Modern hard corals (Class Hexacorallia; Order Scleractinia) are widely studied because of their fundamental role in reef building and their superb fossil record extending back to the Triassic. Nevertheless, interpretations of their evolutionary relationships have been in flux for over a decade. Recent analyses undermine the legitimacy of traditional suborders, families and genera, and suggest that a non-skeletal sister clade (Order Corallimorpharia) might be imbedded within the stony corals. However, these studies either sampled a relatively limited array of taxa or assembled trees from heterogeneous data sets. Here we provide a more comprehensive analysis of Scleractinia (127 species, 75 genera, 17 families) and various outgroups, based on two mitochondrial genes (cytochrome oxidase I, cytochrome b), with analyses of nuclear genes (ß-tubulin, ribosomal DNA) of a subset of taxa to test unexpected relationships. Eleven of 16 families were found to be polyphyletic. Strikingly, over one third of all families as conventionally defined contain representatives from the highly divergent “robust” and “complex” clades. However, the recent suggestion that corallimorpharians are true corals that have lost their skeletons was not upheld. Relationships were supported not only by mitochondrial and nuclear genes, but also often by morphological characters which had been ignored or never noted previously. The concordance of molecular characters and more carefully examined morphological characters suggests a future of greater taxonomic stability, as well as the potential to trace the evolutionary history of this ecologically important group using fossils.
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).
MotivationThe BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community‐led open‐source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.Main types of variables includedThe database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.Spatial location and grainBioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).Time period and grainBioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.Major taxa and level of measurementBioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.Software format.csv and .SQL.
Aim Using high-resolution genetic markers on samples gathered from across their wide distributional range, we endeavoured to delimit species diversity in reef-building Pocillopora corals. They are common, ecologically important, and widespread throughout the Indo-Pacific, but their phenotypic plasticity in response to environmental conditions and their nearly featureless microskeletal structures confound taxonomic assignments and limit an understanding of their ecology and evolution.Location Indo-Pacific, Red Sea, Arabian/Persian Gulf.Methods Sequence analysis of nuclear ribosomal (internal transcribed spacer 2, ITS2) and mitochondrial (open reading frame) loci were combined with population genetic data (seven microsatellite loci) for Pocillopora samples collected throughout the Indo-Pacific, Red Sea and Arabian Gulf, in order to assess the evolutionary divergence, reproductive isolation, frequency of hybridization and geographical distributions of the genus.Results Between five and eight genetically distinct lineages comparable to species were identified with minimal or no hybridization between them. Colony morphology was generally incongruent with genetics across the full range of sampling, and the total number of species is apparently consistent with lower estimates from competing morphologically based hypotheses (about seven or eight taxa). The most commonly occurring genetic lineages were widely distributed and exhibited high dispersal and gene flow, factors that have probably minimized allopatric speciation. Uniquely among scleractinian genera, this genus contains a monophyletic group of broadcast spawners that evolved recently from an ancestral brooder.Main conclusions The delineation of species diversity guided by genetics fundamentally advances our understanding of Pocillopora geographical distributions, ecology and evolution. Because traditional diagnostic features of colony and branch morphology are proving to be of limited utility, the identification of Pocillopora species for future ecological and experimental work should rely on genetic characters that will improve research and aid in conservation strategies for these and other reef-building corals, including the detection of real and mistaken endemic populations.
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