Data from: RAD genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (Homarus americanus).

Deciphering genetic structure and inferring connectivity in marine species have been challenging due to weak genetic differentiation and limited resolution offered by traditional genotypic methods. The main goal of this study was to assess how a population genomics framework could help delineate the genetic structure of the American lobster (Homarus americanus) throughout much of the species’ range and increase the assignment success of individuals to their location of origin. We genotyped 10 156 filtered SNPs using RAD sequencing to delineate genetic structure and perform population assignment for 586 American lobsters collected in 17 locations distributed across a large portion of the species’ natural distribution range. Our results revealed the existence of a hierarchical genetic structure, first separating lobsters from the northern and southern part of the range (FCT = 0.0011; P-value = 0.0002) and then revealing a total of 11 genetically distinguishable populations (mean FST = 0.00185; CI: 0.0007–0.0021, P-value < 0.0002), providing strong evidence for weak, albeit fine-scale population structuring within each region. A resampling procedure showed that assignment success was highest with a subset of 3000 SNPs having the highest FST. Applying Anderson's (Molecular Ecology Resources, 2010, 10, 701) method to avoid ‘high-grading bias’, 94.2% and 80.8% of individuals were correctly assigned to their region and location of origin, respectively. Lastly, we showed that assignment success was positively associated with sample size. These results demonstrate that using a large number of SNPs improves fine-scale population structure delineation and population assignment success in a context of weak genetic structure. We discuss the implications of these findings for the conservation and management of highly connected marine species, particularly regarding the geographic scale of demographic independence.

由于传统基因型检测方法存在遗传分化微弱、分辨率有限的局限，解析海洋物种的遗传结构并推断其连通性一直是学界的难题。本研究的核心目标为评估群体基因组学框架能否帮助阐明该物种大部分分布区内美洲螯龙虾（Homarus americanus）的遗传结构，并提升个体溯源至其原产地的成功率。本研究通过RAD测序技术对10156个经过筛选的单核苷酸多态性（Single Nucleotide Polymorphisms，SNPs）进行基因分型，对分布于该物种自然分布区大部分区域的17个采样点的586只美洲螯龙虾开展遗传结构解析与群体溯源分析。研究结果显示存在层级化遗传结构：首先将分布区南北两侧的美洲螯龙虾区分开（FCT=0.0011；P值=0.0002），随后进一步揭示出共计11个遗传上可区分的群体（平均FST=0.00185；置信区间（Confidence Interval，CI）：0.0007~0.0021，P值<0.0002），有力证明了各区域内虽存在微弱但可识别的精细尺度群体结构。重采样分析显示，选取FST值最高的3000个SNPs子集时，个体溯源成功率最高。采用Anderson于2010年发表于《分子生态学资源》（Molecular Ecology Resources, 2010, 10, 701）的方法以规避“高分偏倚”后，分别有94.2%和80.8%的个体被正确划归至其所属区域与原产地。此外，本研究还证实个体溯源成功率与样本量呈正相关关系。上述结果表明，在遗传结构微弱的研究背景下，使用大量SNPs可提升精细尺度群体结构的解析精度与群体溯源成功率。本研究最后探讨了该研究结果对高度连通海洋物种的保护与管理的启示，尤其是针对种群独立的地理尺度相关议题。