Population genetics of Apostichopus californicus along the Northeastern Pacific Coast

A growing body of evidence suggests that spatial population structure can develop in marine species despite large population sizes and high gene flow. Characterizing population structure is important for the effective management of exploited species, as it can be used to identify appropriate scales of management in fishery and aquaculture contexts. The California sea cucumber, Apostichopus californicus, is one such exploited species whose management could benefit from further characterization of population structure. Using restriction site-associated DNA (RAD) sequencing, we developed 2,075 single nucleotide polymorphisms (SNPs) to quantify genetic structure over a broad section of the species’ range along the North American west coast and within the Salish Sea, a region supporting the Washington State A. californicus fishery and developing aquaculture production of the species. We found evidence for population structure (global fixation index (FST) = 0.0068) with limited dispersal driv..., Approximately 50 adult A. californicus were collected by scuba divers from nine collection sites along the Pacific Coast of North America, ranging from Alaska to Oregon, including four collection sites within the southern Salish Sea. For each animal, a tissue sample was excised from a radial muscle band and stored in 100% ethanol.
DNA was extracted from tissue samples using the EZNA Mollusc DNA Kit (OMEGA Bio-tek, Norcross, GA, USA) and the Qiagen DNeasy Kit (Qiagen, Germantown, MD, USA). DNA was quantified using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific, Waltham, MA, USA) and DNA quality was checked by gel electrophoresis. DNA concentration was normalized to 500 ng in 20 μL of PCR-grade water. We selected samples with high DNA quality for restriction site associated DNA (RAD) sequencing and RAD libraries were prepared following standard protocols1. Briefly, DNA samples were barcoded with an individual six-base identifier sequence attached to an Illumina P1 adapte..., Raw data files (*.fastq) are too large to open, but can be accessed with Unix commands and dDocent, an open source pipeline for genotyping restriction site-associated DNA sequencing data.
R (e.g., packages adegenet and genepop) and text editors (e.g., Text Wrangler) can be used to open the genepop files and fasta files of putatively adaptive loci.
R (e.g., tidyverse), Microsoft Excel, and text editors (e.g., Text Wrangler) can be used to open the environ_data.csv file, containing environmental data from each collection site.
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越来越多的研究证据表明，即便种群规模庞大且基因流水平较高，海洋物种仍可形成空间种群结构（spatial population structure）。对种群结构进行解析，对于开发利用物种的有效管理具有重要意义，可帮助确定渔业与水产养殖场景下适宜的管理尺度。加州海参（Apostichopus californicus）便是此类开发利用物种之一，其种群结构的进一步解析可为该物种的管理提供助力。
本研究采用限制性酶切位点相关DNA（restriction site-associated DNA, RAD）测序技术，开发出2075个单核苷酸多态性（single nucleotide polymorphisms, SNPs）标记，以量化该物种北美西海岸广域分布范围及萨利什海（Salish Sea）内的遗传结构；萨利什海区域支撑着华盛顿州A. californicus渔业，并正发展该物种的水产养殖产业。本研究发现了种群结构存在的证据（全局固定指数（fixation index, FST）= 0.0068），有限扩散驱动……
约50头成年A. californicus个体由水肺潜水员从北美太平洋沿岸9个采样点采集，采样范围从阿拉斯加州延伸至俄勒冈州，其中包含萨利什海南部的4个采样点。对每头个体，均从其放射状肌肉带切取组织样品，并保存于无水乙醇中。
研究人员采用EZNA软体动物DNA试剂盒（OMEGA Bio-tek，美国佐治亚州诺克罗斯市）与Qiagen DNeasy试剂盒（Qiagen，美国马里兰州日耳曼敦市）从组织样品中提取DNA。使用Quant-iT PicoGreen双链DNA检测试剂盒（赛默飞世尔科技，美国马萨诸塞州沃尔瑟姆市）对DNA进行定量，并通过凝胶电泳检测DNA质量。将DNA浓度归一化至20 μL PCR级水中含500 ng DNA。选取高质量DNA样品用于限制性酶切位点相关DNA测序，并按照标准实验方案1制备RAD文库。简要而言，DNA样品通过与连接有Illumina P1接头的单条6碱基识别序列进行条形码标记……
原始数据文件（*.fastq）体积过大无法直接打开，但可通过Unix命令与dDocent——一款用于限制性酶切位点相关DNA测序数据基因分型的开源分析管道——进行访问。
可使用R语言（例如adegenet与genepop包）及文本编辑器（例如Text Wrangler）打开genepop文件与推定适应性位点的FASTA文件。
可使用R语言（例如tidyverse包）、微软Excel及文本编辑器（例如Text Wrangler）打开environ_data.csv文件，该文件包含各采样点的环境数据。