Funding Information This research was funded via a Ph.D. scholarship, Smart State PhD Funding, and ISRS Fellowship at James Cook University (Z. R.) and Chadwick Biodiversity Fellowship at the Australian Museum (Z. R.).
Rarity and genetic diversity in Indo–Pacific Acropora corals
Article first published online: 6 JUL 2012
© 2012 The Authors. Ecology and Evolution published by Blackwell Publishing Ltd.
This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
Ecology and Evolution
Volume 2, Issue 8, pages 1867–1888, August 2012
How to Cite
Richards, Z. T. and van Oppen, Madeleine. J. H. (2012), Rarity and genetic diversity in Indo–Pacific Acropora corals. Ecology and Evolution, 2: 1867–1888. doi: 10.1002/ece3.304
- Issue published online: 6 AUG 2012
- Article first published online: 6 JUL 2012
- Manuscript Accepted: 25 MAY 2012
- Manuscript Revised: 24 MAY 2012
- Manuscript Received: 7 MAR 2012
- James Cook University
- Australian Museum
- 1999. Genetic variation and clonal structure in the scleractinian coral Pocillopora damicornis in the Ryukyu Archipelago, southern Japan. Mar. Biol. 134:753–760. , and .
- 2008. Genetic connectivity in corals on the flower garden banks and surrounding oil/gas platforms, Gulf of Mexico. J. Exp. Mar. Biol. Ecol. 365:1–12. , , and .
- 1994. Molecular markers, natural history and evolution. Chapman and Hall, New York.
- 1994. Evidence for restricted gene flow in the viviparous coral Seriatopora hystrix on Australia's Great Barrier Reef. Evolution 48:1183–1201. , and .
- 2000. Genotypic diversity and gene flow in brooding and spawning corals along the Great Barrier Reef, Australia. Evolution 54:1590–1605. , and .
- 2004. Climate change, genotypic diversity and gene flow in reef-building corals. Ecol. Lett. 7:273–278. , and .
- 1997. Genetic differentiation, reproductive mode and gene flow in the brooding coral Pocillopora damicornis along the Great Barrier Reef, Australia. Mar. Ecol. Prog. Ser. 159:175–187. , , and .
- 2002. Soft-coral natural chimerism: a window in ontogeny allows the creation of entities comprised of incongruous parts. Mar. Ecol. Prog. Ser. 231:91–99. , , and .
- 1994. Genetic analysis of a rare and a widespread species of Echinacea (Asteraceae). Evolution 48:180–188. , , and .
- 2005a. Regionally isolated populations of an imperiled Caribbean coral, Acropora palmata . Mol. Ecol. 14:1377–1390. , , and .
- 2005b. Mendlian microsatellite loci for the Caribbean coral Acropora palmata . Mar. Ecol. Prog. Ser. 231:91–99. , , and .
- 2006. Geographic variation in clonal structure in a reef-building Caribbean coral, Acropora palmata . Ecol. Monogr. 76:503–519. , , and .
- 2010. Host population genetic structure and zooxanthellae diversity of two reef-building coral species along the Florida Reef Tract and wider Caribbean. Coral Reefs 29:835–842. , , , and .
- 2006. Population size does not influence mitochondrial genetic diversity in animals. Science 312:570–571. , , and .
- 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Stat. Soc. B 57:289–300. , and .
- 2001. The control of false discovery rate under dependency. Ann. Stat. 29:1165–1188. , and .
- 2002. Mechanisms and rates of genome expansion and contraction in flowering plants. Biomed. Life Sci. 115:29–36.
- 1995. Variation in the genetic composition of coral (Pocillopora damicornis and Acropora palifera) populations from different reef habitats. Mar. Biol. 121:731–739. , , and .
- 2010. Genetic divergence across habitats in the widespread coral Seriatopora hystrix and its associated Symbiodinium. Plos One 5:e10871. , , , , , and , et al.
- 1984. On the relationship between abundance and distribution. Am. Nat. 124:225–279.
- 2007. Thermal stress and coral cover as drivers of coral disease outbreaks. PLoS Biol. 5:e124. doi: 10.1371/journal.pbio.0050124 , , , , , , et al.
