[1] | Hughes TP, Baird AH, Bellwood DR, Card M, Connolly SR, et al. (2003) Climate change, human impacts, and the resilience of coral reefs. Science 301: 929–933. doi:10.1126/science.1085046.
|
[2] | Bruno JF, Selig ER, Casey KS, Page CA, Willis BL, et al. (2007) Thermal stress and coral cover as drivers of coral disease outbreaks. PLoS Biol 5: e124. doi:10.1371/journal.pbio.0050124.
|
[3] | Hoegh-Guldberg O, Mumby PJ, Hooten AJ, Steneck RS, Greenfield P, et al. (2007) Coral reefs under rapid climate change and ocean acidification. Science 318: 1737–1742. doi:10.1126/science.1152509.
|
[4] | Knowlton N, Jackson JBC (2008) Shifting baselines, local impacts, and global change on coral reefs. PLoS Biol 6: e54. doi:10.1371/journal.pbio.0060054.
|
[5] | De'ath G, Lough JM, Fabricius KE (2009) Declining coral calcification on the Great Barrier Reef. Science 323: 116–119. doi:10.1126/science.1165283.
|
[6] | Veron JEN, Hoegh-Guldberg O, Lenton TM, Lough JM, Obura DO, et al. (2009) The coral reef crisis: the critical importance of <350 ppm CO2. Mar Poll Bull 58: 1428–1436. doi:10.1016/j.marpolbul.2009.09.009.
|
[7] | Hughes TP (1994) Catastrophes, phase shifts, and large-scale degradation of a Caribbean coral reef. Science 265: 1547–1551. doi:10.1126/science.265.5178.1547.
|
[8] | McCook LJ (1999) Macroalgae, nutrients and phase shifts on coral reefs: scientific issues and management consequences for the Great Barrier Reef. Coral Reefs 18: 357–367. doi:10.1007/s003380050213.
|
[9] | Pandolfi JM, Jackson JBC, Baron N, Bradbury RH, Guzman HM, et al. (2005) Are U.S. coral reefs on the slippery slope to slime? Science 308: 1742–1743. doi:10.1126/science.1104258.
|
[10] | Hughes TP, Rodrigues MJ, Bellwood DR, Ceccarelli D, Hoegh-Guldberg O, et al. (2007) Phase shifts, herbivory, and the resilience of coral reefs to climate change. Curr Biol 17: 360–365. doi:10.1016/j.cub.2006.12.049.
|
[11] | Carpenter KE, Abrar M, Aeby GS, Aronson RB, Banks S, 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.
|
[12] | Polidoro BA, Elfes CT, Sanciangco JC, Pippard H, Carpenter KE (2011) Conservation status of marine biodiversity in Oceania: an analysis of marine species on the IUCN Red List of Threatened Species. J Mar Biol 2011: 247030. doi:10.1155/2011/247030.
|
[13] | Roberts CM, McClean CJ, Veron JEN, Hawkins JP, Allen GR, et al. (2002) Marine biodiversity hotspots and conservation priorities for tropical reefs. Science 295: 1280–1284. doi:10.1126/science.1067728.
|
[14] | 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.
|
[15] | Margules CR, Pressey RL (2000) Systematic conservation planning. Nature 405: 243–253. doi:10.1038/35012251.
|
[16] | Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature 403: 853–858. doi:10.1038/35002501.
|
[17] | Murdoch W, Polasky S, Wilson KA, Possingham HP, Kareiva P, et al. (2007) Maximizing return on investment in conservation. Biol Conserv 139: 375–388. doi:10.1016/j.biocon.2007.07.011.
|
[18] | IUCN (2001) IUCN Red List Categories and Criteria: Version 3.1. Gland, Switzerland and Cambridge, UK: IUCN. 30 p.
|
[19] | Mace GM, Collar NJ, Gaston KJ, Hilton-Taylor C, Ak?akaya HR, et al. (2008) Quantification of extinction risk: IUCN's system for classifying threatened species. Conserv Biol 22: 1424–1442. doi:10.1111/j.1523-1739.2008.01044.x.
