mazur M, Meibom A. 2011 The ancient evolutionary origins of Scleractinia revealed by azooxanthellate corals. BMC Evol. Biol. 11, 316. (doi:10.1186/1471-2148-11-316)
59. Wood HM, Matzke NJ, Gillespie RG, Griswold CE. 2013 Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders. Syst. Biol. 62, 264-284. (doi:10.1093/sysbio/sys092)
60. Rambaut A, Drummond AJ. 2009 Tracer: MCMC trace analysis tool. Version 1.5.
61. Kuhn TS, Mooers AØ, Thomas GH. 2011 A simple polytomy resolver for dated phylogenies. Methods Ecol. Evol. 2, 427-436. (doi:10.1111/j.2041-210X. 2011.00103.x)
62. Veron JEN, DeVantier LM, Turak E, Green AL, Kininmonth S, Stafford-Smith MG, Peterson N. 2009 Delineating the coral triangle. Galaxea 11, 91-100. (doi:10.3755/galaxea.11.91)
63. Veron JEN, DeVantier LM, Turak E, Green AL, Kininmonth S, Stafford-Smith MG, Peterson N. 2011 The Coral Triangle. In Coral reefs: an ecosystem in transition (eds Z Dubinsky, N Stambler), pp. 47-55. Dordrecht, The Netherlands: Springer.
64. Hughes TP, Connolly SR, Keith SA. 2013 Geographic ranges of reef corals (Cnidaria: Anthozoa: Scleractinia) in the Indo-Pacific. Ecology 94, 1659. (doi:10.1890/13-0361.1)
65. Darling ES, Alvarez-Filip L, Oliver TA, McClanahan TR, Coˆte´ IM. 2012 Evaluating life-history strategies of reef corals from species traits. Ecol. Lett. 15, 1378-1386. (doi:10.1111/j.1461-0248.2012.01861.x)
66. Davies TJ et al. 2008 Phylogenetic trees and the future of mammalian biodiversity. Proc. Natl Acad. Sci. USA 105, 11 556-11 563. (doi:10.1073/pnas.0801917105)
67. Webb CO. 2000 Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. Am. Nat. 156, 145-155. (doi:10.1086?303378)
68. Vellend M, Cornwell WK, Magnuson-Ford K, Mooers AØ. 2010 Measuring phylogenetic biodiversity. In Biological diversity: frontiers in measurement and assessment, pp. 194-207. Oxford, UK: Oxford University Press.
69. Colless DH. 1982 Review of ‘Phylogenetics: the theory and practice of phylogenetic systematics’. Syst. Zool. 31, 100-104. (doi:10.2307/2413420)
70. Pybus OG, Harvey PH. 2000 Testing macroevolutionary models using incomplete molecular phylogenies. Proc. R. Soc. Lond. B 267, 2267-2272. (doi:10.1098/rspb.2000.1278)
71. Blum MGB, Francois O, Janson S. 2006 The mean, variance and limiting distribution of two statistics sensitive to phylogenetic tree balance. Ann. Appl. Probab. 16, 2195-2214. (doi:10.1214?105051606000000547)
72. Pybus OG, Rambaut A, Holmes EC, Harvey PH. 2002 New inferences from tree shape: numbers of missing taxa and population growth rates. Syst. Biol. 51, 881-888. (doi:10.1080/1063515 0290155881)
73. Purvis A, Agapow PM, Gittleman JL, Mace GM. 2000 Nonrandom extinction and the loss of evolutionary history. Science 288, 328-330. (doi:10.1126?science.288.5464.328)
74. Parhar RK, Mooers AØ. 2011 Phylogenetically clustered extinction risks do not substantially prune the tree of life. PLoS ONE 6, e23528. (doi:10.1371?journal.pone.0023528)
75. R Core Team. 2013 R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing.
76. Paradis E, Claude J, Strimmer K. 2004 APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289-290. (doi:10.1093?bioinformatics/btg412)
77. Bortolussi N, Durand E, Blum M, François O. 2006 apTreeshape: statistical analysis of phylogenetic tree shape. Bioinformatics 22, 363-364. (doi:10.1093?bioinformatics/bti798)
78. Orme CDL, Freckleton RP, Thomas GH, Petzoldt T, Fritz SA, Isaac NJB, Pearse WD. 2013 caper: Comparative analyses of phylogenetics and evolution in R. R Package Version 0.5.2.
79. Bates D, Maechler M, Bolker B, Walker S. 2014 lme4: Linear mixed-effects models using Eigen and S4. R Package Version 1.0-6.
80. Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, Ackerly DD, Blomberg SP, Webb CO. 2010 Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26, 1463-1464. (doi:10. 1093/bioinformatics/btq166)
81. Zupan L et al. 2014 Spatial mismatch of phylogenetic diversity across three vertebrate groups and protected areas in Europe. Divers. Distrib. 20, 674-685. (doi:10.1111/ddi.12186)
82. Allen GR. 2000 Indo-Pacific coral-reef fishes as indicators of conservation hotspots. Proc. 9th Int. Coral Reef Symp., Bali, Indonesia, 23-27 October 2000, vol. 2, pp. 921-926.