- 1992. Effective size of nonrandom mating populations. Genetics 130:909–916. , and .
- 2008. One-third of reef-building corals face elevated extinction risk from climate change and local impacts. Science 321:560–563. , , , , , , et al.
- 1999. Density-dependant variation in lifetime breeding success and natural and sexual selection in Soay rams. Am. Nat. 154:730–746. , , , , , , et al.
- 2011. Population genetics of an ecosystem-defining reef coral Pocillopora damicornis in the tropical Eastern Pacific. PLoS One 6:e21200. , and .
- 2000. Reproductive isolation and genetic differentiation of a scleractinian coral Mycedium elephantotus . Mar. Ecol. Prog. Ser. 201:179–187. , , and .
- 2006. High genetic diversity in a rare and endangered sunflower as compared to a common congener. Mol. Ecol. 15:2345–2355. , , , and .
- 1993. Population genetic consequences of small population size: implications for plant conservation. Annu. Rev. Ecol. Syst. 24:217–242. , and .
- 1998. Microsatellites and minisatellites for molecular ecology: theoretical and empirical considerations. Pp. 55–86 in G. Carvalho , ed. Advances in molecular ecology, Amsterdam, IOS Press. , and .
- 2002. Rarity, fragmentation and extiction risk in desert fishes. Ecology 83:3250–3256. , , , and .
- 2007. Sexual vs. asexual reproduction in an ecosystem engineer: the massive coral Montastraea annularis . J. Anim. Ecol. 76:382–391. , , and .
- 2012. Connectivity of Caribbean coral populations: complementary insights from empirical and modelled gene flow. Mol. Ecol. 21:1143–1157. , , , , , , et al.
- 1996. Relationship of genetic variation to population size in wildlife. Conserv. Biol. 10:1500–1508.
- 2012. How closely does genetic diversity in finite populations conform to predictions of neutral theory? Large deficits in regions of low recombination. Heredity 108:167–178.
- 2010. Introduction to conservation genetics. 2nd ed. Cambridge University Press, Cambridge, U. K. , , and .
- 2005. Increasing intraspecific diversity enhances settling success in a marine invertebrate. Ecology 86:3219–3224. , , , , and .
- 1994. Rarity. Chapman and Hall, London.
- 2001. Is the population size of a species relevant to its evolution? Int. J. Org. Evol. 55:2161.
- 2002. Substantial asexual recruitment of mushroom corals contributes little to population genetics of adults in conditions of chronic sedimentation. Mar. Ecol. Prog. Ser. 235:81–91. .
- 2000. Patterns of genetic variation in rare and widespread plant congeners. Am. J. Bot. 87:783–792. , and .
- 2004. Genetic differentiation among populations of the Mediterranean hermaphroditic brooding coral Balanophyllia europaea (Scleractinia: Dendrophylliidae). Mar. Biol. 145:1075–1083. , , and .
- 2010. Limited gene flow in the brooding coral Favia fragum (Esper, 1797). Mar. Biol. 157:2591–2602. , , , and .
- 2012. Population structure and connectivity in the Atlantic scleractinian coral Montastrea cavernosa (Linnaeus, 1767). Mar. Ecol. 33:32–48. , , and .
- 1987. The demography of chance extinction. Pp. 11–43 in M. E. Soule , (ed). Viable populations for conservation. Cambridge University Press, Cambridge, U.K. .
- 2001. Fstat version 1.2: a computer program to calculate Fstastics. J. Hered. 86:485–486.
- 1990. Allozyme diversity in plant species. Pp. 43–63 in A. D. H. Brown , M. T. Clegg , A. L. Kahler , and B. S. Weir , eds. Plant population genetics, breeding and germplasm resources, Sinauer, Sunderland. , and .
- 1994. Does variance in reproductive success limit effective population size of marine organisms? Pp. 122–134 in A. Beaumont , ed. Genetics and evolution of aquatic organisms. Chapman and Hall, London. .
- 2009. Complex patterns of population structure and recruitment of Plectopomus leopardus (Pisces: Epinephelidae) in the Indo-West Pacific: implications for fisheries management. Mar. Biol. 156:1595–1607. , , , , and .
