Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria)

Molecular Ecology

Volumn 11, Issue 12, 2002, Pages 2475-2487

  Shearer, T L ^a   Van Oppen, M J H ^b,c   Romano, S L ^d   Worheide G ^e  

^a UNIVERSITY AT BUFFALO   (United States)

^b AUSTRALIAN INSTITUTE OF MARINE SCIENCE   (Australia)

^c JAMES COOK UNIVERSITY   (Australia)

^d UNIVERSITY OF THE VIRGIN ISLANDS   (United States)

^e UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

Anthozoa; Coral; Evolution; Mitochondrial DNA; Relative rate

Indexed keywords

ANIMALS; ANTHOZOA; CYTOCHROME B GROUP; DNA, MITOCHONDRIAL; DNA, PROTOZOAN; ELECTRON TRANSPORT COMPLEX IV; EVOLUTION, MOLECULAR; GENETIC MARKERS; RNA, RIBOSOMAL, 16S; VARIATION (GENETICS);

ANIMALIA; ANTHOZOA; CNIDARIA; INVERTEBRATA; METAZOA;

EID: 0036897723     PISSN: 09621083     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-294X.2002.01652.x     Document Type: Review

References (170)

1. Adjeroud M, Tsuchiya M (1999) Genetic variation and clonal structure in the scleractinian coral Pocillopora damicornis in the Ryukyu Archipelago, southern Japan. Marine Biology, 134, 753-760.
2. Arndt A, Marquez C, Lambert P, Smith MJ (1996) Molecular phylogeny of eastern Pacific sea cucumbers (Echinodermata: Holothuroidea) based on mitochondrial DNA sequence. Molecular Phylogenetics and Evolution, 6, 425-437.
3. Avise JC (1994) Molecular Markers, Natural History and Evolution, Chapman & Hall, New York.
4. Avise JC, Arnold J, Ball RM et al. (1987) Intraspecific phylogeography: The mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics, 18, 489-522.
5. Avise JC, Nelson WS, Sugita H (1994) A speciational history of living fossils: Molecular evolutionary patterns in horseshoe crabs. Evolution, 48, 1986-2001.
6. Ayre DJ (1984) The effects of sexual and asexual reproduction on geographic variation in the sea anemone Actinia tenebrosa. Oecologia, 62, 222-229.
7. Ayre DJ, Dufty S (1994) Evidence for restricted gene flow in the viviparous coral Seriatopora hystrix on Australia's Great Barrier Reef. Evolution, 48, 1183-1201.
8. Ayre DJ, Hughes TP (2000) Genotypic diversity and gene flow in brooding and spawning corals along the Great Barrier Reef, Australia. Evolution, 54, 1590-1605.
9. Ayre DJ, Hughes TP, Standish RS (1997) Genetic differentiation, reproductive mode, and gene flow in the brooding coral Pocillopora damicornis along the Great Barrier Reef, Australia. Marine Ecology Progress Series, 159, 175-187.
10. Ayre DJ, Veron JEN, Dufty SL (1991) The corals Acropora palifera and Acropora cuneata are genetically and ecologically distinct. Coral Reefs, 10, 13-18.
11. Ayre DJ, Willis BL (1988) Population structure in the coral Pavona cactus: Clonal genotypes show little phenotypic plasticity. Marine Biology, 99, 495-505.
12. Baco AR, Smith CR, Peek AS, Roderick GK, Vrijenhoek RC (1999) The phylogenetic relationships of whale-fall vesicomyid clams based on mitochondrial COI DNA sequences. Marine Ecology Progress Series, 182, 137-147.
13. Baldwin BS, Black M, Sanjur O et al. (1996) A diagnostic molecular marker for zebra mussels (Dreissena polymorpha) and potentially co-occurring bivalves: Mitochondrial COI. Molecular Marine Biology and Biotechnology, 5, 9-14.
14. Barki Y, Douek J, Graur D, Gateno D, Rinkevich B (2000) Polymorphism in soft coral larvae revealed by amplified fragment-length polymorphism (AFLP) markers. Marine Biology, 136, 37-41.
15. Barton NH, Charlesworth B (1984) Genetic revolutions, founder effects, and speciation. Annual Review of Ecology and Systematics, 15, 133-164.
16. Beagley CT, Okada NA, Wolstenholme DR (1996) Two mitochondrial group I introns in a metazoan, the sea anemone Metridium senile: One intron contains genes for subunits 1 and 3 of NADH dehydrogenase. Proceedings of the National Academy of Sciences of the USA, 93, 5619-5623.
17. Beagley CT, Okimoto R, Wolstenholme DR (1998) The mitochondrial genome of the sea anemone Metridium senile (Cnidaria): Introns, a paucity of tRNA genes, and a near standard genetic code. Genetics, 148, 1091-1108.
