References
- Baums IB, Boulay JN, Polato NR, Hellberg ME. 2012. No gene flow across the Eastern Pacific Barrier in the reef-building coral Porites lobata. Mol Ecol. 21:5418–5433.
- Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler P. 2013. MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phyl Evol. 69:313–319.
- Boore JL. 1999. Animal mitochondrial genomes. Nucleic Acids Res. 27:1767–1780.
- Brown DP, Basch L, Barshis D, Forsman Z, Fenner D, Goldberg J. 2009. American Samoa’s island of giants: massive Porites colonies at Ta’u island. Coral Reefs. 28:735–735.
- Dana JD. 1846. United States exploring expedition during the years 1838–1842. Zoophytes. 7:1–740
- Del Río-Portilla MA, Vargas-Peralta CE, Paz-García DA, Lafarga De La Cruz F, Balart EF, García-de-León FJ. 2016. The complete mitochondrial DNA of endemic Eastern Pacific coral (Porites panamensis). Mitochondrial DNA. 27:738–739.
- Forsman Z, Wellington GM, Fox GE, Toonen RJ. 2015. Clues to unraveling the coral species problem: distinguishing species from geographic variation in Porites across the Pacific with molecular markers and microskeletal traits. Peer J. 3:e751.
- Forsman ZH, Barshis DJ, Hunter CL, Toonen RJ. 2009. Shape-shifting corals: molecular markers show morphology is evolutionarily plastic in Porites. BMC Evol Biol. 9:45.
- Franklin EC, Jokiel PL, Donahue MJ. 2013. Predictive modeling of coral distribution and abundance in the Hawaiian Islands. Mar Ecol Prog Ser. 481:121–132.
- Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 59:307–321.
- Hebert PDN, Cywinska A, Ball SL, de Waard JR. 2003. Biological identifications through DNA barcodes. Proc R Soc B: Biol Sci. 270:313–321.
- Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 25:1754–1760.
- Lin MF, 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.
- Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, et al. 2015. Rfam 12.0: updates to the RNA families database. Nucleic Acids Res. 43:D130–D137.
- Prada C, DeBiasse MB, Neigel JE, Yednock B, Stake JL, Forsman ZH, Baums IB, Hellberg ME. 2014. Genetic species delineation among branching Caribbean Porites corals. Coral Reefs. 33:1019–1030.
- Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 61:539–542.
- Schattner P, Brooks AN, Lowe TM. 2005. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 33(Web Server):W686–W689.
- Shearer TL, van Oppen MJH, Romano SL, Wörheide G. 2002. Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol Ecol. 11:2475–2487.
- Toonen RJ, Puritz JB, Forsman ZH, Whitney JL, Fernandez-Silva I, Andrews KR, Bird CE. 2013. ezRAD: a simplified method for genomic genotyping in non-model organisms. PeerJ. 1:e203.
- Veron J. 2013. Overview of the taxonomy of zooxanthellate Scleractinia. Zool J Linn Soc. 169:485–508.
- Veron JEN. 2000. Corals of the world. Australia: Australian Institute of Marine Science and CRR Qld Pty Ltd.
- Wyman SK, Jansen RK, Boore JL. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics. 20:3252–3255.