83. Roberts CM et al. 2002 Marine biodiversity hotspots and conservation priorities for tropical reefs. Science 295, 1280-1284. (doi:10.1126/science.1067728)
84. Hoeksema BW. 2007 Delineation of the Indo-Malayan centre of maximum marine biodiversity: the Coral Triangle. In Biogeography, time, and place: distributions, barriers, and islands (ed. W Renema), pp. 117-178. Dordrecht, The Netherlands: Springer.
85. van Hooidonk RJ, Maynard JA, Planes S. 2013 Temporary refugia for coral reefs in a warming world. Nat. Clim. Change 3, 508-511. (doi:10.1038?nclimate1829)
86. Romano SL, Palumbi SR. 1996 Evolution of scleractinian corals inferred from molecular systematics. Science 271, 640-642. (doi:10.1126?science.271.5249.640)
87. Romano SL, Cairns SD. 2000 Molecular phylogenetic hypotheses for the evolution of scleractinian corals. Bull. Mar. Sci. 67, 1043-1068.
88. Graham NAJ, Wilson SK, Jennings S, Polunin NVC, Bijoux JP, Robinson J. 2006 Dynamic fragility of oceanic coral reef ecosystems. Proc. Natl Acad. Sci. USA 103, 8425-8429. (doi:10.1073/pnas.0600693103)
89. Wilson SK, Graham NAJ, Pratchett MS, Jones GP, Polunin NVC. 2006 Multiple disturbances and the global degradation of coral reefs: are reef fishes at risk or resilient? Glob. Change Biol. 12, 2220-2234. (doi:10.1111/j.1365-2486.2006.01252.x)
90. Chong-Seng KM, Mannering TD, Pratchett MS, Bellwood DR, Graham NAJ. 2012 The influence of coral reef benthic condition on associated fish assemblages. PLoS ONE 7, e42167. (doi:10.1371?journal.pone.0042167)
91. Idjadi JA, Edmunds PJ. 2006 Scleractinian corals as facilitators for other invertebrates on a Caribbean reef. Mar. Ecol. Prog. Ser. 319, 117-127. (doi:10. 3354/meps319117)
92. Pratchett MS, Wilson SK, Graham NAJ, Munday PL. 2009 Coral bleaching and consequences for motile reef organisms: past, present and uncertain future effects. In Ecological studies: coral bleaching (eds MJH van Oppen, JM Lough), pp. 139-158. Berlin, Germany: Springer.
93. Fabricius KE, De’ath G, Noonan S, Uthicke S. 2014 Ecological effects of ocean acidification and habitat complexity on reef-associated macroinvertebrate communities. Proc. R. Soc. B 281, 20132479. (doi:10.1098/rspb.2013.2479)
94. Willis BL, Page CA, Dinsdale EA. 2004 Coral disease on the Great Barrier Reef. In Coral health and disease (eds E Rosenberg, Y Loya), pp. 69-104. Berlin, Germany: Springer.
95. Séré MG, Schleyer MH, Quod JP, Chabanet P. 2012 Porites white patch syndrome: an unreported coral disease on Western Indian Ocean reefs. Coral Reefs 31, 739. (doi:10.1007/s00338-012-0897-9)
96. Tilman D, May RM, Lehman CL, Nowak MA. 1994 Habitat destruction and the extinction debt. Nature 371, 65-66. (doi:10.1038/371065a0)
97. Díaz M, Madin JS. 2011 Macroecological relationships between coral species’ traits and disease potential. Coral Reefs 30, 73-84. (doi:10. 1007/s00338-010-0668-4)
98. Darling ES, McClanahan TR, Côte IM. 2013 Life histories predict coral community disassembly under multiple stressors. Glob. Change Biol. 19, 1930-1940. (doi:10.1111/gcb.12191)
99. Baird AH, Guest JR, Willis BL. 2009 Systematic and biogeographical patterns in the reproductive biology of scleractinian corals. Annu. Rev. Ecol. Evol. Syst. 40, 551-571. (doi:10.1146/annurev.ecolsys.110308. 120220)
100. Kerr AM, Baird AH, Hughes TP. 2011 Correlated evolution of sex and reproductive mode in corals (Anthozoa: Scleractinia). Proc. R. Soc. B 278, 75-81. (doi:10.1098/rspb.2010.1196)
101. Mouquet N et al. 2012 Ecophylogenetics: advances and perspectives. Biol. Rev. 87, 769-785. (doi:10. 1111/j.1469-185X.2012.00224.x)
102. Purvis A, Hector A. 2000 Getting the measure of biodiversity. Nature 405, 212-219. (doi:10.1038?35012221)
103. Kelly S, Grenyer R, Scotland RW. 2014 Phylogenetic trees do not reliably predict feature diversity. Divers. Distrib. 20, 600-612. (doi:10.1111?ddi.12188)
104. Jablonski D. 2002 Survival without recovery after mass extinctions. Proc. Natl Acad. Sci. USA 99, 8139-8144. (doi:10.1073/pnas.102163299)