18. Beaton MJ, Roger AJ, Cavalier-Smith T (1998) Sequence analysis of the mitochondrial genome of Sarcophyton glaucum: Conserved gene order among octocorals. Journal of Molecular Evolution, 47, 697-708.
19. Beauchamp KA, Powers DA (1996) Sequence variation of the first internal spacer (ITS-1) of ribosomal DNA in ahermatypic corals from California. Molecular Marine Biology and Biotechnology, 5, 357-362.
20. Best BA, Thomas WK (1993) Anthozoan mtDNA: A fundamentally different rate of evolution. American Zoologist, 33, 99A.
21. Birky CW, Maruyama T, Fuerst P (1983) An approach to population and evolutionary genetic theory for genes in mitochondria and chloroplasts, and some results. Genetics, 103, 513-527.
22. Boore JL (1999) Animal mitochondrial genomes. Nucleic Acids Research, 27, 1767-1780.
23. Braga E, Zardoya R, Meyer A, Yen J (1999) Mitochondrial and nuclear rRNA based copepod phylogeny with emphasis on the Euchaetidae (Calanoida). Marine Biology, 133, 79-90.
24. Bridge D, Cunningham CW, Desalle R, Buss LW (1995) Class level relationships in the phylum Cnidaria: Molecular and morphological evidence. Molecular Biology and Evolution, 12, 679-689.
25. Bridge D, Cunningham CW, Schierwater B, Desalle R, Buss LW (1992) Class level relationships in the phylum Cnidaria: Evidence from mitochondrial genome structure. Proceedings of the National Academy of Sciences of the USA, 89, 8750-8753.
26. Brown WM (1985) The mitochondrial genome of animals. In: Molecular Evolutionary Genetics (ed. MacIntyre R.), pp. 95-130. Plenum, New York.
27. Brown WM, George M, Wilson AC (1979) Rapid evolution of animal mitochondrial DNA. Proceedings of the National Academy of Sciences of the USA, 76, 1967-1971.
28. Brown WM, Prager EM, Wang A, Wilson AC (1982) Mitochondrial DNA sequences of primates: Tempo and mode of evolution. Journal of Molecular Evolution, 18, 225-239.
29. Bucklin A, Frost BW, Kocher TD (1995) Molecular systematics of six Calanus and three Metridia species (Calanoida, Copepoda). Marine Biology, 121, 655-664.
30. Bucklin A, Guarnieri M, McGillicuddy DJ, Hill RS (2001) Spring evolution of Pseudocalanus spp. abundance on Georges Bank based on molecular discrimination of P. moultoni and P. newmani. Deep Sea Research Part II - Topical Studies in Oceanography, 48, 589-608.
31. Burnett WJ, Benzie JAH, Beardmore JA, Ryland JS (1994) High genetic variability and patchiness in a common Great Barrier Reef zoanthid (Palythoa caesia). Marine Biology, 121, 153-160.
32. Burnett WJ, Benzie JAH, Beardmore JA, Ryland JS (1995) Patterns of genetic subdivision in populations of a clonal cnidarian, Zoanthus coppingeri, from the Great Barrier Reef. Marine Biology, 122, 665-673.
33. Burton RS, Lee BN (1994) Nuclear and mitochondrial gene genealogies and allozyme poiymorphism across a major phylogeographic break in the copepod Tigriopus californicus. Proceedings of the National Academy of Sciences of the USA, 91, 5197-5201.
34. Canapa A, Marota I, Rollo F, Olmo E (1996) Phylogenetic analysis of Veneridae (Bivalvia): Comparison of molecular and palaeontological data. Journal of Molecular Evolution, 43, 517-522.
35. Cappola VA, Fautin DG (2000) Corallimorpharia (Cnidaria, Anthozoa): An order, a coral, or a sea anemone? Ninth International Coral Reef Symposium, Volume Abstracts (eds Hopley D, Hopley P, Tamelander J, Done T), p. 17. Smithsonian Tropical Research Institute, Bali, Indonesia.
36. Chen CA, Yu JK (2000) Universal primers for amplification of mitochondrial small subunit ribosomal RNA-encoding gene in scleractinian corals. Marine Biotechnology, 2, 146-153.
37. Chi NW, Kolodner RD (1994) Purification and characterization of msh1, a yeast mitochondrial protein that binds to DNA mismatches. Journal of Biological Chemistry, 269, 29984-29992.
38. Clark-Walker GD (1991) Contrasting mutation rates in mitochondrial and nuclear genes of yeast versus mammals. Current Genetics, 20, 195-198.
39. Clayton DA (1982) Replication of animal mitochondrial DNA. Cell, 28, 693-705.
40. Coffroth MA, Lasker HR, Diamond ME, Bruenn JA, Bermingham E (1992) DNA fingerprints of a gorgonian coral: A method for detecting clonal structure in a vegetative species. Marine Biology, 114, 317-325.
