DOI: 10.5061/dryad.9kd51c5jr
title: Final filtered loci dataset for Rostroraja eglanteria

description: Skates are benthic elasmobranchs that are highly vulnerable to incidental
 fishery bycatch, are discarded at sea, and are poorly accounted for in
 catch records. Many aspects of skate life history, such as population
 structure, are not well understood. Without this knowledge, their
 continued indiscriminate harvest may have deleterious effects on
 scientific, conservation, and management efforts. The Clearnose Skate
 (Rostroraja eglanteria) is seasonally migratory and widely distributed in
 the coastal waters of the eastern United States and in the northeastern
 Gulf of Mexico. This study used molecular techniques to assess the
 population structure of Clearnose Skate so that it may serve as a valuable
 biological reference point for further research and management. Specimens
 were collected from 2014 to 2019 by fisheries-independent surveys, and
 examined on broad and small geographic scales. High-throughput
 genotyping-by-sequencing was used to identify single nucleotide
 polymorphisms (SNPs), resulting in two datasets; one consisting of 8,914
 loci (outlier and neutral) and the other comprised of 30 outlier loci.
 Results from all analyses and using both datasets indicated large and
 significant genetic differences between specimens from the Gulf of Mexico
 and specimens from the U.S East Coast. Using the outlier dataset, small
 but significant differences were also found among specimens from the U.S.
 East Coast with a subtle break near the North Carolina and South Carolina
 border. These genetic differences were spatially autocorrelated,
 indicating a genetic gradient consistent with an isolation-by-distance
 model. The genetic differentiation between the Gulf of Mexico and the U.S.
 East Coast is likely due to the physical barriers such as Florida and the
 Gulf Stream current, while the subtle structure along the U.S. East Coast
 is likely due to recent isolation caused by reduced dispersal and local
 temperature preferences.
description: Tissue samples were collected by fishery-independent survey crews
 and sent to the Fisheries Genetics lab at the Virginia Institute of Marine
 Science. DNA was extracted using either Qiagen™<sup>
 </sup>DNeasy Blood and Tissue kit (QIAGEN Sciences, Germantown, MD),
 or Puramag™ carboxylated magnetic beads (MCLAB, South San Francisco,
 CA).  Extractions yielding high molecular weight DNA
 and a concentration of at least 50 ng/uL were sent to Diversity Arrays
 Technology (DArT Pty Ltd, Canberra, AU) for high-throughput genotyping by
 sequencing using DArTseq<sup>TM</sup> (Sansaloni et al. 2011).
 Briefly, restriction endonucleases were used to reduce the complexity of
 the genome followed by hybridization to microarrays and sequencing on an
 Illumina HiSeq 2500 (Illumina, San Diego, CA, USA). SNPs were identified
 using a proprietary data pipeline developed by DArT PL (DArTsoft14) where
 fragments were aligned to the <i>Leucoraja erinacea</i>
 reference genome (Wang et al. 2012), and matched with individual specimens
 and their associated metadata
 (http://www.diversityarrays.com/software.html).
description: Original SilicoDArT file, metadata file, unfiltered genlight
 file, and R scripts are available upon request.