|
[20] | Rodrigues ASL, Ak?akaya HR, Andelman SJ, Bakarr MI, Boitani L, et al. (2004) Global gap analysis: priority regions for expanding the global protected-area network. Bioscience 54: 1092–1100. doi:10.1641/0006-3568(2004)054[1092:GGAPRF]2?.0.CO;2.
|
[21] | Rodrigues ASL, Pilgrim JD, Lamoreux JF, Hoffman M, Brooks TM (2006) The value of the IUCN Red List for conservation. Trends Ecol Evol 21: 71–76. doi:10.1016/j.tree.2005.10.010.
|
[22] | Hoffmann M, Brooks TM, da Fonseca GAB, Gascon C, Hawkins AFA, et al. (2008) Conservation planning and the IUCN Red List. Endang Species Res 6: 113–125. doi:10.3354/esr00087.
|
[23] | May RM (1990) Taxonomy as destiny. Nature 347: 129–130. doi:10.1038/347129a0.
|
[24] | Altschul SF, Lipman DL (1990) Equal animals. Nature 348: 493–494. doi:10.1038/348493c0.
|
[25] | Witting L, Loeschcke V (1995) The optimization of biodiversity conservation. Biol Conserv 71: 205–207. doi:10.1016/0006-3207(94)00041-N.
|
[26] | Mace GM, Gittleman JL, Purvis A (2003) Preserving the tree of life. Science 300: 1707–1709. doi:10.1126/science.1085510.
|
[27] | de Queiroz K (2011) Branches in the lines of descent: Charles Darwin and the evolution of the species concept. Biol J Linn Soc 103: 19–35. doi:10.1111/j.1095-8312.2011.01634.x.
|
[28] | Pavoine S, Ollier S, Dufour AB (2005) Is the originality of a species measurable? Ecol Lett 8: 579–586. doi:10.1111/j.1461-0248.2005.00752.x.
|
[29] | Isaac NJB, Turvey ST, Collen B, Waterman C, Baillie JEM (2007) Mammals on the EDGE: conservation priorities based on threat and phylogeny. PLoS ONE 2: e296. doi:10.1371/journal.pone.0000296.
|
[30] | Agnarsson I, Kuntner M, May-Collado LJ (2010) Dogs, cats, and kin: a molecular species-level phylogeny of Carnivora. Mol Phylogenet Evol 54: 726–745. doi:10.1016/j.ympev.2009.10.033.
|
[31] | Kuntner M, May-Collado LJ, Agnarsson I (2011) Phylogeny and conservation priorities of afrotherian mammals (Afrotheria, Mammalia). Zool Scr 40: 1–15. doi:10.1111/j.1463-6409.2010.00452.x.
|
[32] | Collen B, Turvey ST, Waterman C, Meredith HMR, Kuhn TS, et al. (2011) Investing in evolutionary history: implementing a phylogenetic approach for mammal conservation. Philos Trans R Soc B-Biol Sci 366: 2611–2622. doi:10.1098/rstb.2011.0109.
|
[33] | May-Collado LJ, Agnarsson I (2011) Phylogenetic analysis of conservation priorities for aquatic mammals and their terrestrial relatives, with a comparison of methods. PLoS ONE 6: e22562. doi:10.1371/journal.pone.0022562.t005.
|
[34] | Nee S, May RM (1997) Extinction and the loss of evolutionary history. Science 278: 692–694. doi:10.1126/science.278.5338.692.
|
[35] | McKinney ML (1997) Extinction vulnerability and selectivity: combining ecological and paleontological views. Annu Rev Ecol Syst 28: 495–516. doi:10.1146/annurev.ecolsys.28.1.495.
|
[36] | Russell GJ, Brooks TM, McKinney MM, Anderson CG (1998) Present and future taxonomic selectivity in bird and mammal extinctions. Conserv Biol 12: 1365–1376. doi:10.1111/j.1523-1739.1998.96332.x.
|
[37] | 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.
|
[38] | Purvis A (2008) Phylogenetic approaches to the study of extinction. Annu Rev Ecol Evol Syst 39: 301–319. doi:10.1146/annurev-ecolsys-063008-102010.