41. Collins TM, Frazer K, Palmer AR, Vermeij GJ, Brown WM (1996) Evolutionary history of northern hemisphere Nucella (Gastropoda, Muricidae): Molecular, morphological, ecological, and paleontological evidence. Evolution, 50, 2287-2304.
42. Dawson MN, Jacobs DK (2001) Molecular evidence for cryptic species of Aurelia aurita (Cnidaria, Scyphozoa). Biological Bulletin, 200, 92-96.
43. DeGiorgi C, Martiradonna A, Lanave C, Saccone C (1996) Complete sequence of the mitochondrial DNA in the sea urchin Arbacia lixula: Conserved features of the echinoid mitochondrial genome. Molecular Phylogenetics and Evolution, 5, 323-332.
44. Diekmann OE, Bak RPM, Stam WT, Olsen JL (2001) Molecular genetic evidence for probable reticulate speciation in the coral genus Madracis from a Caribbean fringing reef slope. Marine Biology, 139, 221-233.
45. Duret L (2000) tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. Trends in Genetics, 16, 287-289.
46. Edmands S, Moberg PE, Burton RS (1996) Allozyme and mitochondrial DNA evidence of population subdivision in the purple sea urchin Strongylocentrotus purpuratus. Marine Biology, 126, 443-450.
47. Edmands S, Potts DC (1997) Population genetic structure in brooding sea anemones (Epiactis spp.) with contrasting reproductive modes. Marine Biology, 127, 485-498.
48. Erpenbeck D, Breeuwer JAJ, van der Velde HC, Van Soest RWM (2002) Unravelling host and symbiont phylogenies of halichondrid sponges (Demospongiae, Porifera) using a mitochondrial marker. Marine Biology, 141, 377-386.
49. Ferris SD, Sage RD, Prager EM, Ritte U, Wilson AC (1983) Mitochondrial DNA evolution in mice. Genetics, 105, 681-721.
50. France SC, Hoover LL (2001a) DNA sequences of the mitochondrial COI gene have low levels of divergence among deep-sea octocorals (Cnidaria: Anthozoa). Hydrobiologia, 471, 149-155.
51. France SC, Hoover LL (2001b) Analysis of variation in mitochondrial DNA sequences (ND3, ND4L, MSH) among Octocorallia (=Alcyonaria) (Cnidaria: Anthozoa). Bulletin of the Biological Society of Washington, 10, 110-118.
52. France SC, Kocher TD (1996) Geographic and bathymetric patterns of mitochondrial 16S rRNA sequence divergence among deep sea amphipods, Eurythenes gryllus. Marine Biology, 126, 633-643.
53. France SC, Rosel PE, Agenbroad JE, Mullineaux LS, Kocher TD (1996) DNA sequence variation of mitochondrial large-subunit rRNA provides support for a two-subclass organization of the Anthozoa (Cnidaria). Molecular Marine Biology and Biotechnology, 5, 15-28.
54. Fukami H, Omori M, Hatta M (2000) Phylogenetic relationships in the coral family Acroporidae, reassessed by inference from mitochondrial genes. Zoological Science, 17, 689-696.
55. Geller JB, Walton ED (2001) Breaking up and getting together: Evolution of symbiosis and cloning by fission in sea anemones (genus Anthopleura) inferred from a molecular phylogeny. Evolution, 55, 1781-1794.
56. Geller JB, Walton ED, Grosholz ED, Ruiz GM (1997) Cryptic invasions of the crab Carcinus detected by molecular phylogeography. Molecular Ecology, 6, 901-906.
57. Harrison MK, Crespi BJ (1999) Phylogenetics of Cancer crabs (Crustacea: Decapoda: Brachyura). Molecular Phylogenetics and Evolution, 12, 186-199.
58. Hart MW, Byrne M, Smith MJ (1997) Molecular phylogenetic analysis of life history evolution in Asterinid starfish. Evolution, 51, 1848-1861.
59. Hatta M, Fukami H, Wang WQ et al. (1999) Reproductive and genetic evidence for a reticulate evolutionary history of mass-spawning corals. Molecular Biology and Evolution, 16, 1607-1613.
60. Hellberg ME (1994) Relationships between inferred levels of gene flow and geographic distance in a philopatric coral, Balanophyllia elegans. Evolution, 48, 1829-1854.
61. Hellberg ME (1996) Dependence of gene flow on geographic distance in two solitary corals with different larval dispersal capabilities. Evolution, 50, 1167-1175.
62. Hellberg ME (1998) Sympatric sea shells along the sea's shore: The geography of speciation in the marine gastropod Tegula. Evolution, 52, 1311-1324.
63. Higuchi R, Bowman B, Freiberger M, Ryder OA, Wilson AC (1984) DNA sequences from the Quagga, an extinct member of the horse family. Nature, 312, 282-284.
