Extensive sharing of mitochondrial COI and CYB haplotypes among reef-building staghorn corals (Acropora spp.) in Sabah, North Borneo

References

• Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215:403–410.
   PubMed Web of Science ®Google Scholar
• Belle EMS, Piganeau G, Gardner M, Eyre-Walker A. 2005. An investigation of the variation in the transition bias among various animal mitochondrial DNA. Gene. 355:58–66.
   PubMed Web of Science ®Google Scholar
• Bofkin L, Goldman N. 2007. Variation in evolutionary processes at different codon positions. Mol Biol Evol. 24:513–521.
   PubMed Web of Science ®Google Scholar
• Brown WM, Matthew G Jr, Wilson AC. 1979. Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci USA. 76:1967–1971.
   PubMed Web of Science ®Google Scholar
• Chen CA, Chang C-C, Wei NV, Chen C-H, Lein Y-T, Lin H-E, Dai C-F, Wallace CC. 2004. Secondary structure and phylogenetic utility of the ribosomal internal transcribed spacer 2 (ITS2) in scleractinian corals. Zool Stud. 43:759–771.
   Web of Science ®Google Scholar
• Chen I-P, Tang C-Y, Chiou C-Y, Hsu J-H, Wei NV, Wallace CC, Muir P, Wu H, Chen CA. 2009. Comparative analyses of coding and noncoding DNA regions indicate that Acropora (Anthozoa: Scleractina) possesses a similar evolutionary tempo of nuclear vs. mitochondrial genomes as in plants. Mar Biotechnol. 11:141–152.
   PubMed Web of Science ®Google Scholar
• Chiou CY, Chen IP, Chen C, Wu HJ, Wei NV, Wallace CC, Chen CA. 2008. Analysis of Acropora muricata calmodulin (CaM) indicates that scleractinian corals possess the ancestral exon/intron organization of the eumetazoan CaM gene. J Mol Evol. 66:317–324.
   PubMed Web of Science ®Google Scholar
• Coleman AW, van Oppen MJH. 2008. Secondary structure of the rRNA ITS2 region reveals key evolutionary patterns in acroporid corals. J Mol Evol. 67:389–396.
   PubMed Web of Science ®Google Scholar
• Fay JC, Wu CI. 2003. Sequence divergence, functional constraint, and selection in protein evolution. 4:213–235.
   Google Scholar
• Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Marine Biol Biotechnol. 3:294–299.
   PubMedGoogle Scholar
• Forsman ZH, Hunter CL, Fox GE, Wellington GM. 2006. Is the ITS region the solution to the “species problem” in corals? Intragenomic variation and alignment permutation in Porites, Siderastrea and outgroup taxa. In: Suzuki Y, Nakamori T, Hidaka M, Kayanne H, Casareto BE, Nadaoka K, Yamano H, Tsuchiya M, editors. Proceedings of the 10th International Coral Reef Symposium; Jun 28–Jul 2; Okinawa. Tokyo: Japanese Coral Reef Society. p. 14–23.
   Google Scholar
• Fukami H, Chen CA, Budd AF, Collins A, Wallace C, Chuang Y-Y, Chen C, Dai C-F, Iwao K, Sheppard C, 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.
   PubMed Web of Science ®Google Scholar
• Fukami H, Omori M, Hatta M. 2000. Phylogenetic relationships in the coral family Acroporidae, reassessed by inference from mitochondrial genes. Zoolog Sci. 17:689–696.
   PubMed Web of Science ®Google Scholar
• Hebert PDN, Cywinska A, Ball SL, deWaard JR. 2003. Biological identifications through DNA barcodes. Proc Roy Soc Lond B. 270:313–321.
   PubMed Web of Science ®Google Scholar
• Huang D, Meier R, Todd PA, Chou LM. 2008. Slow mitochondrial COI sequence evolution at the base of the metazoan tree and its implications for DNA barcoding. J Mol Evol. 66:167–174.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Kretz K, Callen W, Hedden V. 1994. Cycle sequencing (manual supplement). PCR Methods Appl. 3:S107–S112.
   PubMedGoogle Scholar
• Kryazhimskiy J, Plotkin JB. 2008. The population genetics of dN/dS. PLoS Genet. 4:e1000304.
   PubMed Web of Science ®Google Scholar
• Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 33:1870–1874.
   PubMed Web of Science ®Google Scholar
• Lawrie DS, Messer PW, Hershberg R, Petrov DA. 2013. Strong purifying selection at synonymous sites in D. melanogaster. PLoS Genet. 9:e1003527.
   PubMed Web of Science ®Google Scholar
• Leigh JW, Bryant D. 2015. PopART: full-feature software for haplotype network construction. Methods Ecol Evol. 6:1110–1116.
   Web of Science ®Google Scholar
• Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 25:1451–1452.
   PubMed Web of Science ®Google Scholar
• Liu S-YV, Chan C-LC, Hsieh HJ, Fontana S, Wallace CC, Chen CA. 2015. Massively parallel sequencing (MPS) assays for sequencing mitochondrial genomes: the phylogenomic implications for Acropora staghorn corals (Scleractinia; Acroporidae). Mar Biol. 162:1383–1392.
   Web of Science ®Google Scholar
• Lyons DM, Lauring AS. 2017. Evidence for the selective basis of transition-to-transversion substitution bias in two RNA viruses. Mol Biol Evol. 34:3205–3215.
   PubMed Web of Science ®Google Scholar
• Meyer CP, Paulay G. 2005. DNA barcoding: error rates based on comprehensive sampling. PLoS Biol. 3:e422.
