Benestan Laura, Gosselin Thierry, Perrier Charles, Sainte-Marie Bernard, Rochette Rémy, Bernatchez Louis
Institut de Biologie Intégrative des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada, G1V0A6.
Pêches et Océans Canada, Institut Maurice-Lamontagne, CP 1000, Mont-Joli, Quebec, Canada, G5H 3Z4.
Mol Ecol. 2015 Jul;24(13):3299-315. doi: 10.1111/mec.13245. Epub 2015 Jun 15.
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.
由于传统基因型方法提供的遗传分化较弱且分辨率有限，解析海洋物种的遗传结构和推断其连通性一直具有挑战性。本研究的主要目标是评估种群基因组框架如何有助于描绘美洲龙虾（美洲螯龙虾）在其大部分分布范围内的遗传结构，并提高个体归属于其起源地的成功率。我们使用RAD测序对10156个过滤后的单核苷酸多态性（SNP）进行基因分型，以描绘遗传结构并对在该物种自然分布范围的很大一部分内的17个地点收集的586只美洲龙虾进行种群归属分析。我们的结果揭示了一种分层遗传结构的存在，首先将分布范围北部和南部的龙虾分开（FCT = 0.0011；P值 = 0.0002），然后总共揭示了11个遗传上可区分的种群（平均FST = 0.00185；置信区间：0.0007 - 0.0021，P值 < 0.0002），这为每个区域内虽微弱但精细尺度的种群结构提供了有力证据。重采样程序表明，使用具有最高FST的3000个SNP子集时，归属成功率最高。应用安德森（2010年，《分子生态学资源》，第10卷，第701页）的方法以避免“高分级偏差”，分别有94.2%和80.8%的个体被正确归属于其区域和起源地。最后，我们表明归属成功率与样本量呈正相关。这些结果表明，在遗传结构较弱的情况下，使用大量SNP可改善精细尺度的种群结构描绘和种群归属成功率。我们讨论了这些发现对高度连通的海洋物种的保护和管理的影响，特别是关于人口统计学独立的地理尺度。