64. Hill RS, Allen LD, Bucklin A (2001) Multiplexed species-specific PCR protocol to discriminate four N. Atlantic Calanus species, with an mtCOI gene tree for ten Calanus species. Marine Biology, 139, 279-287.
65. Hrincevich AW, Foltz DW (1996) Mitochondrial DNA sequence variation in a sea star (Leptasterias spp.) species complex. Molecular Phylogenetics and Evolution, 6, 408-415.
66. Hudson RR, Kreitman M, Aguade M (1987) A test of neutral molecular evolution based on nucleotide data. Genetics, 116, 153-159.
67. Hunt A, Ayre DJ (1989) Population structure in the sexually reproducing sea anemone Oulactis muscosa. Marine Biology, 102, 537-544.
68. Hunter CL (1985) Assessment of clonal diversity and population structure of Porites compressa (Cnidaria, Scleractinia). In: Proceedings of the 5th International Coral Reef Congress (eds Delesalle B, Galzin R, Salvat B), pp. 69-74. Antenne Museum-EPHE, Tahiti.
69. Hunter CL (1993) Genotypic variation and clonal structure in coral populations with different disturbance histories. Evolution, 47, 1213-1228.
70. Kimura M, Weiss GH (1964) The stepping stone model of population structure and the decrease of genetic correlation with distance. Genetics, 49, 561-576.
71. Knowlton N, Mate JL, Guzman HM, Rowan R, Jara J (1997) Direct evidence for reproductive isolation among the three species of the Montastraea annularis complex in Central America (Panama and Honduras). Marine Biology, 127, 705-711.
72. Knowlton N, Weigt LA (1998) New dates and new rates for divergence across the Isthmus of Panama. Proceedings of the Royal Society of London Series B, Biological Sciences, 265, 2257-2263.
73. Knowlton N, Weigt LA, Solorzano LA, Mills DK, Bermingham E (1993) Divergence in proteins, mitochondrial DNA, and reproductive compatibility across the Isthmus of Panama. Science, 260, 1629-1632.
74. Knowlton N, Weil E, Weigt LA, Guzman HM (1992) Sibling species in Montastraea annularis, coral bleaching, and the coral climate record. Science, 255, 330-333.
75. Kojima SR, Seqawa T, Kobayashi T et al. (1995) Phylogenetic relationships among species of Calyptogena (Bivalvia: Vesicomyidae) collected around Japan revealed by nucleotide sequences of mitochondrial genes. Marine Biology, 122, 401-407.
76. Krieger J, Fuerst PA (2002) Evidence for a slowed rate of molecular evolution in the order Acipenseriformes. Molecular Biology and Evolution, 19, 891-897.
77. Kumar S (1996) PHYLTEST: A Program for Testing Phylogenetic Hypotheses, Version 2.0. Institute of Molecular and Evolutinary Genetics and Department of Biology, Pennsylvania State University, University Park, PA.
78. Laroche J, Li P, Maggia L, Bousquet J (1997) Molecular evolution of angiosperm mitochondrial introns and exons. Proceedings of the National Academy of Sciences of the USA, 94, 5722-5727.
79. Lee CE (2000) Global phylogeography of a cryptic copepod species complex and reproductive isolation between genetically proximate 'populations'. Evolution, 54, 2014-2027.
80. LeGoff MC, Rogers AD (2002) Characterization of 10 microsatellite loci for the deep-sea coral Lophelia pertusa (Linnaeus 1758). Molecular Ecology Notes, 2, 164-166.
81. Lessios HA, Kessing BD, Robertson DR (1998) Massive gene flow across the world's most potent marine biogeographic barrier. Proceedings of the Royal Society of London Series B, Biological Sciences, 265, 583-588.
82. Lessios HA, Kessing BD, Robertson DR, Paulay G (1999) Phylogeography of the pantropical sea urchin Eucidaris in relation to land barriers and ocean currents. Evolution, 53, 806-817.
83. Lopez JV, Kersanach R, Rehner SA, Knowlton N (1999) Molecular determination of species boundaries in corals: Genetic analysis of the Montastraea annularis complex using amplified fragment length polymorphisms and a microsatellite marker. Biological Bulletin, 196, 80-93.
84. Lynch M, Jarrell PE (1993) A method for calibrating molecular clocks and its application to animal mitochondrial DNA. Genetics, 135, 1197-1208.
85. Maier E, Tollrian R, Nurnberger B (2001) Development of species-specific markers in an organism with endosymbionts: Microsatellites in the scleractinian coral Seriatopora hystrix. Molecular Ecology Notes, 1, 157-159.