- 2009. Ecological impacts of genotypic diversity in the clonal seagrass Zostera marina . Ecology 90:1412–1419. , and .
- 1992. The evolutionary ecology of corals. Trends Ecol. Evol. 7:285–295. , , and .
- 2008. Ecological consequences of genetic diversity. Ecol. Lett. 11:609–623. , , , , and .
- 1987. The pollination ecology of co-occurring geographically restricted and widespread species of Astragalus (Fabaceae). Biol. Conserv. 39:179–193.
- 1991. Patterns of genetic variation and breeding systems in rare plants species. Pp. 87–98 in D. A. Falk , K. E. Holsinger , eds. Genetics and conservation of rare plants. Oxford University Press, New York. .
- 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge.
- 1971. Theoretical aspects of population genetics. Princeton University Press, Princeton, NJ. , and .
- 2008. Genetic structure of Heliofungia actiniformis (Scleractinia: Fungiidae) populations in the Indo-Malay Archipelago: implications for live coral trade management efforts. Conserv. Genet. 10:241–249. doi: 10.1007/s10592-008-9566-5 , , , and .
- 2012. Extensive sympatry, cryptic diversity and introgression throughout the geographic distribution of two coral species complexes. Mol. Ecol. 21:2224–2238. , and .
- 1987. Effective population size, genetic variation and their use in population mangement. Pp. 87–123 in M. E. Soule , ed. Viable populations for conservation. Cambridge University Press, Cambridge, U.K. , and .
- 2010. Biodiversity and climate change: integrating evolutionary and ecological responses of species and communities. Annu. Rev. Ecol. Evol. Syst. 41:321–350. , , , and .
- 2001. Genetic data analysis. Computer program for the analysis of allelic data. Version 1(d16c). Available at http://Lewis.eeb.uconn.edu/lewishome/software.html. , and .
- 2000. The evolutionary fate and consequences of duplicated genes. Science 290:1151–1155. , and .
- 2011. Acropora austera connectivity in the south-western Indian Ocean assessed using nuclear intron sequence data. Mar. Biol. 158:613–621. , , and .
- 2004. Unexpected patterns of genetic structuring among locations but not colour morphs in Acropora nasuta (Cnidaria; Scleractinia). Mol. Ecol. 13:3–90. , , , , and .
- 2005. Patterns of genetic variation do not correlate with geographical distance in the reef-building coral Pocillopora meandrina in the South Pacific. Mol. Ecol. 14:1861–1868. , , and .
- 2005. Isolation by distance in the scleractinian coral Seriatopora hystrix from the Red Sea. Mar. Biol. 147:1109–1120. , , , and .
- 2002. The highly cross-fertile coral species, Acropora hyacinthus and A. cytherea, constitute statistically distinguishable lineages. Mol. Ecol. 11:1339–1349. , , , , and .
- 2000. Bleaching of corals on the Great Barrier Reef: differential susceptibilities among taxa. Coral Reefs 19:155–163. , and .
- 2004. The role of sexual and asexual reproduction in structuring high latitude populations of the reef coral Pocillopora damicornis . Heredity 92:557–568. , and .
- 2008a. Population structure is not a simple function of reproductive mode and larval type: insights from tropical corals. J. Anim. Ecol. 77:713–724. , and .
- 2008b. Protection of genetic diversity and maintenance of connectivity among reef corals within marine protected areas. Conserv. Biol. 22:1245–1254. , and .
- 1997. No clear genetic distinction between morphological species within the coral genus Platygyra. Bull. Mar. Sci. 61:907–917. , and .
- 2010. Gene flow and genetic diversity of a broadcast-spawning coral in Northern Peripheral Populations. PLoS One 5:e11149. , , , and .
- 2006. Beyond Bonferroni: less conservative analyses for conservation genetics. Conserv. Genet. 7:783–787.
- 1987. Molecular evolutionary genetics. Columbia University Press, New York.
- 2008. Genetic variation and population structuring in two brooding coral species (Siderastrea stellata and Siderastrea radians) from Brazil. Genetica 132:243–254. , , , and .
