DOI: 10.5061/dryad.3bk3j9khp
title: Genomic and phenotypic divergence informs translocation strategies for an endangered freshwater fish

description: Translocation, the movement of organisms for conservation purposes, can
 result in unintended introgression if genetic material flows between
 populations in new ways. The Bluemask Darter Etheostoma akatulo is a
 federally endangered species of freshwater fish inhabiting the Caney Fork
 River system and three of its tributaries (Collins River, Rocky River, and
 Cane Creek) in Tennessee. The current conservation strategy for Bluemas­k
 Darters involves translocating the progeny of broodstock from the Collins
 River, in the west, to the Calfkiller River, in the east, where the
 species had been extirpated. In this study, we use ddRAD sequence data
 from across the extant range to assess this translocation strategy in
 light of population structure, phylogeny, and demography. We also include
 museum specimen data to assess morphological variation among extant and
 extirpated populations. Our analyses reveal substantial genetic and
 phenotypic disparities between a western population in the Collins River
 and an eastern population encompassing the Rocky River, Cane Creek, and
 upper Caney Fork, the two of which shared common ancestry more than
 100,000 years ago. Furthermore, morphological analyses classify 12 of 13
 Calfkiller River specimens with phenotypes consistent with the eastern
 population. These results suggest that current translocations perturb the
 evolutionary boundaries between two delimited populations. Instead, we
 suggest that repopulating the Calfkiller River using juveniles from the
 Rocky River could balance conflicting signatures of demography, diversity,
 and divergence. Beyond conservation, the microgeographic structure of
 Bluemask Darter populations adds another puzzle to the phylogeography of
 the hyper diverse freshwater fishes in eastern North America.
description: Raw ddRAD sequence data (Data/fastqs/*): We
 sampled specimens of <em>Etheostoma akatulo</em> from sites
 among the four tributaries of the Caney Fork River system that span the
 complete extant range of the species. Samples (collected by J.W.S. under
 permit from the TVA) were small tissue biopsies from the upper lobe of the
 caudal fin. To minimize injury and mortality, tissue biopsies were only
 sampled from individuals with a total length &gt; 30 mm and all
 specimens were released at their collection site. We also included several
 previously collected specimens of other species closely related to
 <em>E. akatulo</em> to serve as outgroups for phylogenetic and
 molecular divergence time analyses: two specimens of <em>E.
 stigmaeum</em> (from Crooked Creek, Jefferson County, AL, USA), two
 specimens of <em>E. meadiae</em> (Copper Creek, Scott County,
 VA, USA), two specimens of <em>E. jessiae</em> (McNair Creek,
 Franklin County, KY, USA), and one specimen of <em>E.
 chlorosoma</em> (Wildcat Creek, Calloway County, KY, USA). We
 extracted genomic DNA from our ethanol-preserved tissue specimens using
 the Qiagen DNeasy Blood and Tissue Kit following the manufacturer's
 protocol (Qiagen, Valencia, CA, USA). After ddRAD library
 preparation, libraries were sequenced for 100 bp, single-end reads on an
 Illumina HiSeq2000 at the Genomics & Cell Characterization Core
 Facility, University of Oregon (Eugene, OR, USA). Specimen metadata is
 available in the Data/akatulo_genetic_metadata.tsv file.
 Morphological data (Data/akatulo_morphology_data.tsv):
 Courtesy of Dr. Steve Layman and the Auburn University Museum of
 Natural History. See Layman, S. R., & Mayden, R. L. (2009). A New
 Species of the Darter Subgenus Doration (Percidae:
 <em>Etheostoma</em>) from the Caney Fork River System,
 Tennessee. Copeia, 2009(1), 157–170.
description: Instructions on using these files and replicating analyses are
 available in the README.md file. Each script contains a documented header
 and in-line documentation. NOTE that the precise site
 info, latitude, and longtidue columns have been masked in accordance with
 Dryad submission protocols for imperiled species (see README_MASKING in
 Data/ folder).