86. Marquez LM, van Oppen MJH, Willis BL, Miller DJ (2000) Reticulate evolution in the Acropora hyacinthus group: Results from mitochondrial and nuclear markers. In: Ninth International Coral Reef Symposium, Volume Abstracts (eds Hopley D, Hopley P, Tamelander J, Done T), p. 19. Smithsonian Tropical Research Institute, Bali, Indonesia.
87. Marquez LM, van Oppen MJH, Willis BL, Miller DJ (2002a) Sympatric populations of the highly cross-fertile coral species Acropora hyacinthus and A. cytherea are genetically distinct. Proceedings of the Royal Society of London, Series B, 269, 1289-1294.
88. Marquez LM, van Oppen MJH, Willis BL, Reyes A, Miller DJ (2002b) The highly cross-fertile coral species, Acropora hyacinthus and A. cytherea, constitute statistically distinguishable lineages. Molecular Ecology, 11, 1339-1349.
89. Martin AP (1999) Substitution rates of organelle and nuclear genes in sharks: Implicating metabolic rate (again). Molecular Biology and Evolution, 16, 996-1002.
90. McFadden CS (1999) Genetic and taxonomic relationships among Northeastern Atlantic and Mediterranean populations of the soft coral Alcyonium coralloides. Marine Biology, 133, 171-184.
91. McFadden CS, Donahue R, Hadland BK, Weston R (2001) A molecular phylogenetic analysis of reproductive trait evolution in the soft coral genus Alcyonium. Evolution, 55, 54-67.
92. McFadden CS, Hutchinson MB (2001) Hybrid origin of soft coral species suggested by ribosomal DNA sequence heterogeneity. American Zoologist, 41, 1519.
93. McFadden CS, Tullis I, Hutchinson MB, Winner K (2000) Rates of evolution of cnidarian mitochondrial genes. American Zoologist, 40, 1124-1124.
94. McInerney JO (1998) Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proceedings of the National Academy of Sciences of the USA, 95, 10698-10703.
95. McKnight ML, Shaffer HB (1997) Large, rapidly evolving intergenic spacers in the mitochondrial DNA of the salamander family Ambystomatidae (Amphibia: Caudata). Molecular Biology and Evolution, 14, 1167-1176.
96. Medina M (1998) Molecular Systematics and Population Genetics of Sea Hares (Gastropoda: Opistobranchia: Anaspidea). Univeristy of Miami, Florida.
97. Medina M, Weil E, Szmant AM (1999) Examination of the Montastraea annularis species complex (Cnidaria: Scleractinia) using ITS and COI sequences. Marine Biotechnology, 1, 89-97.
98. Metz EC, Gomez-Gutierrez G, Vacquier VD (1998a) Mitochondrial DNA and bindin gene sequence evolution among allopatric species of the sea urchin genus Arbacia. Molecular Biology and Evolution, 15, 185-195.
99. Metz EC, Robles-Sikisaka R, Vacquier VD (1998b) Nonsynonymous substitution in abalone sperm fertilization genes exceeds substitution in introns and mitochondrial DNA. Proceedings of the National Academy of Sciences of the USA, 95, 10676-10681.
100. Miller KJ (1998) Short-distance dispersal of black coral larvae: Inference from spatial analysis of colony genotypes. Marine Ecology Progress Series, 163, 225-233.
101. Miller K, Babcock R (1997) Conflicting morphological and reproductive species boundaries in the coral genus Platygyra. Biological Bulletin, 192, 98-110.
102. Moore WS (1995) Inferring phylogenies from mtDNA variation: Mitochondrial-gene trees versus nuclear-gene trees. Evolution, 49, 718-726.
103. Moore J, Willmer P (1997) Convergent evolution in invertebrates. Biological Reviews of the Cambridge Philosophical Society, 72, 1-60.
104. Moritz C, Dowling TE, Brown WM (1987) Evolution of animal mitochondrial DNA: Relevance for population biology and systematics. Annual Review of Ecology and Systematics, 18, 269-292.
105. Musto H, Cruveiller W, D'Onofrio G, Romero H, Bernardi G (2001) Translational selection on codon usage in Xenopus laevis. Molecular Biology and Evolution, 18, 1703-1707.
106. Nei M, Maruyama T, Chakraborty R (1975) The bottleneck effect and genetic variability in populations. Evolution, 29, 1-10.
107. O'Foighil D, Gaffney PM, Wilbur AE, Hilbish TJ (1998) Mitochondrial cytochrome oxidase I gene sequences support an Asian origin for the Portuguese oyster Crassostrea angulata. Marine Biology, 131, 497-503.
