Data from: Genomic data reject the hypothesis of sympatric ecological speciation in a clade of Desmognathus salamanders

Closely related taxa with dissimilar morphologies are often considered to have diverged via natural selection favoring different phenotypes. However, some studies have found these scenarios to be paired with limited or no genetic differentiation. Desmognathus quadramaculatus and D. marmoratus are sympatric salamander species thought to represent a case of ecological speciation based on distinct morphologies, but the results of previous studies have not resolved corresponding patterns of lineage divergence. Here, we use genome-wide data to test this hypothesis of ecological speciation. Population structure analyses partitioned individuals geographically, but not morphologically, into two adjacent regions of western North Carolina: Pisgah and Nantahala. Phylogenetic analyses confirmed the nominal species are non-monophyletic and resolved deep divergence between the two geographic clusters. Model-testing overwhelmingly supported the hypothesis that lineage divergence followed geography. Finally, ecological niche modeling showed that Pisgah and Nantahala individuals occupy different climatic niches, and geographic boundaries for the two lineages correspond to a difference in precipitation regimes across southern Appalachia. Overall, we reject the previous hypothesis of ecological speciation based on microhabitat partitioning. Instead, our results suggest that there are two cryptic lineages, each containing the same pair of morphotypes.Concatenated nexus file for BEAST (outgroup data set)Data file used for BEAST analysis, including D. carolinensis outgroup individuals.quads_out_concat.nexVCF file containing SNPs for DAPC (ingroup data set)Single nucleotide polymorphism data set with only in-group individuals, used in DAPC and for calculating f-statistics. (See "Population assignments" file for corresponding population data for individual IDs.)quads_no.recode.vcfPopulation assignmentsFile containing (1) ID codes, (2) species assignments, (3) population assignments, (4) latitude, and (5) longitude used in DAPC analyses and ecological niche modeling. Species assignment codes: Q = D. quadramaculatus, M = D. marmoratus, C = D. carolinensis. Population assignment codes: P = Pisgah, N = Nantahala, C = D. carolinensis.quads_out_pops.csvBPP loci data setReduced data set of 500 random loci used in Bayesian Phylogeography and Phylogenetics analyses.desmogs.lociInterleaved nexus file for SVDquartets (ingroup data set)In-group data set used for SVDquartets analysisquads_no_out.nexVCF file containing SNPs for DAPC (outgroup data set)Single nucleotide polymorphism data for all individuals. Used for DAPC analyses and calculating f-statistics. (See "Population assignments" file for corresponding population data for individual IDs.)quads_out.recode.vcfTreeMix/F4 data setData set used for TreeMix and F4 analyses. The data is in plink stratified allele frequency format, which can be converted to work in TreeMix and F4 using TreeMix's inbuilt conversion script. For more details see the TreeMix Bitbucket site: https://bitbucket.org/nygcresearch/treemix/wiki/Home F4 is available to download here: https://github.com/mmatschiner/F4plink.frq.strat.gzLink to raw dataThis is a text file that contains a link to the demultiplexed raw sequencing data for all individuals used in this study. The fastq files are named using each individual's ID; more information about individuals can be found in the "Population assignment" file. Note that the gzipped directory is 31Gb.desmog_raw_data_link.txtFunding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: DEB-13550