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Open Access Highly Accessed Research article

Molecules and fossils reveal punctuated diversification in Caribbean “faviid” corals

Sonja A Schwartz1*, Ann F Budd2 and David B Carlon3

Author Affiliations

1 Department of Environmental Science, Policy & Management, University of California, Berkeley, CA, 94720, USA

2 Department of Geoscience, University of Iowa, Iowa City, IA, 52242, USA

3 Department of Biology, University of Hawaii at Manoa, Honolulu, HI, 96822, USA

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BMC Evolutionary Biology 2012, 12:123  doi:10.1186/1471-2148-12-123

Published: 25 July 2012

Additional files

Additional file 1:

Alleles and Accession Numbers by Species. Number of individuals sequenced per species (n), the number of alleles isolated per locus per species, and Genbank accession numbers. All species carried unique alleles, except for the two Manicina species. The two last rows give the number of unique alleles in the combined Manicina data sets (Manicina spp.) and the combined 6 ingroup species. (PDF 42 kb)

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Additional file 2:

Gene trees for (A)CaM, (B)MaSC-1, and (C)Pax-C. Alleles are designated by locus_allele number. Node labels indicate Bayesian posterior probabilities/Maximum likelihood bootstrap support, -- < 50% ML support. Two-tone boxes indicate alleles shared between taxa. All trees produced in MrBayes v3.1 (generations = 5,000,000, nruns = 2, nchains = 4.) The models of evolution were GTR + G for Cam and Pax-C and GTR for MaSC-1. See Additional File 3 for individual genotypes.

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Additional file 3:

Sampling and genotype data for all individual corals. Samples and multilocus genotypes used in gene and concatenated trees. Heterozygous genotypes that could not be resolved by cloning or PHASE 2.1.1 are indicated as ‘?/?+’; and ‘0’ indicates PCR failure or poor sequence quality. The two last columns designate which samples were used in the concatenated ML/Bayes trees (Figure 1) and the BEAST analysis (Figure 2).

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Additional file 4:

Primers used for direct sequencing. Sequences and annealing temperatures for primers used in this study.

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Additional file 5:

Stratigraphic Ranges of the Fossil Caribbean Faviidae. Compiled first and last occurrence data, references, and notes for all Caribbean fossil faviid species.

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