108. O'Foighil D, Hilbish TJ, Showman RM (1996) Mitochondrial gene variation in Mercenaria clam sibling species reveals a relict secondary contact zone in the western Gulf of Mexico. Marine Biology, 126, 675-683.
109. O'Foighil D, Jozefowicz CJ (1999) Amphi-Atlantic phylogeography of direct-developing lineages of Lasaea, a genus of brooding bivalves. Marine Biology, 135, 115-122.
110. Odorico DM, Miller DJ (1997) Variation in the ribosomal internal transcribed spacers and 5.8S rDNA among five species of Acropora (Cnidaria; Scleractinia): Patterns of variation consistent with reticulate evolution. Molecular Biology and Evolution, 14, 465-473.
111. van Oppen MJH, Catmull J, McDonald BJ, Hislop NR, Hagerman PJ, Miller DJ (2002b) The mitochondrial genome of Acropora tenuis (Cnidaria; Scleractinia) contains a large group I intron and a candidate control region. Journal of Moluecular Evolution, 55, 1-13.
112. van Oppen MJH, Hislop NR, Hagerman PJ, Miller DJ (1999a) Gene content and organization in a segment of the mitochondrial genome of the scleractinian coral Acropora tenuis: Major differences in gene order within the anthozoan subclass Zoantharia. Molecular Biology and Evolution, 16, 1812-1815.
113. van Oppen MJH, McDonald BJ, Willis B, Miller DJ (2001) The evolutionary history of the coral genus Acropora (Scleractinia, Cnidaria) based on a mitochondrial and a nuclear marker: Reticulation, incomplete lineage sorting, or morphological convergence? Molecular Biology and Evolution, 18, 1315-1329.
114. van Oppen MJH, Willis BL, Miller DJ (1999b) Atypically low rate of cytochrome b evolution in the scleractinian coral genus Acropora. Proceedings of the Royal Society of London Series B, Biological Sciences, 266, 179-183.
115. van Oppen MJH, Willis BL, van Rheede T, Miller DJ (2002a) Spawning time, reproductive compatibilities and genetic structuring in the Acropora aspera group: Evidence for natural hybridisation and semi-permeable species boundaries in corals. Molecular Ecology, 11, 1363-1376.
116. van Oppen MJH, Willis BL, van Vugt HWJA, Miller DJ (2000) Examination of species boundaries in the Acropora cervicornis group (Scleractinia, Cnidaria) using nuclear DNA sequence analyses. Molecular Ecology, 9, 1363-1373.
117. Palmer JD, Adams KL, Cho Y, Parkinson CL, Qiu YL, Song K (2000) Dynamic evolution of plant mitochonrial genomes: Mobile genes and introns and highly variable mutation rates. Proceedings of the National Academy of Sciences of the USA, 97, 6960-6966.
118. Palmer JD, Herbon LA (1989) Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. Journal of Molecular Evolution, 28, 87-97.
119. Palumbi SR (1996) What can molecular genetics contribute to marine biogeography? An urchin's tale. Journal of Experimental Marine Biology and Ecology, 203, 75-92.
120. Palumbi SR, Grabowsky G, Duda T, Geyer L, Tachino N (1997) Speciation and population genetic structure in tropical Pacific sea urchins. Evolution, 51, 1506-1517.
121. Palumbi SR, Kessing BD (1991) Population biology of the trans-Arctic exchange: mtDNA sequence similarity between Pacific and Atlantic sea urchins. Evolution, 45, 1790-1805.
122. Palumbi SR, Metz EC (1991) Strong reproductive isolation between closely related tropical sea urchins (genus Echinometra). Molecular Biology and Evolution, 8, 227-239.
123. Palumbi SR, Wilson AC (1990) Mitochondrial DNA diversity in the sea urchins Strongylocentrotus purpruatus and S. drobachiensis. Evolution, 44, 403-415.
124. Pesole G, Gissi C, De Chirico A, Saccone C (1999) Nucleotide substitution rate of mammalian mitochonridal genomes. Journal of Molecular Evolution, 48, 427-434.
125. Pont-Kingdon GA, Beagley CT, Okimoto R, Wolstenholme DR (1994) Mitochondrial DNA of the sea anemone, Metridium senile (Cnidaria): Prokaryote-like genes for tRNA (f-Met) and small subunit ribosomal RNA, and standard genetic code specificities for AGR and ATA codons. Journal of Molecular Evolution, 39, 387-399.
126. Pont-Kingdon GA, Okada NA, Macfarlane JL et al. (1995) A coral mitochondrial mutS gene. Nature, 375, 109-111.