|
[39] | Loya Y, Sakai K, Yamazato K, Nakano Y, Sambali H, et al. (2001) Coral bleaching: the winners and the losers. Ecol Lett 4: 122–131. doi:10.1046/j.1461-0248.2001.00203.x.
|
[40] | van Woesik R, Sakai K, Ganase A, Loya Y (2011) Revisiting the winners and the losers a decade after coral bleaching. Mar Ecol-Prog Ser 434: 67–76. doi:10.3354/meps09203.
|
[41] | Bellwood DR, Hughes TP (2001) Regional-scale assembly rules and biodiversity of coral reefs. Science 292: 1532–1534. doi:10.1126/science.1058635.
|
[42] | Fukami H, Chen CA, Budd AF, Collins A, Wallace CC, et al. (2008) Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria). PLoS ONE 3: e3222. doi:10.1371/journal.pone.0003222.
|
[43] | Díaz M, Madin J (2011) Macroecological relationships between coral species' traits and disease potential. Coral Reefs 30: 73–84. doi:10.1007/s00338-010-0668-4.
|
[44] | Faith DP (1992) Conservation evaluation and phylogenetic diversity. Biol Conserv 61: 1–10. doi:10.1016/0006-3207(92)91201-3.
|
[45] | Forsman ZH, Birkeland C (2009) Porites randalli: a new coral species (Scleractinia, Poritidae) from American Samoa. Zootaxa 2244: 51–59.
|
[46] | Hoeksema BW (2009) Attached mushroom corals (Scleractinia: Fungiidae) in sediment-stressed reef conditions at Singapore, including a new species and a new record. Raffles Bull Zool S22: 81–90.
|
[47] | Wallace CC, Turak E, DeVantier LM (2011) Novel characters in a conservative coral genus: three new species of Astreopora (Scleractinia: Acroporidae) from West Papua. J Nat Hist 45: 1905–1924. doi:10.1080/00222933.2011.573098.
|
[48] | Cairns SD (2009) Phylogenetic list of 722 valid Recent azooxanthellate scleractinian species, with their junior synonyms and depth ranges. In: Roberts JM, Wheeler A, Freiwald A, Cairns SD, editors. Cold-Water Corals: The Biology and Geology of Deep-Sea Coral Habitats. New York: Cambridge University Press. Available: http://www.lophelia.org/online-appendice?s. Accessed 2011 Jun 6.
|
[49] | Baum BR (1992) Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41: 3–10. doi:10.2307/1222480.
|
[50] | Ragan MA (1992) Phylogenetic inference based on matrix representation of trees. Mol Phylogenet Evol 1: 53–58. doi:10.1016/1055-7903(92)90035-F.
|
[51] | Kerr AM (2005) Molecular and morphological supertree of stony corals (Anthozoa: Scleractinia) using matrix representation parsimony. Biol Rev 80: 543–558. doi:10.1017/S1464793105006780.
|
[52] | Romano SL, Palumbi SR (1996) Evolution of scleractinian corals inferred from molecular systematics. Science 271: 640–642. doi:10.1126/science.271.5249.640.
|
[53] | Romano SL, Cairns SD (2000) Molecular phylogenetic hypotheses for the evolution of scleractinian corals. Bull Mar Sci 67: 1043–1068.
|
[54] | Bininda-Emonds ORP, Gittleman JL, Steel MA (2002) The (super)tree of life: procedures, problems, and prospects. Annu Rev Ecol Syst 33: 265–289. doi:10.1146/annurex.ecolysis.33.010802.15051?1.
|
[55] | Bininda-Emonds ORP (2004) The evolution of supertrees. Trends Ecol Evol 19: 315–322. doi:10.1016/j.tree.2004.03.015.
|
[56] | Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30: 3059–3066. doi:10.1093/nar/gkf436.
|
[57] | Katoh K, Toh H (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9: 286–298. doi:10.1093/bib/bbn013.
|
[58] | 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.
|
[59] | Stamatakis A, Hoover P, Rougemont J (2008) A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 57: 758–771. doi:10.1080/10635150802429642.