   PubMed Web of Science ®Google Scholar
• Miller DJ, Hayward DC, Reece-Hoyes JS, Scholten I, Catmull J, Gehring WJ, Patrick C, Larsen JE, Ball EE. 2000. Pax gene diversity in the basal cnidarian Acropora millepora (Cnidaria, Anthozoa): implications for the evolution of the Pax gene family. Proc Natl Acad Sci USA. 97:4475–4480.
   PubMed Web of Science ®Google Scholar
• Nei M, Gojobori T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 3:418–426.
   PubMed Web of Science ®Google Scholar
• Nei M, Miller JC. 1990. A simple method for estimating average number of nucleotide substitutions within and between populations from restriction data. Genetics. 125:873–879.
   PubMed Web of Science ®Google Scholar
• Nei M, Tajima F. 1981. DNA polymorphism detectable by restriction endonucleases. Genetics. 97:145–163.
   PubMed Web of Science ®Google Scholar
• 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. Mol Biol Evol. 14:465–473.
   PubMed Web of Science ®Google Scholar
• Pont-Kingdon GA, Beagley CT, Okimoto R, Wolstenholme DR. 1994. Mitochondrial DNA of the sea anemone, Metridium senile (Cnidaria): prokaryote-like genes for tRNAf-met and small-subunit ribosomal RNA and standard genetic code specificities for AGR and ATA codons. J Mol Evol. 39:387–399.
   PubMed Web of Science ®Google Scholar
• Richards ZT, Miller DJ, Wallace CC. 2013. Molecular phylogenetics of geographically restricted Acropora species: implications for threatened species conservation. Mol Phylogenet Evol. 69:837–851.
   PubMed Web of Science ®Google Scholar
• Richards ZT, van Oppen MJH, Wallace CC, Willis B, Miller DJ. 2008. Some rare indo-pacific coral species are probable hybrids. PLoS One. 3:e3240.
   PubMed Web of Science ®Google Scholar
• Robert R, Lee DJH, Rodrigues KF, Muhammad Ali SH, Waheed Z, Kumar SV. 2016. Consolidated checklist of hard corals of the genus Acropora Oken, 1815 (Scleractinia: Acroporidae) in North Borneo, East Malaysia. Zootaxa. 4200:259–304.
   Web of Science ®Google Scholar
• Rosser NL, Thomas L, Stankowski S, Richards ZT, Kennington WJ, Johnson MS. 2017. Phylogenomics provides new insight into evolutionary relationships and genealogical discordance in the reef-building coral genus Acropora. Proc Roy Soc Lond B. 284:20162182.
   PubMed Web of Science ®Google Scholar
• Saccone C, De Giorgi C, Gissi C, Pesole G, Reyes A. 1999. Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system. Gene. 238:195–209.
   PubMed Web of Science ®Google Scholar
• Shearer TL, van Oppen MJH, Romano SL, Wörheide G. 2002. Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol Ecol. 11:2475–2487.
   PubMed Web of Science ®Google Scholar
• Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673–4680.
   PubMed Web of Science ®Google Scholar
• Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG. 2012. Primer3 – new capabilities and interfaces. Nucleic Acids Res. 40:e115.
   PubMed Web of Science ®Google Scholar
• van Oppen MJH, Willis BL, Miller DJ. 1999. Atypically low rate of cytochrome b evolution in the scleractinian coral genus Acropora. Proc Roy Soc Lond B. 266:179–183.
   PubMed Web of Science ®Google Scholar
• van Oppen MJH, Willis BL, Rheede TV, Miller DJ. 2002. Spawning times, reproductive compatibilities and genetic structuring in the Acropora aspera group: evidence for natural hybridization and semi-permeable species boundaries in corals. Mol Ecol. 11:1363–1376.
   PubMed Web of Science ®Google Scholar
• 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. Mol Ecol. 9:1363–1373.
   PubMed Web of Science ®Google Scholar
• 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? Mol Biol Evol. 18:1315–1329.
   PubMed Web of Science ®Google Scholar
• Veron JEN, Odorico DM, Chen CA, Miller DJ. 1995. Reassessing evolutionary relationships of scleractinian corals. Coral Reefs. 15:1–9.
   Web of Science ®Google Scholar
• Vollmer SV, Palumbi SR. 2002. Hybridization and the evolution of reef coral diversity. Science. 296:2023–2025.
   PubMed Web of Science ®Google Scholar
• Vollmer SV, Palumbi SR. 2004. Testing the utility of internally transcribed spacer sequences in coral phylogenetics. Mol Ecol. 13:2763–2772.
   PubMed Web of Science ®Google Scholar
• Waheed Z, Benzoni F, van der Meij SET, Terraneo TI, Hoeksema BW. 2015. Scleractinian corals (Fungiidae, Agariciidae and Euphylliidae) of Pulau Layang-Layang, Spratly Islands, with a note on Pavona maldivensis (Gardiner, 1905). Zookeys. 517:1–37.
   Google Scholar
• 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.
   Web of Science ®Google Scholar
• Wei N-WV, Wallace CC, Dai C-F, Pillay KRM, Chen CA. 2006. Analyses of the ribosomal internal transcribed spacers (its) and the 5.8S gene indicate that extremely high rDNA heterogeneity is a unique feature in the scleractinian coral genus Acropora (Scleractinia; Acroporidae). Zool Stud. 45:404–418.
   Web of Science ®Google Scholar