DOI: 10.5061/dryad.3r2280gpx
title: Data from: Extensive admixture among karst-obligate salamanders reveals evidence of recent divergence and gene exchange through aquifers

description: Karst ecosystems often contain extraordinary biodiversity, but the complex
 underground aquifers of karst regions present challenges for assessing and
 conserving stygobiont diversity and investigating their evolutionary
 history. We examined the karst-obligate salamanders of the Eurycea
 neotenes species complex in the Edwards Plateau region of central Texas
 using population genomics data to address questions about population
 connectivity and the potential for gene exchange within the underlying
 aquifer system. The Eurycea neotenes species complex has historically been
 divided into three nominal species, but their status, and spatial extent
 of species ranges, have remained uncertain. We discovered evidence of
 extensive admixture within the species complex and with adjacent lineages.
 We observed relatively low levels of differentiation among all sampling
 localities which supports the hypothesis of recent divergence. Nominal
 taxonomy, aquifer region and geography accounted for a modest amount of
 the overall population genomic variation, but these predictors were
 largely confounded and difficult to disentangle. Importantly, the taxonomy
 of the three nominal species does not reflect the admixture apparent in
 clustering analyses. Inference of migration events revealed a complex
 pattern of gene exchange, suggesting that Eurycea salamanders have a
 dynamic history of dispersal through the aquifer system. These results
 highlight the need for greater understanding of how stygobiont populations
 are connected via dispersal and gene exchange through karst aquifers.
 These results also highlight the applicability of population genomics data
 as a powerful lever for investigating connectivity among populations in
 systems where direct detection of dispersal paths is difficult, as in
 underground, aquatic systems.
description: Matrix of posterior genotype probabilities for 607 salamanders at
 16,094 SNP loci generated by genotyping-by-sequencing methods (similar to
 ddRAD.seq methods). The hierarchical Bayesian clustering algorithm ENTROPY
 was used to generate these genotype probabilities. A locality file is
 included along with a script and matrix of predictors for Redundancy
 Analysis and script and data object for Bayesian Linear Mixed Model are
 included.
description: # Data from: Extensive admixture among karst-obligate salamanders reveals
 evidence of recent divergence and gene exchange through aquifers
 [https://doi.org/10.5061/dryad.3r2280gpx](https://doi.org/10.5061/dryad.3r2280gpx) Files included here contain scripts and data for partitioning population genomic variation using RDA and a Bayesian Linear Mixed Model. ## Description of the data and file structure gprobmean.csv is the matrix of posterior genotype estimates for 607 salamanders for 16,094 SNP loci locality_dat.csv contains information about sampling localities predictors_dbmem.csv contains categorical predictors for nominal taxon, major aquifer, and eight Moran's Eigenvector maps for all individuals RDAscript.R is a script to perform Redundancy Analyses using the gprobmean.csv and predictors_dbmem.csv files described above IBDanalyses_BLMM.R is the script to perform Bayesian Linear Mixed Model analyses using JAGS and includes code for a function for running these analyses. It is to be used with the RData object IBD_BLMM.RData IBD_BLMM.RData includes the matrix of pairwise, linearized Fst values, the matrix of pairwise geographic distances between localities, and indexing matrices for the categorical predictors: nominal taxonomy and major aquifer. This object also includes all results files for all analyses, though these can be re-run with the above script. To be loaded with IBDanalyses_BLMM.R interactivePCA_1v2.html is an interactive version of the Principal Components Analysis that can be viewed in a web browser. ## Sharing/Access information The DNA sequence data analysed used to generate the posterior genotype estimates have been archived on NCBI’s SRA  (PRJNA1057889): * [https://www.ncbi.nlm.nih.gov/search/all/?term=PRJNA1057889](https://www.ncbi.nlm.nih.gov/search/all/?term=PRJNA1057889) ## Change log: compared to previous, no data has changed. IBDanalyses_BLMM.R has been updated to include calculation of wAIC and LOOIC (leave-one-out information criteria) for all of the Bayesian linear mixed models. file added: interactivePCA_1v2.html