|
[60] | Miller MA, Pfeiffer W, Schwartz T (2010) Creating the CIPRES Science Gateway for inference of large phylogenetic trees. pp. 1–8. doi:10.1109/GCE.2010.5676129.
|
[61] | Budd AF, Smith ND (2005) Diversification of a new Atlantic clade of scleractinian reef corals: insights from phylogenetic analysis of morphologic and molecular data. Paleontol Soc Pap 11: 103–128.
|
[62] | Cairns SD (1997) A generic revision and phylogenetic analysis of the Turbinoliidae (Cnidaria: Scleractinia). Smithsonian Contrib Zool 591: 1–55.
|
[63] | Cairns SD (2001) A generic revision and phylogenetic analysis of the Dendrophylliidae (Cnidaria: Scleractinia). Smithsonian Contrib Zool 615: 1–75.
|
[64] | Daly M, Fautin DG, Cappola VA (2003) Systematics of the Hexacorallia (Cnidaria: Anthozoa). Zool J Linn Soc 139: 419–437. doi:10.1046/j.1096-3642.2003.00084.x.
|
[65] | Hoeksema BW (1989) Taxonomy, phylogeny and biogeography of mushroom corals (Scleractinia: Fungiidae). Zool Verh Leiden 254: 1–295.
|
[66] | Hoeksema BW (1993) Historical biogeography of Fungia (Pleuractis) spp. (Scleractinia: Fungiidae), including a new species from the Seychelles. Zool Meded Leiden 67: 639–654.
|
[67] | Pandolfi JM (1992) Successive isolation rather than evolutionary centres for the origination of Indo-Pacific reef corals. J Biogeogr 19: 593–609. doi:10.2307/2845703.
|
[68] | Pires DO, Castro CB (1997) Scleractinia and Corallimorpharia: An analysis of cnidae affinity. Proc 8th Int Coral Reef Symp 2: 1581–1586.
|
[69] | Wallace CC (1999) Staghorn Corals of the World: A Revision of the Coral Genus Acropora. Collingwood: CSIRO Publishing. 421 p.
|
[70] | Swofford DL (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sunderland: Sinauer Associates.
|
[71] | Benzoni F, Stefani F, Stolarski J, Pichon M, Mitta G, et al. (2007) Debating phylogenetic relationships of the scleractinian Psammocora: molecular and morphological evidences. Contrib Zool 76: 35–54.
|
[72] | Benzoni F, Stefani F, Pichon M, Galli P (2010) The name game: morpho-molecular species boundaries in the genus Psammocora (Cnidaria, Scleractinia). Zool J Linn Soc 160: 421–456. doi:10.1111/j.1096-3642.2010.00622.x.
|
[73] | Best MB, Hoeksema BW (1987) New observations on scleractinian corals from Indonesia: 1. Free-living species belonging to the Faviina. Zool Meded Leiden 61: 387–403.
|
[74] | Chevalier J-P (1971) Les scléractiniaires de la Mélanésie Francaise (Nouvelle Calédonie, Iles Chesterfield, Iles Loyauté, Nouvelles Hébrides). Première partie. Expéd Fran?aise Récifs Coralliens Nouvelle Calédonie 5: 1–307.
|
[75] | Claereboudt MR (1990) Galaxea paucisepta nom. nov. (for G. pauciradiata), rediscovery and redescription of a poorly known scleractinian species (Oculinidae). Galaxea 9: 1–8.
|
[76] | Claereboudt MR, Al-Amri IS (2004) Calathiscus tantillus, a new genus and new species of scleractinian coral (Scleractinia, Poritidae) from the Gulf of Oman. Zootaxa 532: 1–8.
|
[77] | Ditlev H (2003) New scleractinian corals (Cnidaria: Anthozoa) from Sabah, North Borneo. Description of one new genus and eight new species, with notes on their taxonomy and ecology. Zool Meded Leiden 77: 193–219.
|
[78] | Fenner DP (1993) Species distinctions among several Caribbean stony corals. Bull Mar Sci 53: 1099–1116.
|
[79] | Gittenberger A, Reijnen BT, Hoeksema BW (2011) A molecularly based phylogeny reconstruction of mushroom corals (Scleractinia: Fungiidae) with taxonomic consequences and evolutionary implications for life history traits. Contrib Zool 80: 107–132.
