DOI: 10.5061/dryad.3k5c0sh
title: Data from: Species delimitation in endangered groundwater salamanders: implications for aquifer management and biodiversity conservation

description: Groundwater-dependent species are among the least-known components of
 global biodiversity, as well as some of the most vulnerable because of
 rapid groundwater depletion at regional and global scales. The karstic
 Edwards–Trinity aquifer system of west-central Texas is one of the most
 species-rich groundwater systems in the world, represented by dozens of
 endemic groundwater-obligate species with narrow, naturally fragmented
 distributions. Here, we examine how geomorphological and hydrogeological
 processes have driven population divergence and speciation in a radiation
 of salamanders (Eurycea) endemic to the Edwards–Trinity system using
 phylogenetic and population genetic analysis of genome-wide DNA sequence
 data. Results revealed complex patterns of isolation and reconnection
 driven by surface and subsurface hydrology, resulting in both adaptive and
 non-adaptive population divergence and speciation. Our results uncover new
 cryptic species diversity and refine the borders of several threatened and
 endangered species. The U.S. Endangered Species Act has been used to bring
 state regulation to unrestricted groundwater withdrawals in the Edwards
 (Balcones Fault Zone) Aquifer, where listed species are found. However,
 the Trinity and Edwards–Trinity (Plateau) aquifers harbor additional
 species with similarly small ranges that currently receive no protection
 from regulatory programs designed to prevent groundwater depletion. Based
 on regional climate models that predict increased air temperature,
 together with hydrologic models that project decreased springflow, we
 conclude that Edwards–Trinity salamanders and other co-distributed
 groundwater-dependent organisms are highly vulnerable to extinction within
 the next century.
description: Structure input file for
 the northern clade.A Structure data file
 consisting of 131 individuals genotyped at 647 loci. See README file for
 MAINPARAMS and EXTRAPARAMS settings.Sept.strStructure input file for E. chisholmensis and E. naufragia populations.A Structure data file consisting of 53 E. chisholmensis and E. naufragia samples genotyped at 647 loci. See README file for MAINPARAMS and EXTRAPARAMS settings.chinau.strStructure input file for E. tonkawae.A Structure data file consisting of 78 E. tonkawae samples genotyped at 647 loci. See README file for MAINPARAMS and EXTRAPARAMS settings.tonk.strStructure input file for the southeastern clade.A Structure data file consisting of 73 individuals from the southeastern clade (excluding Typhlomolge) genotyped at 146 loci. See README file for MAINPARAMS and EXTRAPARAMS settings.EBlep.strStructure input file for the southwestern clade.A Structure data file consisting of 82 individuals from the southwestern clade genotyped at 604 loci. See README file for MAINPARAMS and EXTRAPARAMS settings.WBlep.strStructure input file for E. sp. 2.A Structure data file consisting of 36 individual E. sp. 2 samples genotyped at 604 loci. See README file for MAINPARAMS and EXTRAPARAMS settings.sp2.strStructure input file for E. troglodytes and E. sp. 3.A Structure data file consisting of 46 E. troglodytes and E. sp. 3 samples genotyped at 604 loci. See README file for MAINPARAMS and EXTRAPARAMS settings.trogsp3.strStructure input file for E. troglodytes.A Structure data file consisting of 26 individual E. troglodytes genotyped at 604 loci. See README file for MAINPARAMS and EXTRAPARAMS settings.trog.strStructure