Final filtered loci dataset for Rostroraja eglanteria

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).

鳐类（skates）是底栖板鳃亚纲鱼类（elasmobranchs），极易受到渔业兼捕副渔获物的影响，常被弃置于海中，且渔获记录中对其统计严重不足。目前人们对鳐类生活史的诸多方面（如种群结构）仍知之甚少。若缺乏此类认知，持续无差别捕捞可能会对科学研究、物种保护及渔业管理工作造成不利影响。

亮鼻鳐（Clearnose Skate, Rostroraja eglanteria）具有季节性洄游特性，广泛分布于美国东海岸海域及墨西哥湾东北部水域。本研究借助分子技术对亮鼻鳐的种群结构进行评估，以期为后续相关研究与渔业管理提供有价值的生物学参考基准。

研究样本于2014至2019年间通过渔业独立调查采集，并在大尺度与小尺度地理范围内开展检测。研究采用高通量测序分型技术（high-throughput genotyping-by-sequencing）筛选单核苷酸多态性（single nucleotide polymorphisms, SNPs），最终得到两组数据集：一组包含8914个基因座（涵盖异常位点与中性位点），另一组仅包含30个异常位点基因座。

所有分析基于两组数据集均得出一致结论：墨西哥湾与美国东海岸的亮鼻鳐样本之间存在显著且大规模的遗传分化。基于异常位点数据集的分析还显示，美国东海岸内部的样本亦存在微小但显著的遗传差异，在北卡罗来纳州与南卡罗来纳州边境附近存在一处细微的遗传分界。上述遗传差异具有空间自相关性，表明其遗传梯度符合距离隔离模型。墨西哥湾与美国东海岸之间的遗传分化，可能由佛罗里达半岛及湾流等物理屏障造成；而美国东海岸内部的细微遗传结构，则可能源于扩散能力减弱与局部温度偏好所导致的近期隔离。

方法
组织样本由渔业独立调查团队采集，并送往弗吉尼亚海洋科学研究所渔业遗传学实验室进行处理。DNA提取可采用Qiagen™ DNeasy血液与组织试剂盒（QIAGEN Sciences, 日耳曼敦，马里兰州）或Puramag™羧基化磁珠（MCLAB, 南旧金山，加利福尼亚州）完成。

提取得到的高分子量DNA且浓度不低于50 ng/uL的样本，将被送往多样性阵列技术公司（Diversity Arrays Technology, DArT Pty Ltd, 堪培拉，澳大利亚），通过DArTseq™技术进行高通量测序分型（Sansaloni等，2011）。简言之，研究人员首先利用限制性内切酶降低基因组复杂度，随后将其与微阵列杂交，并在Illumina HiSeq 2500测序仪（Illumina, 圣地亚哥，加利福尼亚州，美国）上完成测序。单核苷酸多态性的识别依托DArT PL公司开发的专有数据流程（DArTsoft14）完成：将测序片段比对至斑纹鳐（Leucoraja erinacea）参考基因组（Wang等，2012），并与个体样本及其关联元数据进行匹配（http://www.diversityarrays.com/software.html）。