DOI: 10.5061/dryad.jq2bvq8g6
title: Data from: Conservation genomics of the threatened Trispot Darter (Etheostoma trisella)

description: The southeastern United States is a hotspot of biodiversity, but aquatic
 habitats are fragmented by anthropogenic activities such as hydrologic
 alteration. Small-stream-inhabiting fish can suffer population declines,
 loss of genetic diversity, and migration impediment from riverine
 impoundment. The Trispot Darter (Etheostoma trisella) is a small,
 freshwater fish endemic to the southeastern United States. E. trisella was
 previously believed to be extinct and has now been listed as threatened
 under the U.S. Endangered Species Act, due to destruction of its limited
 habitat and a restricted range. We used mitochondrial DNA (NADH
 dehydrogenase subunit 2 gene), seven microsatellite loci, and 9732 single
 nucleotide polymorphisms (SNPs) to evaluate population structure and
 diversity in E. trisella. Mitochondrial data provided evidence of
 historical connectivity between populations, with haplotype sharing across
 populations and weak support for population structure. Microsatellite and
 SNP data, however, indicate that populations have more recently become
 isolated. Furthermore, we detect three distinct management units (i.e.,
 genetic groups) which reflect isolated geographic localities (i.e., Little
 Canoe Creek, Ballplay Creek, and a system including the Conasauga and
 Coosawattee rivers). We also detected a recent bottleneck event in the
 Ballplay Creek population as well as a low effective population size.
 Tests of isolation by distance further suggest that populations are
 structured by riverine isolation rather than geographic distance. A better
 understanding about the distribution, abundance, and habitat occupancy of
 all E. trisella populations will be important for informing future
 decisions for conservation of the species.
description: Genomic DNA was isolated from tissue using the DNeasy Blood and
 Tissue Kit following the manufacturer’s instructions (QIAGEN). The quality
 of DNA was verified by electrophoresis using a 1.5% agarose gel stained
 with ethidium bromide. DNA quantity was determined using a NanoDrop 2000
 Spectrophotometer (Thermo Fisher Scientific). Purified DNA was stored at
 -4 °C until further analysis. Genotyping by DArTseq™ analysis was
 performed at Diversity Arrays Technology Pty, Ltd. (DArT; Canberra, ACT,
 Australia) utilizing DArT complexity reduction methods and next generation
 sequencing (Kilian et al. 2012).
description: # Etheostoma\_trisella\_population\_genomics\_2023
 [https://doi.org/10.5061/dryad.jq2bvq8g6](https://doi.org/10.5061/dryad.jq2bvq8g6) This repository contains the data used to perform population genomic and phylogenetic analyses for *Etheostoma trisella* collected in the United States. The data are the result of DArTSeq: a combination of DArT complexity reduction with sequencing on the Next Generation Sequencing platforms. It represents combined marker discovery and genotyping for SNPs. Approximately 50,000 DNA fragments from DArT representations were assayed for polymorphism. We detect three distinct management units (i.e., genetic groups) which reflect isolated geographic localities (i.e., Little Canoe Creek, Ballplay Creek, and a system including the Conasauga and Coosawattee rivers). We also detected a recent bottleneck event in the Ballplay Creek population as well as a low effective population size. Tests of isolation by distance further suggest that populations are structured by riverine isolation rather than geographic distance. ## Description of the data and file structure The SNP report file in .csv format includes data for 93 *Etheostoma trisella* specimens. The file includes columns for AlleleID, CloneID, AlleleSequence, TrimmedSequence, SNP, SnpPosition, CallRate, OneRatioRef, OneRatioSnp, FreqHomRe, FreqHomSnp, FreqHets, PICRef, PICSnp, AvgPIC, AvgCountRef, AvgCountSnp, RepAvg. Binary states for loci are also indicated for each specimen. Specimens are named with a unique number identifier followed by collection locality. ## Sharing/Access information Not applicable. ## Code/Software Not applicable.