input file for E. sp. 3.A Structure data file consisting of 20 E. sp. 3 samples genotyped at 604 loci. See README file for MAINPARAMS and EXTRAPARAMS settings.sp3.strNexus file for 74,955 SNPs from 94 populations.Data are 74,955 SNPs from 94 populations of Eurycea. For populations represented by more than one sampled individual, only those SNPs that are fixed within the population are used to create the exemplar sequence using the 'populations' program in Stacks. Details needed to reproduce the RAxML analysis are provided in the README file.74955.nexBarcode files for demultiplexing raw reads.A zip archive of seven text files containing sample names and associated barcodes for demultiplexing raw reads from pooled samples. See the attached README file for the steps taken to demultiplex in Stacks and ipyrad and produce assemblies for downstream analyses.barcodes.zipJA14785_pool1_CGTACG_L004_R1 raw readsJA14785_pool1_CGTACG_L004_R1_001.fastq.gzJA14785_pool1_CGTACG_L004_R2 raw readsJA14785_pool1_CGTACG_L004_R2_001.fastq.gzJA14785_pool2_ATTGGG_L003_R1 raw readsJA14785_pool2_ATTGGG_L003_R1_001.fastq.gzJA14785_pool2_ATTGGG_L003_R2 raw readsJA14785_pool2_ATTGGG_L003_R2_001.fastq.gzJA14785_pool2_ATTGGG_L004_R1 raw readsJA14785_pool2_ATTGGG_L004_R1_001.fastq.gzJA14785_pool2_ATTGGG_L004_R2 raw readsJA14785_pool2_ATTGGG_L004_R2_001.fastq.gzJA14785_pool3_GTATTA_L003_R1 raw readsJA14785_pool3_GTATTA_L003_R1_001.fastq.gzJA14785_pool3_GTATTA_L003_R2 raw readsJA14785_pool3_GTATTA_L003_R2_001.fastq.gzJA14785_pool3_GTATTA_L004_R1 raw readsJA14785_pool3_GTATTA_L004_R1_001.fastq.gzJA14785_pool3_GTATTA_L004_R2 raw readsJA14785_pool3_GTATTA_L004_R2_001.fastq.gzJA14300_ddRAD_Pool1_CGTACG_L008_R1 raw readsJA14300_ddRAD_Pool1_CGTACG_L008_R1_001.fastq.gzJA14300_ddRAD_Pool1_CGTACG_L008_R2 raw readsJA14300_ddRAD_Pool1_CGTACG_L008_R2_001.fastq.gzJA14300_ddRAD_Pool1_CGTACG_L006_R1 raw readsJA14300_ddRAD_Pool1_CGTACG_L006_R1_001.fastq.gzJA14300_ddRAD_Pool1_CGTACG_L006_R2 raw readsJA14300_ddRAD_Pool1_CGTACG_L006_R2_001.fastq.gzJA14300_ddRAD_Pool2_TAAGAA_L008_R1 raw readsJA14300_ddRAD_Pool2_TAAGAA_L008_R1_001.fastq.gzJA14300_ddRAD_Pool2_TAAGAA_L008_R2 raw readsJA14300_ddRAD_Pool2_TAAGAA_L008_R2_001.fastq.gzJA14300_ddRAD_Pool3_ACGATT_L008_R1 raw readsJA14300_ddRAD_Pool3_ACGATT_L008_R1_001.fastq.gzJA14300_ddRAD_Pool3_ACGATT_L008_R2 raw readsJA14300_ddRAD_Pool3_ACGATT_L008_R2_001.fastq.gzJA14300_ddRAD_Pool4_GTATTA_L008_R1 raw readsJA14300_ddRAD_Pool4_GTATTA_L008_R1_001.fastq.gzJA14300_ddRAD_Pool4_GTATTA_L008_R2 raw readsJA14300_ddRAD_Pool4_GTATTA_L008_R2_001.fastq.gzJA14785_pool1_CGTACG_L003_R1 raw readsJA14785_pool1_CGTACG_L003_R1_001.fastq.gzJA14785_pool1_CGTACG_L003_R2 raw readsJA14785_pool1_CGTACG_L003_R2_001.fastq.gzThe NCBI SRA identifier for demultiplexed reads.PRJNA504898 is the BioProject Accession identifier for demultiplexed fastq files in the NCBI Sequence Read Archive (SRA). Reads were demultiplexed using the process_radtags program in the Stacks software pipeline and using ipyrad. See the README associated with the barcodes file for more information.Input files for BPP analyses.An archive containing the input files necessary to replicate the BPP analyses, including an excel workbook listing different combinations of priors tested.BPP_infiles.zipInfiles and R code for hierarchical F-statistic analyses.An archive containing the three input files and R code for hierarchical F-statistic analyses using the HierFstat package in R. Each input file has a corresponding excel worksheet listing the subbasin, watershed, and subpopulation names that are coded as integers in the input files.HierFstat_infiles.zip