|
[80] | Head SM (1983) An undescribed species of Merulina and a new genus and species of siderastreid coral from the Red Sea. J Nat Hist 17: 419–435. doi:10.1080/00222938300770281.
|
[81] | Huang D, Licuanan WY, Baird AH, Fukami H (2011) Cleaning up the “Bigmessidae”: molecular phylogeny of scleractinian corals from Faviidae, Merulinidae, Pectiniidae and Trachyphylliidae. BMC Evol Biol 11: 37. doi:10.1186/1471-2148-11-37.
|
[82] | Kitahara MV, Cairns SD, Stolarski J, Blair D, Miller DJ (2010) A comprehensive phylogenetic analysis of the Scleractinia (Cnidaria, Anthozoa) based on mitochondrial CO1 sequence data. PLoS ONE 5: e11490. doi:10.1371/journal.pone.0011490.
|
[83] | Lin M-F, Luzon KS, Licuanan WY, Ablan-Lagman MC, Chen CA (2011) Seventy-four universal primers for characterizing the complete mitochondrial genomes of scleractinian corals (Cnidaria; Anthozoa). Zool Stud 50: 513–524.
|
[84] | Locke JM, Weil E, Coates KA (2007) A newly documented species of Madracis (Scleractinia: Pocilloporidae) from the Caribbean. Proc Biol Soc Wash 120: 214–226. doi:10.2988/0006-324X(2007)120[214:ANDSOM]2.?0.CO;2.
|
[85] | Moll H, Best MB (1984) New scleractinian corals (Anthozoa: Scleractinia) from the Spermonde Archipelago, South Sulawesi, Indonesia. Zool Meded Leiden 58: 47–58.
|
[86] | Scheer G, Pillai CSG (1983) Report on the stony corals from the Red Sea. Zoologica 131: 1–198.
|
[87] | Vaughan TW (1901) The stony corals of the Porto Rican waters. Bull US Fish Commiss 1900 2: 289–320.
|
[88] | Veron JEN, Pichon M, Wijsman-Best M (1977) Scleractinia of Eastern Australia. Part II. Families Faviidae, Trachyphylliidae. Townsville: Australian Institute of Marine Science. 233 p.
|
[89] | Veron JEN, Pichon M (1980) Scleractinia of Eastern Australia. Part III. Families Agariciidae, Siderastreidae, Fungiidae, Oculinidae, Merulinidae, Mussidae, Pectiniidae, Caryophylliidae, Dendrophylliidae. Townsville: Australian Institute of Marine Science. 422 p.
|
[90] | Veron JEN (1986) Corals of Australia and the Indo-Pacific. Sydney: Angus & Robertson. 644 p.
|
[91] | Veron JEN (1990) New Scleractinia from Japan and other Indo-West Pacific countries. Galaxea 9: 95–173.
|
[92] | Veron JEN (2000) Corals of the World. Townsville: Australian Institute of Marine Science. 1382 p.
|
[93] | Veron JEN (2002) New Species Described in Corals of the World. Townsville: Australian Institute of Marine Science. 209 p.
|
[94] | Wallace CC, Chen CA, Fukami H, Muir PR (2007) Recognition of separate genera within Acropora based on new morphological, reproductive and genetic evidence from Acropora togianensis, and elevation of the subgenus Isopora Studer, 1878 to genus (Scleractinia: Astrocoeniidae; Acroporidae). Coral Reefs 26: 231–239. doi:10.1007/s00338-007-0203-4.
|
[95] | Wells JW (1937) New genera of Mesozoic and Cenozoic corals. J Paleontol 11: 73–77.
|
[96] | Wijsman-Best M (1972) Systematics and ecology of New Caledonian Faviinae (Coelenterata – Scleractinia). Contrib Zool 42: 3–90.
|
[97] | Yabe H, Sugiyama T (1941) Recent reef-building corals from Japan and the south sea islands under the Japanese mandate. II. Sci Rep T?hoku Imp Univ 2nd Ser (Geol) Spec Vol 2: 67–91.
