DOI: 10.5061/dryad.33h50
title: Data from: Unexpected cryptic species diversity in the widespread coral Seriatopora hystrix masks spatial-genetic patterns of connectivity

description: 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 (&lt;10 km).
 Moreover, the magnitude of genetic differentiation between different
 clusters (&gt;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.
description: Genotypes_Seriatopora
 spp. GBRGenotype data for all
 965 individuals at 10 lociGenotypes0316.csvPopulation Allele Frequencies_ Seriatopora spp. GBRThe input population allele frequencies used to calculate Da distance for 30 populations examined in the study.PopAlleleFreqNJtree.csvDa Distance Matrix_Seriatopora spp. GBRInput file of Da Distance used to calculate NJ trees.DaDistMatrixNJtree.csvPairwise Population G"st Matrix_Seriatopora spp. GBRMatrix of pairwise population G"st estimates.GstMatrix.csvPairwise Population Fst Matrix_Seriatopora spp. GBRMatrix of pairwise population Fst estimates.FstMatrix.csvPairwise Population Geographic Distance Matrix_Seriatopora spp. GBRMatrix of pairwise geographic distances among populations, Ln(d+1)GeoDistMatrix.csvStructure input_Seriatopora spp. GBRInput file used for hierarchical structure analyses.Structure input.csvStructure parameters_Seriatopora spp. GBRThe parameters used for hierarchical structure analyses: project parameters, correlated allele frequency model parameters, independent allele frequency model parameters.Structure parameters.csvMedium length mtDNA haplotype alignment_Seriatopora spp.Alignment of mtDNA haplotypes used in the medium length alignment (~811bp)Medium_mtDNAhapalign.csvShort length mtDNA haplotype alignment_Seriatopora spp.Alignment of mtDNA haplotypes used at shortest length (629bp)Short_mtDNAhapalign.csvLong length mtDNA haplotype alignment_Seriatopora spp.MtDNA haplotype alignment of longest length sequences: 1388bpLong_mtDNAhapalign.csvW. Lizard mtDNA sequence alignment_Seriatopora spp. GBRAlignment of full sequences of all 39 individuals sequenced from the W. Lizard site in this study.WL_fullseqalignment.csvMaster Worksheet of All Data 2re _Seriatopora spp. GBRThis 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.Species_Master Table2_042315.xlsMaster Summary Table 2re_Seriatopora spp. GBRThis 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.Master Table 2.csv