Gray seal RAD loci

Catalog of 244,822 RAD loci consensus sequences resulting from ddRAD sequencing of genomic DNA from 56 gray seals sampled in the Northwest Atlantic. The gray seals selected to build the RAD catalog included 7 individuals from each of the following sampling locations and cohorts - Gulf of St Lawrence, Canada: 2015; Sable Island, NS, Canada: 1973-74, 1985, 1998, 2004, and 2015; Muskeget Island, MA, USA: 2002 and 2015-16. The details of the ddRAD protocol and bioinformatic processing are described in detail in the Methods section and Appendix S1 of Cammen et al. (2018). In brief, ddRAD was conducted with restriction enzymes SBfI-HF and MspI, size selection by 1.5x beads, and 50-bp single-end read Illumina Hiseq 2500 sequencing. Sequences were processed using Stacks v1.21 to build loci de novo using the following parameters, selected using the r80 optimization approach: m = 2, M = 2, and n = 2. File is in FASTA format and each sequence is identified by a numerical locus ID.

本RAD序列集包含西北大西洋海域56只灰海豹的基因组DNA经双酶切限制性酶切位点相关DNA（double digest Restriction-site Associated DNA sequencing, ddRAD）测序得到的244822个限制性酶切位点相关DNA（Restriction-site Associated DNA, RAD）位点一致性序列。用于构建该RAD序列集的灰海豹样本按采样地点与年份队列分组，每组均包含7只个体：加拿大圣劳伦斯湾（2015年）；加拿大新斯科舍省萨布尔岛（1973-1974年、1985年、1998年、2004年及2015年）；美国马萨诸塞州马斯基特岛（2002年与2015-2016年）。ddRAD实验流程与生物信息学分析的详细步骤已在Cammen等人2018年发表研究的方法部分及附录S1中完整记载。简言之，本研究采用SBfI-HF与MspI两种限制性内切酶开展ddRAD实验，通过1.5倍体积磁珠进行片段大小筛选，并使用Illumina HiSeq 2500平台完成50bp单端读长测序。序列分析采用Stacks v1.21软件进行从头组装以构建RAD位点，参数通过r80优化方法确定，具体设置为m=2、M=2及n=2。本数据集文件采用FASTA格式，每条序列以数字位点ID作为唯一标识。