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.解析海洋物种的遗传结构并推断其种群连通性，因传统基因型分型方法的遗传分化信号微弱、分辨率不足，长期以来极具挑战。 本研究的核心目标为评估群体基因组学（population genomics）框架，能否在美洲螯龙虾（Homarus americanus）的大部分自然分布范围内，厘清其遗传结构，并提升个体溯源至原产地的种群归属成功率。我们采用RAD测序（RAD sequencing）对10156个经过过滤的单核苷酸多态性（single nucleotide polymorphism, SNPs）位点进行基因分型，对采自覆盖该物种自然分布大范围区域的17个采样点的586只美洲螯龙虾开展遗传结构解析与种群归属分析。 研究结果揭示了层级式遗传结构的存在：首先将分布范围内的龙虾划分为北部与南部类群（FCT = 0.0011；P值=0.0002），随后进一步识别出总计11个遗传可区分的种群（平均FST = 0.00185；置信区间（confidence interval, CI）：0.0007–0.0021，P值<0.0002），有力证实了两个区域内均存在微弱但精细的种群遗传结构。重采样分析显示，选取FST值最高的3000个SNPs子集时，种群归属成功率可达最高。采用Anderson于2010年发表于《Molecular Ecology Resources》（第10卷，第701页）的方法以规避‘高分偏倚（high-grading bias）’，个体的区域归属正确率与采样点归属正确率分别达到94.2%与80.8%。最后，本研究证实种群归属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可提升精细尺度的种群遗传结构解析能力与种群归属成功率。我们还讨论了本研究结果对高度连通海洋物种的保护与管理的启示，尤其聚焦于种群人口学独立性的地理尺度议题。