127. Pont-Kingdon G, Okada NA, Macfarlane JL et al. (1998) Mitochondrial DNA of the coral Sarcophyton glaucum contains a gene for a homologue of bacterial MutS: A possible case of gene transfer from the nucleus to the mitochondrion. Journal of Molecular Evolution, 46, 419-431.
128. Ridgway T, Hoegh-Guldberg O, Ayre DJ (2001) Panmixia in Pocillopora verrucosa from South Africa. Marine Biology, 139, 175-181.
129. Romano SL, Cairns SD (2000) Molecular phylogenetic hypotheses for the evolution of scleractinian corals. Bulletin of Marine Science, 67, 1043-1068.
130. Romano SL, Palumbi SR (1996) Evolution of scleractinian corals inferred from molecular systematics. Science, 271, 640-642.
131. Romano SL, Palumbi SR (1997) Molecular evolution of a portion of the mitochondrial 16S ribosomal gene region in scleractinian corals. Journal of Molecular Evolution, 45, 397-411.
132. Romano SL, Richmond RH (2000) Molecular tools for assessing genetic variation within scleractinian coral species. In: Ninth International Coral Reef Symposium, Volume Abstracts (eds Hopley D, Hopley P, Tamelander J, Done, T), p. 21. Smithsonian Tropical Research Institute, Bali, Indonesia.
133. Schneider A, Marechal-Drouard L. (2000) Mitochondrial tRNA import: Are there distinct mechanisms? Trends in Cell Biology, 10, 509-513.
134. Sharp PM, Li WH (1989) On the rate of DNA sequence evolution in Drosophila. Journal of Molecular Evolution, 28, 398-402.
135. Sharp PM, Stenico M, Peden JF, Lloyd AT (1993) Codon usage: Mutational bias, translational selection, or both. Biochemical Society Transactions, 21, 835-841.
136. Shields DC, Sharp PM, Higgins DG, Wright F (1988) Silent sites in Drosophila genes are not neutral: Evidence of selection among synonymous codons. Molecular Biology and Evolution, 5, 704-716.
137. Snell TL (1997)Morphological and Genetic Variation in the Scleractinian Coral Montastraea cavernosa, p. 104. Louisiana State University, Baton Rouge, LA.
138. Snell TL (2000) Low levels of mitochondrial sequence variation in scleractinian corals. In: Ninth International Coral Reef Symposium, Volume Abstracts (eds Hopley D, Hopley P, Tamelander J, Done, T), p. 21. Smithsonian Tropical Research Institute, Bali, Indonesia.
139. Snell TL, Coffroth MA (1999) Use of intersimple sequence repeats in analyzing intra- and interspecific variability in scleractinian corals. American Zoologist, 39, 727.
140. Snell TL, Foltz DW, Sammarco PW (1998) Variation in morphology vs conservation of a mitochondrial gene in Montastraea cavernosa (Cnidaria, Scleractinia). Gulf of Mexico Science, 2, 188-195.
141. Song JI, Suh JH, Kim SJ (2000) Geographic variation of Granulilittorina exigua (Littorinidae, Gastropoda) in Korea based on the mitochondrial cytochrome b gene sequence. Korean Journal of Biological Science, 4, 267-272.
142. Stenico M, Lloyd AT, Sharp PM (1994) Codon usage in Caenorhabditis elegans: Delineation of translational selection and mutational biases. Nucleic Acids Research, 22, 2437-2446.
143. Stobart B, Benzie JAH (1994) Allozyme electrophoresis demonstrates that the scleractinian coral Montipora digitata is two species. Marine Biology, 118, 183-190.
144. Stoddart JA (1984a) Genetic differentiation amongst populations of the coral Pocillopora damicornis off southwestern Australia. Coral Reefs, 3, 149-156.
145. Stoddart JA (1984b) Genetical structure within populations of the coral Pocillopora damicornis. Marine Biology, 81, 19-30.
146. Sturmbauer C, Levinton JS, Christy J (1996) Molecular phylogeny analysis of fiddler crabs: Test of the hypothesis of increasing behavioral complexity in evolution. Proceedings of the National Academy of Sciences of the USA, 93, 10855-10857.
147. van Syoc RJ (1994) Genetic divergence between subpopulations of the eastern Pacific goose barnacle Pollicipes elegans: Mitochondrial cytochrome c subunit 1 nucleotide sequences. Molecular Marine Biology and Biotechnology, 3, 338-346.
148. Szmant AM, Weil E, Miller MW, Colon DE (1997) Hybridization within the species complex of the scleractinan coral Montastraea annularis. Marine Biology, 129, 561-572.
