Bayou Darter next-gen sequence data and analyses

Bayou Darters (Nothonotus rubrus) are a small benthic fish endemic to Bayou Pierre, Mississippi. The entire range of the species is threatened by geomorphic change due to accelerated erosion, channel incision, and channel evolution processes stemming from the migration of the Mississippi River and human alterations to the landscape. Bayou Darters have disappeared from much of mainstem Bayou Pierre, but have expanded their range upstream into formerly unoccupied tributaries, in concert with upstream progression of channel evolution processes. In this dataset, we document an effort to understand whether upstream dispersal into tributaries is affecting gene flow through fragmentation of populations. We used Next-Gen sequencing approaches to develop high-resolution molecular datasets to assess population structure, patterns of heterozygosity, and effective populations size, throughout the contemporary distribution of the species. 

Methods
We sampled Nothonotus rubrus from 19 sites representing the known contemporary distribution of the species. We targeted a minimum of 5 individuals per site. Tissue samples were collected with fin clips (~0.1g) from individual N. rubrus. Tissue samples were stored in 95% etOH on ice, and individuals were released alive at their locality of capture. We extracted DNA using DNEasy blood and tissue kits (Qiagen), constructed libraries with the EcoT221 restriction enzyme, and sequenced tissues on an Illumina Hi-Seq platform. We used Genotype-By-Sequencing to identify SNPs and R package vcftools to filter SNPs and individuals for quality controls. We analyzed data using multiple approaches, including STRUCTURE, Principle Coordinates Analysis, NeEstimator V2.1, and measurements of heterozygosity and pairwise Fst calculated from filtered SNP data.