|
[98] | Bininda-Emonds ORP, Beck RMD, Purvis A (2005) Getting to the roots of matrix representation. Syst Biol 54: 668–672. doi:10.1080/10635150590947113.
|
[99] | Jones KE, Bininda-Emonds ORP, Gittleman JL (2005) Bats, clocks, and rocks: diversification patterns in Chiroptera. Evolution 59: 2243–2255. doi:10.1111/j.0014-3820.2005.tb00932.x.
|
[100] | Maddison WP, Mooers A? (2007) Tuatara: Conservation Priority in a Phylogenetic Context. Version 1.0. Available: http://mesquiteproject.org/packages/tuat?ara. Accessed 2011 Jun 20.
|
[101] | Redding DW, Mooers A? (2006) Incorporating evolutionary measures into conservation prioritization. Conserv Biol 20: 1670–1678. doi:10.1111/j.1523-1739.2006.00555.x.
|
[102] | Mooers A?, Faith DP, Maddison WP (2008) Converting endangered species categories to probabilities of extinction for phylogenetic conservation prioritization. PLoS ONE 3: e3700. doi:10.1371/journal.pone.0003700.
|
[103] | Blomberg SP, Garland T Jr, Ives AR (2003) Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57: 717–745. doi:10.1111/j.0014-3820.2003.tb00285.x.
|
[104] | Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, et al. (2010) Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26: 1463–1464. doi:10.1093/bioinformatics/btq166.
|
[105] | Fritz SA, Purvis A (2010) Selectivity in mammalian extinction risk and threat types: a new measure of phylogenetic signal strength in binary traits. Conserv Biol 24: 1042–1051. doi:10.1111/j.1523-1739.2010.01455.x.
|
[106] | Orme D, Freckleton RP, Thomas G, Petzoldt T, Fritz SA (2008) CAIC: Comparative Analyses Using Independent Contrasts. R Package Version 1.0.4-94. Available: http://r-forge.r-project.org/projects/ca?ic. Accessed 2011 Jun 20.
|
[107] | Felsenstein J (1985) Phylogenies and the comparative method. Am Nat 125: 1–15. doi:10.1086/284325.
|
[108] | 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.
|
[109] | Fritz SA, Purvis A (2010) Phylogenetic diversity does not capture body size variation at risk in the world's mammals. Proc R Soc B-Biol Sci 277: 2435–2441. doi:10.1098/rspb.2010.0030.
|
[110] | Nystr?m M, Graham NAJ, Lokrantz J, Norstr?m AV (2008) Capturing the cornerstones of coral reef resilience: linking theory to practice. Coral Reefs 27: 795–809. doi:10.1007/s00338-008-0426-z.
|
[111] | Redding DW, Hartmann K, Mimoto A, Bokal D, DeVos M, et al. (2008) Evolutionarily distinctive species often capture more phylogenetic diversity than expected. J Theor Biol 251: 606–615. doi:10.1016/j.jtbi.2007.12.006.
|
[112] | Maherali H, Klironomos JN (2007) Influence of phylogeny on fungal community assembly and ecosystem functioning. Science 316: 1746–1748. doi:10.1126/science.1143082.
|
[113] | Cadotte MW, Cardinale BJ, Oakley TH (2008) Evolutionary history and the effect of biodiversity on plant productivity. Proc Natl Acad Sci USA 105: 17012–17017. doi:10.1073/pnas.0805962105.
|
[114] | 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.
|
[115] | Redding DW, DeWolff CV, Mooers A? (2010) Evolutionary distinctiveness, threat status, and ecological oddity in primates. Conserv Biol 24: 1052–1058. doi:10.1111/j.1523-1739.2010.01532.x.
|
[116] | Connolly J, Cadotte MW, Brophy C, Dooley á, Finn J, et al. (2011) Phylogenetically diverse grasslands are associated with pairwise interspecific processes that increase biomass. Ecology 92: 1385–1392. doi:10.1890/10-2270.1.
|
[117] | Flynn DFB, Mirotchnick N, Jain M, Palmer MI, Naeem S (2011) Functional and phylogenetic diversity as predictors of biodiversity–ecosystem function relationships. Ecology 92: 1573–1581. doi:10.1890/10-1245.1.
