Abstract
The taxonomy of corals of the genus Seriatopora has not previously been studied using molecular sequence markers. As a first step toward a re-evaluation of species boundaries in this genus, mitochondrial sequence variability was analyzed in 51 samples collected from Okinawa, New Caledonia, and the Philippines. Four clusters of sequences were detected that showed little concordance with species currently recognized on a morphological basis. The most likely explanation is that the skeletal characters used for species identification are highly variable (polymorphic or phenotypically plastic); alternative explanations include introgression/hybridization, or deep coalescence and the retention of ancestral mitochondrial polymorphisms. In all individuals sequenced, two copies of trnW were found on either side of the atp8 gene near the putative D-loop, a novel mitochondrial gene arrangement that may have arisen from a duplication of the trnW-atp8 region followed by a deletion of one atp8.
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References
Arndt A, Smith M (1998) Mitochondrial gene rearrangement in the sea cucumber genus Cucumaria. Mol Biol Evol 15:1009–1016
Cantatore P, Gadaleta MN, Roberti M, Saccone C, Wilson AC (1987) Duplication and remoulding of tRNA genes during the evolutionary rearrangement of mitochondrial genomes. Nature 329:853–855
Chen C, Dai C-F, Plathong S, Chiou C-Y, Chen CA (2008) The complete mitochondrial genomes of needle corals, Seriatopora spp. (Scleractinia: Pocilloporidae): an idiosyncratic atp8, duplicated trnW gene, and hypervariable regions used to determine species phylogenies and recently diverged populations. Mol Phylogenet Evol 46:19–33
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Flot J-F, Tillier S (2006) Molecular phylogeny and systematics of the scleractinian coral genus Pocillopora in Hawaii. Proc 10th Int Coral Reef Symp 1:24–29
Flot J-F, Tillier S (2007) The mitochondrial genome of Pocillopora (Cnidaria: Scleractinia) contains two variable regions: the putative D-loop and a novel ORF of unknown function. Gene 401:80–87
Flot J-F, Magalon H, Cruaud C, Couloux A, Tillier S (2008) Patterns of genetic structure among Hawaiian corals of the genus Pocillopora yield clusters of individuals that are compatible with morphology. Comptes Rendus Biologies 331:239–247
Fukami H, Budd AF, Paulay G, Solé-Cava A, Chen CA, Iwao K, Knowlton N (2004) Conventional taxonomy obscures deep divergence between Pacific and Atlantic corals. Nature 427:832–835
Fukami H, Chen C, Chiou C-Y, Knowlton N (2007) Novel group I introns encoding a putative homing endonuclease in the mitochondrial cox1 gene of scleractinian corals. J Mol Evol 64:591–600
Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704
Maier E, Tollrian R, Nürnberger B (2001) Development of species-specific markers in an organism with endosymbionts: microsatellites in the scleractinian coral Seriatopora hystrix. Mol Ecol Notes 1:157–159
Medina M, Collins AG, Takaoka TL, Kuehl JV, Boore JL (2006) Naked corals: skeleton loss in Scleractinia. Proc Natl Acad Sci USA 103:9096–9100
Moritz C (1991) Evolutionary dynamics of mitochondrial DNA duplications in parthenogenetic geckos, Heteronotia binoei. Genetics 129:221–230
Moritz C, Brown W (1986) Tandem duplication of D-loop and ribosomal RNA sequences in lizard mitochondrial DNA. Science 233:1425–1427
Quinn TW, Wilson AC (1993) Sequence evolution in and around the mitochondrial control region in birds. J Mol Evol 37:417–425
Rawlings TA, Collins TM, Bieler R (2003) Changing identities: tRNA duplication and remolding within animal mitochondrial genomes. Proc Natl Acad Sci USA 100:15700–15705
Shearer TL, Coffroth MA (2008) Barcoding corals: limited by interspecific divergence, not intraspecific variation. Mol Ecol Resources 8:247–255
Shearer TL, van Oppen MJH, Romano SL, Wörheide G (2002) Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol Ecol 11:2475–2487
Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599
Underwood JN, Souter PB, Ballment ER, Lutz AH, van Oppen MJH (2006) Development of 10 polymorphic microsatellite markers from herbicide-bleached tissues of the brooding pocilloporid coral Seriatopora hystrix. Mol Ecol Notes 6:176–178
van Oppen MJH, Wörheide G, Takabayashi M (2002) Nuclear markers in evolutionary and population genetic studies of scleractinian corals and sponges. Proc 9th Int Coral Reef Symp 1:131–138
Veron JEN, Stafford-Smith M (2000) Corals of the world. Australian Institute of Marine Science, Townsville
Acknowledgments
J.-F. Flot received a PhD scholarship and teaching assistantship from the French Ministry of Research and Education, and support from the MNHN program Structure et évolution des écosystèmes. We thank Eric Folcher, Catherine Geoffray, Jean-Louis Menou, and Mark Vergara for their help in the field; thanks also to Céline Bonillo, Josie Lambourdière, Julien Lorion, Annie Tillier, and two anonymous reviewers. This project was part of agreement n°2005/67 between Genoscope and MNHN on the project ‘Macrophylogeny of life’ directed by Guillaume Lecointre; support from the Consortium National de Recherche en Génomique is gratefully acknowledged.
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Flot, JF., Licuanan, W.Y., Nakano, Y. et al. Mitochondrial sequences of Seriatopora corals show little agreement with morphology and reveal the duplication of a tRNA gene near the control region. Coral Reefs 27, 789–794 (2008). https://doi.org/10.1007/s00338-008-0407-2
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DOI: https://doi.org/10.1007/s00338-008-0407-2