Conventional taxonomy obscures deep divergence between Pacific and Atlantic corals

Abstract

sequenced as described in ref. 18. Internal primers McytbseqF (5 0-ATT GAC TAT GGC GAC CGC TTT T-3 0) and McytbseqR (5 0-GAA TAA AAT TCT CTG CGT CTC C-3 0) for cytB were used in addition to PCR primers. Primers to amplify the b-tubulin gene (intron and exon regions), designed on the basis of sequence data of Montastraea faveolata 19 , were TubulinF (5 0-GCA TGG GAA CGC TCC TTA TTT-3 0) and TubulinR (5 0-ACA TCT GTT GAG TGA GTT CTG-3 0). They amplify a region corresponding to amino acid positions 144-299 within exon 4 of the human and Drosophila b-tubulin gene; the beginning of the intron corresponds to position 247, and the flanking exons have 99% amino acid similarity to the corresponding vertebrate sequence. Depending on the genus, one, two or three bands of about 600 bases, 1.0-1.5 kilobases (kb) and more than 2.0 kb were amplified by PCR with the above-described protocol. The size difference between bands was due to the length of the intron. Because most genera had a 1.0-1.5-kb band, this was used for phylogenetic analyses. Diploastrea and Solenastrea had only the 600-base-pair (bp) band, and no bands could be amplified for Acanthastrea rotundoflora and Favites chinensis; consequently these four taxa were not analysed for b-tubulin. Amplified fragments of the b-tubulin gene were separated by agarose electrophoresis, cloned with the pGEM-T System (Promega) and sequenced for both strands. At least five clones obtained from each of two independent PCRs were analysed. If only one sequence occurred more than once, this sequence was used in the phylogenetic analyses; otherwise the two most abundant sequences were used. DNA phylogenetic analyses Only the exon regions of the b-tubulin gene (444 bp) were analysed, because the intron was too variable for alignment. Phylogenetic analyses were performed with PAUP* 20. DNA sequences of the entire cytB gene and the COI gene excluding the third codon position (total length 1,557 bases) were combined on the basis of nucleotide saturation analyses and the incongruence length difference test. Phylogenetic trees were constructed on the basis of neighbour-joining (NJ), maximum-parsimony (MP) and maximum-likelihood (ML) methods with the use of PAUP*. The NJ analysis was done with a two-parameter model 21. In MP and ML analyses, heuristic searches with TBR branch swapping and 25 random additions of taxa were performed. For ML analysis, we used Modeltest 22 to find an appropriate model of evolution. For mitochondrial genes the K81uf model 23 with gamma parameter (G) and proportion of invariable positions (I) was chosen. For b-tubulin we chose the TrN model 24 with G and I. Bootstrapping was used to evaluate support for trees (1,000 replicates for NJ and MP; 300 bootstraps with the fast-stepwise heuristic search for ML).

The New Systematics of Scleractinia: Integrating Molecular and Morphological Evidence

“…Therefore, these genes are more informative for reconstructing deep coral phylogenies. Other than the 16S rDNA that established widespread subordinal non-monophyly Palumbi 1996, 1997;Le GoffVitry et al 2004), 12S rDNA, cytochrome b and cytochrome c oxidase subunit I (COI) were purposed for corals relatively early (Medina et al 1999;van Oppen et al 1999;Fukami et al 2000) and have been used for inferring large scleractinian trees effectively (Chen et al 2002;Fukami et al 2004bFukami et al , 2008Barbeitos et al 2010;Kitahara et al 2010bKitahara et al , 2013Stolarski et al 2011;Arrigoni et al 2012Arrigoni et al , 2014cHuang 2012;Huang andRoy 2013, 2015;Marcelino et al 2013;Curnick et al 2015; Fig. 4.1).…”

“…These include amplifications of the Pax-C intron (van Oppen et al 2001(van Oppen et al , 2004Márquez et al 2002;Richards et al 2008Richards et al , 2013, β-tubulin (Fukami et al 2004b;Stefani et al 2008a), ITS (Medina et al 1999;van Oppen et al 2000Diekmann et al 2001;Rodriguez-Lanetty and Hoegh-Guldberg 2002;Márquez et al 2003;Chen et al 2004;Vollmer and Palumbi 2004;Forsman et al 2005Forsman et al , 2006Forsman et al , 2009Forsman et al , 2010Forsman et al , 2015Wei et al 2006;Stefani et al 2011;Kitano et al 2013Kitano et al , 2014, and 28S rDNA Cuif et al 2003;Wolstenholme et al 2003). For regions that have not diverged considerably between paralogues, such as the ITS, mixed PCR products can be split into two dominant sequences based on phase reconstruction of forward and reverse chromatograms of distinct lengths (Flot and Tillier 2006;Flot et al 2006).…”

A biophysical perspective on dispersal and the geography of evolution in marine and terrestrial systems

“…The growth of molecular biology, satellite oceanography and chemical tagging methods (among other technologies) since the early 1990s has provided alternative perspectives. Studies applying these techniques have often emphasized abundant cryptic taxa (Knowlton 1993(Knowlton , 2000Goetze 2003;Dawson 2004;Fukami et al 2004), considerable oceanographic structure with ecological and evolutionary consequences (Longhurst 1998;Sotka et al 2004;Hare et al 2005), interacting biological and physical restrictions on dispersal Cowen et al 2006), a high percentage of self-recruitment (Swearer et al 1999;Cowen et al 2000;Jones et al 2005) and strong phylogeographic structure on scales of tens of meters to tens of kilometres (Taylor & Hellberg 2003;Dawson & Hamner 2005). Re-evaluating all available data leads to the conclusion that a variety of processes, acting at various spatial and temporal scales, influence modern patterns of marine biogeography (see also Rosenblatt 1963).…”

Genetic and morphological differentiation in the hermatypic coral Galaxea fascicularis in Okinawa, Japan

“…In recent years, revised frameworks of the phylogeny of the order Scleractinia have been proposed using molecular tools (e.g. Romano & Palumbi 1996, Fukami et al 2004). On the other hand, the majority of hermatypic corals, including many common species, are yet to be carefully examined for their species status due to the lack of molecular markers and morphological traits that are useful in distinguishing closely related species or cryptic species.…”