|
[118] | Hughes TP, Bellwood DR, Connolly SR (2002) Biodiversity hotspots, centres of endemicity, and the conservation of coral reefs. Ecol Lett 5: 775–784. doi:10.1046/j.1461-0248.2002.00383.x.
|
[119] | Beger M, Jones GP, Munday PL (2003) Conservation of coral reef biodiversity: a comparison of reserve selection procedures for corals and fishes. Biol Conserv 111: 53–62. doi:10.1016/S0006-3207(02)00249-5.
|
[120] | Almany GR, Connolly SR, Heath DD, Hogan JD, Jones GP, et al. (2009) Connectivity, biodiversity conservation and the design of marine reserve networks for coral reefs. Coral Reefs 28: 339–351. doi:10.1007/s00338-009-0484-x.
|
[121] | Carpenter KE, Barber PH, Crandall ED, Ablan-Lagman MC, Ambariyanto , et al. (2011) Comparative phylogeography of the Coral Triangle and implications for marine management. J Mar Biol 2011: 396982. doi:10.1155/2011/396982.
|
[122] | Davies TJ, Fritz SA, Grenyer R, Orme CDL, Bielby J, et al. (2008) Phylogenetic trees and the future of mammalian biodiversity. Proc Natl Acad Sci USA 105: 11556–11563. doi:10.1073/pnas.0801917105.
|
[123] | Parhar RK, Mooers A? (2011) Phylogenetically clustered extinction risks do not substantially prune the Tree of Life. PLoS ONE 6: e23528. doi:10.1371/journal.pone.0023528.
|
[124] | Mooers A? (1995) Tree balance and tree completeness. Evolution 49: 379–384. doi:10.2307/2410349.
|
[125] | Mooers A?, Heard SB (1997) Inferring evolutionary process from phylogenetic tree shape. Q Rev Biol 72: 31–54. doi:10.1086/419657.
|
[126] | Purvis A, Agapow PM (2002) Phylogeny imbalance: taxonomic level matters. Syst Biol 51: 855–854. doi:10.1080/10635150215871.
|
[127] | Blum MGB, Fran?ois O (2006) Which random processes describe the Tree of Life? A large-scale study of phylogenetic tree imbalance. Syst Biol 55: 685–691. doi:10.1080/10635150600889625.
|
[128] | Purvis A, Fritz SA, Rodríguez J, Harvey PH, Grenyer R (2011) The shape of mammalian phylogeny: patterns, processes and scales. Philos Trans R Soc B-Biol Sci 366: 2462–2477. doi:10.1098/rstb.2011.0025.
|
[129] | Colless DH (1982) Review of “Phylogenetics: The Theory and Practice of Phylogenetic Systematics.” Syst Zool 31: 100–104.
|
[130] | Heard SB, Mooers A? (2000) Phylogenetically patterned speciation rates and extinction risks change the loss of evolutionary history during extinctions. Proc R Soc Lond B-Biol Sci 267: 613–620. doi:10.1098/rspb.2000.1046.
|
[131] | Bellwood DR, Hughes TP, Folke C, Nystr?m M (2004) Confronting the coral reef crisis. Nature 429: 827–833. doi:10.1038/nature02691.
|
[132] | Bruno JF, Selig ER (2007) Regional decline of coral cover in the Indo-Pacific: timing, extent, and subregional comparisons. PLoS ONE 2: e711. doi:10.1371/journal.pone.0000711.
|
[133] | Marshall PA, Baird AH (2000) Bleaching of corals on the Great Barrier Reef: differential susceptibilities among taxa. Coral Reefs 19: 155–163. doi:10.1007/s003380000086.
|
[134] | Miller J, Waara R, Muller E, Rogers C (2006) Coral bleaching and disease combine to cause extensive mortality on reefs in US Virgin Islands. Coral Reefs 25: 418. doi:10.1007/s00338-006-0125-6.
|
[135] | 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.
