Data from: Unexpected cryptic species diversity in the widespread coral Seriatopora hystrix masks spatial-genetic patterns of connectivity
Warner, Patricia A., James Cook University
van Oppen, Madeleine J. H., Australian Institute of Marine Science, James Cook University
Willis, Bette L., James Cook University
Published Apr 30, 2015 on Dryad.
Cite this dataset
Warner, Patricia A.; van Oppen, Madeleine J. H.; Willis, Bette L. (2015). Data from: Unexpected cryptic species diversity in the widespread coral Seriatopora hystrix masks spatial-genetic patterns of connectivity [Dataset]. Dryad. https://doi.org/10.5061/dryad.33h50
Mounting evidence of cryptic species in a wide range of taxa highlights the need for careful analyses of population genetic data sets to unravel within-species diversity from potential interspecies relationships. Here, we use microsatellite loci and hierarchical clustering analysis to investigate cryptic diversity in sympatric and allopatric (separated by 450 km) populations of the widespread coral Seriatopora hystrix on the Great Barrier Reef. Structure analyses delimited unique genetic clusters that were confirmed by phylogenetic and extensive population-level analyses. Each of four sympatric yet distinct genetic clusters detected within S. hystrix demonstrated greater genetic cohesion across regional scales than between genetic clusters within regions (<10 km). Moreover, the magnitude of genetic differentiation between different clusters (>0.620 G”ST) was similar to the difference between S. hystrix clusters and the congener S. caliendrum (mean G”ST 0.720). Multiple lines of evidence, including differences in habitat specificity, mitochondrial identity, Symbiodinium associations and morphology, corroborate the nuclear genetic evidence that these distinct clusters constitute different species. Hierarchical clustering analysis combined with more traditional population genetic methods provides a powerful approach for delimiting species and should be regularly applied to ensure that ecological and evolutionary patterns interpreted for single species are not confounded by the presence of cryptic species.
Genotypes_Seriatopora spp. GBR
Genotype data for all 965 individuals at 10 loci
Population Allele Frequencies_ Seriatopora spp. GBR
The input population allele frequencies used to calculate Da distance for 30 populations examined in the study.
Da Distance Matrix_Seriatopora spp. GBR
Input file of Da Distance used to calculate NJ trees.
Pairwise Population G"st Matrix_Seriatopora spp. GBR
Matrix of pairwise population G"st estimates.
Pairwise Population Fst Matrix_Seriatopora spp. GBR
Matrix of pairwise population Fst estimates.
Pairwise Population Geographic Distance Matrix_Seriatopora spp. GBR
Matrix of pairwise geographic distances among populations, Ln(d+1)
Structure input_Seriatopora spp. GBR
Input file used for hierarchical structure analyses.
Structure parameters_Seriatopora spp. GBR
The parameters used for hierarchical structure analyses: project parameters, correlated allele frequency model parameters, independent allele frequency model parameters.
Medium length mtDNA haplotype alignment_Seriatopora spp.
Alignment of mtDNA haplotypes used in the medium length alignment (~811bp)
Short length mtDNA haplotype alignment_Seriatopora spp.
Alignment of mtDNA haplotypes used at shortest length (629bp)
Long length mtDNA haplotype alignment_Seriatopora spp.
MtDNA haplotype alignment of longest length sequences: 1388bp
W. Lizard mtDNA sequence alignment_Seriatopora spp. GBR
Alignment of full sequences of all 39 individuals sequenced from the W. Lizard site in this study.
Master Worksheet of All Data 2re _Seriatopora spp. GBR
This Excel file is a worksheet containing tabs for each csv file uploaded to Dryad: master summary table of all individuals, genotypes, allele frequencies for calculation of Da distance for NJ tree, Da distance matrix, matrix of pairwise population G"st, matrix of pairwise population Fst, matrix of pairwise population geographic distances, structure input, structure parameters, medium length haplotype alignment, short length haplotype alignment, long length haplotype alignment, alignment of full sequences from individuals from W Lizard.
Master Summary Table 2re_Seriatopora spp. GBR
This is a summary table of each individual used in the study, including the following data: sample name, designated species according to publication, population, mtDNA amplicon size, Symbiodinium ITS2 sequence, Lat/ Long, Habitat, Geographic Region, and Genbank Accession numbers.