Extensive admixture among karst-obligate salamanders reveals evidence of recent divergence and gene exchange through aquifers

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 amoun..., 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., , # 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 i...