149. Takezaki N, Razhetsky A, Nei M (1995) Phylogenetic test of the molecular clock and linearized trees. Molecular Biological and Evolution, 12, 823-833.
150. Tomascik T (1990) Growth rates of two morphotypes of Montastrea annularis along a eutrophication gradient, Barbados, WI. Marine Pollution Bulletin, 21, 376-381.
151. Vawter L, Brown WM (1986) Nuclear and mitochondrial DNA comparisons reveal extreme rate variation in the molecular clock. Science, 234, 194-196.
152. van Veghel MLJ (1994) Reproductive characteristics of the polymorphic Caribbean reef building coral Montastrea annularis. I. Gametogenesis and spawning behavior. Marine Ecology Progress Series, 109, 209-219.
153. van Veghel MLJ, Bak RPM (1993) Intraspecific variation of a dominant Caribbean reef building coral, Montastrea annularis: Genetic, behavioral and morphometric aspects. Marine Ecology Progress Series, 92, 255-265.
154. van Veghel MLJ, Bak RPM (1994) Reproductive characteristics of the polymorphic Caribbean reef building coral Montastrea annularis: 3. Reproduction in damaged and regenerating colonies. Marine Ecology Progress Series, 109, 229-233.
155. Vieira CP, Charlesworth D (2001) Low diversity and divergence in the fill gene family of Antirrhinum (Scrophulariaceae). Journal of Molecular Evolution, 52, 171-181.
156. Vollmer SV, Palumbi SR (2000) Using a mult-locus approach to examine species-level relationships in the scleractinian corals. In: Ninth International Coral Reef Symposium, Volume Abstracts (eds Hopley D, Hopley P, Tamelander J, Done, T), p. 23. Smithsonian Tropical Research Institute, Bali, Indonesia.
157. Vollmer SV, Palumbi SR (2002) Hybridization and the evolution of reef coral diversity. Science, 296, 2023-2025.
158. Wallace CC, Willis BL (1994) Systematics of the coral genus Acropora: Implications of new biological findings for species concepts. Annual Review of Ecology and Systematics, 25, 237-262.
159. Yu JK, Wang HY, Lee SC, Dai CF (1999) Genetic structure of a scleractinian coral, Mycedium elephantotus, in Taiwan. Marine Biology, 133, 21-28.
160. Weil E (1992) Genetic and morphological variation in Caribbean and Eastern Pacific Porites (Anthozoa, Scleractinia). Preliminary results. In: Proceedings of the 7th International Coral Reef Symposium, Vol. 2 (ed. Richmond R H.), pp. 643-655. University of Guam Press, Guam.
161. Weil E, Knowlton N (1994) A multi-character analysis of the Caribbean coral Montastraea annularis (Ellis and Solander, 1786) and its two sibling species, M. faveolata (Ellis and Solander, 1786) and M. franksi (Gregory, 1895). Bulletin of Marine Science, 55, 151-175.
162. Willis BL, Ayre DJ (1985) Asexual reproduction and genetic determination of growth form in the coral Pavona cactus: Biochemical genetic and immunogenic evidence. Oecologia, 65, 6516-6525.
163. Willis BL, Babcock RC, Harrison PL, Wallace CC (1997) Experimental hybridization and breeding incompatibilities within the mating systems of mass spawning reef corals. Coral Reefs, 16, S53-S65.
164. Wilson AC, Cann RL, Carr SM et al. (1985) Mitochondrial DNA and two perspectives on evolutionary genetics. Biological Journal of the Linnean Society, 26, 375-400.
165. Wolfe KH, Li WH, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proceedings of the National Academy of Sciences of the USA, 84, 9054-9058.
166. Wolstenholme DR (1992) Animal mitochondrial DNA: Structure and evolution. In: International Review of Cytology (eds Wolstenholme DR, Jeon KW), pp. 173-216. Academic Press, New York.
167. Won JH, Rho BJ, Song JI (2001) A phylogenetic study of the Anthozoa (phylum Cnidaria) based on morphological and molecular characters. Coral Reefs, 20, 39-50.
168. Wörheide G, Degnan BM, Hooper JNA (2000) Population phylogenetics of the common coral reef sponge Leucetta spp. and Pericharax spp. (Porifera: Calcarea) from the Great Barrier Reef and Vanuatu. In: Ninth International Coral Reef Symposium, Volume Abstracts (eds Hopley D, Hopley P, Tamelander J, Done T), p. 23. Smithsonian Tropical Research Institute, Bali, Indonesia.
169. Wörheide G, Hooper JNA, Degnan BM (2002) Phylogeography of
170. Wright S (1943) Isolation by distance. Genetics, 28, 114-138.