- 1984. The evolutionary significance of genetic diversity: ecological, demographic and life history correlates. Pp. 13–213 in G. S. Mani , ed. Evolutionary dynamics of genetic diversity. Springer-Verlag, Berlin. , , and .
- 2003. Genetic structure of the scleractinian coral Platygyra sinensis in Hong Kong. Mar. Biol. 143:963–968. , and .
- 2008. Degree and pattern of gene flow in several scleractinian coral in the Ryukyu Archipelago, Southern Japan. Pac. Sci. 62:413–421.
- 2003. Genetic variation and gene flow of broadcast spawning and planula brooding coral, Goniastrea aspera (Scleractinia), in the Ryukyu Archipelato, southern Japan. Zoolog. Sci. 20:1031–1038. , and .
- 2009. Genetic diversity and connectivity in a brooding reef coral at the limit of its distribution. Proc. Roy. Soc. B. 276:3927–3935. , , and .
- 1970. Evolution by gene duplication. Springer-Verlag, New York.
- 2004. Microchecker: software for identifying and correcting genotyping errors in microsatellite data. Mol. Ecol. Notes 4:535–538. , , , and .
- 2006. Conservation genetics and the resilience of reef-building corals. Mol. Ecol. 15:3863–3883. , and .
- 2000. Examination of species boundaries in the Acropora cervicornis group (Scleractinia, Cnidaria) using nuclear DNA sequence analysis. Mol. Ecol. 9:1363–1373. , , , and .
- 2007. Ten microsatellite loci for the reef-building coral Acropora millepora (Cnidarea, Scleractinia) from the Great Barrier Reef, Australia. Mol. Ecol. Notes 7:436–438. , , , and .
- 2008. Genetic traces of recent long-distant dispersal in a predominantly self-recruiting coral. PLoS One 3:e3401. , , , , and .
- 2011a. Novel genetic diversity through somatic mutations:fuel for adaptation of reef corals? Diversity 3:405–423. , , , , and .
- 2011b. The role of deep reefs in shallow reef recovery: an assessment of vertical connectivity in a brooding coral from west and east Australia. Mol. Ecol. 20:1647–1660. , , and .
- 2011c. Historical and contemporary factors shape the population genetic structure of the broadcast spawning coral, Acropora millepora, on the Great Barrier Reef. Mol. Ecol. 20:4899–4914. , , , and .
- 2003. Population genetics, demographic connectivity, and the design of marine reserves. Ecol. Appl. 13:S146–S158.
- 2008. Ecosystems in action: lessons from marine ecology about recovery, resistance, and reversibility. Bioscience 58:33–42. , , and .
- 2012. The role of genes in understanding the evolutionary ecology of reef building corals. Evol. Ecol. 26:317–335. , , , , and .
- 2012. Genetic connectivity patterns of corals Pocillopora damicornis and Porites panamensis (Anthozoa: Scleractinia) along the West Coast of Mexico. Pac. Sci. 66:43–61. , , , , , , et al.
- 2005. GenAlex 6: genetic analysis in Excel. Population genetic software for teaching and research. Australian National University, Canberra, Australia. , and .
- 1981. Recovery and recolonization of coral reefs. Mar. Ecol. Prog. Ser. 4:105–122.
- 2010. Isolation by distance across the Hawaiian Archipelago in the reef-building coral Porites lobata . Mol. Ecol. 19:4661–4677. , , , and .
- 2009. Chimerism in wild adult populations of the broadcast spawning coral Acropora millepora on the Great Barrier Reef. PLoS One 4:e7751. , , , and .
- 1995. Genepop (Version 1.2). Population genetics software for exact tests and eumenicism. J. Hered. 86:248–249. , and .
- 2010. No two reefs are created equal: fine-scale population structure in the threatened coral species Acropora palmata and A. cervicornis . Aquat. Biol. 10:69–83. , and .
- 2008. Some rare Indo-Pacific coral species are probable hybrids. PLoS One 3:e3240. , , , , and .
- 2001. Panmixia in Pocillopora verrucosa from South Africa. Mar. Biol. 139:175–182. , , and .
- 2002. The phylogeography and connectivity of the latitudinally widespread scleractinian coral Plesiastrea versipora in the Western Pacific. Mol. Ecol. 11:1177–1189. , and .
