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Final filtered loci dataset for Rostroraja eglanteria

Citation

Nelson, Lindsey (2022), Final filtered loci dataset for Rostroraja eglanteria, Dryad, Dataset, https://doi.org/10.5061/dryad.9kd51c5jr

Abstract

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.

Methods

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™ 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 DArTseqTM (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 Leucoraja erinacea reference genome (Wang et al. 2012), and matched with individual specimens and their associated metadata (http://www.diversityarrays.com/software.html).

Usage Notes

Original SilicoDArT file, metadata file, unfiltered genlight file, and R scripts are available upon request.

Funding

Virginia Sea Grant, Virginia Institute of Marine Science, Award: R/721522

Virginia Sea Grant, Virginia Institute of Marine Science, Award: R/72155G

American Museum of Natural History, Award: Lerner-Gray Memorial Fund

International Women's Fishing Association, Award: Scholarship Trust

Virginia Institute of Marine Science Graduate Student Association, Award: Student Research Fund