|
[136] | Yee SH, Santavy DL, Barron MG (2011) Assessing the effects of disease and bleaching on Florida Keys corals by fitting population models to data. Ecol Model 222: 1323–1332. doi:10.1016/j.ecolmodel.2011.01.009.
|
[137] | Weitzman ML (1998) The Noah's Ark problem. Econometrica 66: 1279–1298. doi:10.2307/2999617.
|
[138] | Faith DP, Magallón S, Hendry AP, Conti E, Yahara T, et al. (2010) Evosystem services: an evolutionary perspective on the links between biodiversity and human well-being. Curr Opin Environ Sustain 2: 66–74. doi:10.1016/j.cosust.2010.04.002.
|
[139] | Romano SL, Palumbi SR (1997) Molecular evolution of a portion of the mitochondrial 16S ribosomal gene region in scleractinian corals. J Mol Evol 45: 397–411. doi:10.1007/PL00006245.
|
[140] | Fukami H, Budd AF, Paulay G, Sole-Cava AM, Chen CA, et al. (2004) Conventional taxonomy obscures deep divergence between Pacific and Atlantic corals. Nature 427: 832–835. doi:10.1038/nature02339.
|
[141] | Budd AF, Romano SL, Smith ND, Barbeitos MS (2010) Rethinking the phylogeny of scleractinian corals: a review of morphological and molecular data. Integr Comp Biol 50: 411–427. doi:10.1093/icb/icq062.
|
[142] | Palmer CV, Bythell JC, Willis BL (2010) Levels of immunity parameters underpin bleaching and disease susceptibility of reef corals. FASEB J 24: 1935–1946. doi:10.1096/fj.09-152447.
|
[143] | Veron JEN, DeVantier LM, Turak E, Green AL, Kininmonth S, et al. (2009) Delineating the Coral Triangle. Galaxea 11: 91–100. doi:10.3755/galaxea.11.91.
|
[144] | Cadotte MW, Davies TJ (2010) Rarest of the rare: advances in combining evolutionary distinctiveness and scarcity to inform conservation at biogeographical scales. Divers Distrib 16: 376–385. doi:10.1111/j.1472-4642.2010.00650.x.
|
[145] | Steel M, Mimoto A, Mooers A? (2007) Hedging our bets: the expected contribution of species to future phylogenetic diversity. Evol Bioinform 3: 237–244.
|
[146] | Faith DP (2008) Threatened species and the potential loss of phylogenetic diversity: conservation scenarios based on estimated extinction probabilities and phylogenetic risk analysis. Conserv Biol 22: 1461–1470. doi:10.1111/j.1523-1739.2008.01068.x.
|
[147] | Knowlton N, Nunes F (2008) Atlantic corals—least of our concerns? Science E- Letter. Available: http://www.sciencemag.org/content/321/58?88/560.full/reply#sci_el_11734. Accessed 2011 Sep 5.
|
[148] | Carpenter KE, Polidoro BA, Livingstone SR, Aronson RB, Precht WF (2008) Response to N. Knowlton and F. Nunes' E-Letter. Science E-Letter. Available: http://www.sciencemag.org/content/321/58?88/560.full/reply#sci_el_11734. Accessed 2011 Sep 5.
|
[149] | Maynard JA, Baird AH, Pratchett MS (2008) Revisiting the Cassandra syndrome; the changing climate of coral reef research. Coral Reefs 27: 745–749. doi:10.1007/s00338-008-0432-1.
|
[150] | Fabricius KE, Langdon C, Uthicke S, Humphrey C, Noonan S, et al. (2011) Losers and winners in coral reefs acclimatized to elevated carbon dioxide concentrations. Nat Clim Change 1: 165–169. doi:10.1038/nclimate1122.
|
[151] | Pandolfi JM, Connolly SR, Marshall DJ, Cohen AL (2011) Projecting coral reef futures under global warming and ocean acidification. Science 333: 418–422. doi:10.1126/science.1204794.
|
[152] | Rodolfo-Metalpa R, Houlbrèque F, Tambutté E, Boisson F, Baggini C, et al. (2011) Coral and mollusc resistance to ocean acidification adversely affected by warming. Nat Clim Change 1: 308–312. doi:10.1038/nclimate1200.
|