- 2011. Limited genetic connectivity of Pavona gigantea in the Mexican Pacific. Coral Reefs 30:677–686. , , , , , and .
- 2009. Restoration of coral populations in light of genetic diversity estimates. Coral Reefs 28:727–733. , , and .
- 2006. Genetic structure of a reef-building coral from thermally distinct environments on the Great Barrier Reef. Coral Reefs 25:493–502. , and .
- 2009. Patterns of genetic structuring in the coral Pocillopora damicornis on reefs in East Africa. BMC Ecol. 9:19. doi: 10.1186/1472-6785-9-19 , , , and .
- 2004. Most species are not driven to extinction before genetic factors impact them. Proc. Natl Acad. Sci. USA 101:15261–15264. , , and .
- 2010. The recovery of coral genetic diversity in the Sunda Strait following the 1883 eruption of Krakatau. Coral Reefs 29:547–565. , , , and .
- 1940. The significance of polyploidy in plant evolution. Am. Nat. 74:54–66.
- 1984. Genetic differentiation amongst populations of the coral Pocillopora damicornis off southwestern Australia. Coral Reefs 3:149–156.
- 2003. Genetic variation of the scleractinian coral Stylophora pistillata from western Pacific reefs. Coral Reefs 22:17–22. , , , and .
- 2009. Genetic diversity and divergence among coastal and offshore reefs in a hard coral depend on geographic discontinuity and oceanic currents. Evol. Appl. 2:222–233.
- 2007. Multiple scales of genetic connectivity in a brooding coral on isolated reefs following catastrophic bleaching. Mol. Ecol. 16:771–784. , , , and .
- 2009. Ecologically relevant dispersal of corals on isolated reefs: implications for managing resilience. Ecol. Appl. 19:18–29. , , , and .
- 2002. Hybridization and the evolution of coral reef diversity. Science 296:2023–2025. , and .
- 2006. Staghorn coral Acropora cervicornis: implications for the recovery of endangered reefs. J. Hered. 98:40–50. , and .
- 1985. Animal population genetics and disturbance: the effects of local extinctions and recolonizations on heterozygosity and fitness. Pp. 265–285 in S. T. A. Pickett , P. S. White , eds. The ecology of natural disturbance and patch dynamics. Academic Press, London. .
- 1928. Zusammensetzung von population und korrelationserscheinung vom standpunkt der vererbung-slehre aus betrachtet. Hereditas 11:65–106.
- 1999. Staghorn corals of the world: a revision of the genus Acropora. CSIRO Publishing, Australia.
- 2008. Microsatellite characterization and marker development from public EST and WGS databases in the reef-building coral Acropora millepora (Cnidaria, Anthozoa, Scleractinia). J. Hered. 100:329–337. , , and .
- 2012. Genotypic diversity enhances invasive ability of Spartina alterniflora . Mol. Ecol. 21:2542–2551. , , , , , , et al.
- 2004. Non-random mating and population genetic subdivision of two broadcasting corals at Ningaloo Reef, Western Australia. Mar. Biol. 144:593–603. .
- , and ,
- 2006. Genetic evidence for mixed modes of reproduction in the coral Pocillipora damicornis and its effect on population structure. Mar. Ecol. Prog. Ser. 306:115–124.
- 2003. Community and ecosystem genetics: a consequence of the extended phenotype. Ecology 84:559–573. , , , , , , et al.
- 2006. Limits to the adaptive potential of small populations. Annu. Rev. Ecol. Evol. Syst. 37:433–458. , , and .
- 1922. Coefficients of inbreeding and relationship. Am. Nat. 56:330–338.
- 1931. Evolution in Mendelian populations. Genetics 16:97–159.
- 1996. Comparative population genetic structure of the rare woodland shrub Daviesia suaveolens and its common congener D. mimosoides . Conserv. Biol. 10:1220–1228. , and .
- 1999. Genetic structure of a scleractinian coral, Mycedium elephantotus in Taiwan. Mar. Biol. 133:21–28. , , , and .
- 2003. Evolution by gene duplication: an update. Trends Ecol. Evol. 18:292–298.