Comparative population genetics of the federally endangered Relict Darter, and its sister taxon the Clarks Darter (Teleostei: Percidae)
Kattawar, Jerry; Piller, kyle (2020), Comparative population genetics of the federally endangered Relict Darter, and its sister taxon the Clarks Darter (Teleostei: Percidae), Dryad, Dataset, https://doi.org/10.5061/dryad.fqz612jqb
The southeastern United States harbors one of the most diverse temperate freshwater fish faunas of the world. Unfortunately, due to improper land use practices and habitat degradation, many of the species in this region are imperiled and may become extinct without appropriate conservation efforts. This study examined the population dynamics of an endangered endemic darter of southwest Kentucky, the Relict Darter (Etheostoma chienense) and its sister taxon, the undescribed Clarks Darter (Etheostoma cf. oophylax). Mitochondrial sequence data coupled with SNP data were used to infer population structure, gene flow, genetic variation, and effective population sizes of both species. The results from this study, based on 160 individuals from nine localities, indicate that the endangered Relict Darter possesses limited genetic variation based on mitochondrial DNA haplotypes (N=4). In addition, SNP data (6.8k markers) further indicates limited genetic structure (K=1), as well as a low effective population size (143-918), suggesting that the Relict Darter can be managed as a single, panmictic conservation unit. It is suggested that conservation efforts be taken to protect remaining habitats, augment the system with artificial spawning substrates, and, as a last resort (if needed), supplement the natural population with captive reared individuals. Ethesotoma cf. oophylax showed some genetic variation among distant sites, but more samples are needed throughout the range in order to fully understand the population dynamics of this species.
This dataset was collected at Southeastern Louisiana Univeristy in the Piller lab using ddRADseq. Fin clips were taken from the caudal fin of the fish and placed in 90% ethanol for short term stoarage. DNA was extracted using Promega and Qiagen DNA extraction kits. Double Digest RADseq (Peterson et al. 2012) was implemented for single end Illumina library prep at Southeastern Louisiana Univeristy in the Piller lab. Illumina sequencing on an Illumina Hiseq 4000 was done at University of Oregon. The raw data was processed using ipyrad v0.7.30 and then vcftools. Several standard population genetic analyses were run on these datasets (STRUCTURE, DAPC, pwFst, Effective population size, etc.)
For raw fastq data files go to NCBI SRA project number PRJNA635125.
Here we have provided ipyrad params files, and final alignment files. See paper for details on analyses.
Cooperative Endangered Species Conservation Fund, Award: FAP111-44-00