Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden.
Institute of Marine Research, Tromsø Department, Tromsø, Norway.
PLoS One. 2021 May 27;16(5):e0251976. doi: 10.1371/journal.pone.0251976. eCollection 2021.
The diverse biology and ecology of marine organisms may lead to complex patterns of intraspecific diversity for both neutral and adaptive genetic variation. Sebastes mentella displays a particular life-history as livebearers, for which existence of multiple ecotypes has been suspected to complicate the genetic population structure of the species. Double digest restriction-site associated DNA was used to investigate genetic population structure in S. mentella and to scan for evidence of selection. In total, 42,288 SNPs were detected in 277 fish, and 1,943 neutral and 97 tentatively adaptive loci were selected following stringent filtration. Unprecedented levels of genetic differentiation were found among the previously defined 'shallow pelagic', 'deep pelagic' and 'demersal slope' ecotypes, with overall mean FST = 0.05 and 0.24 in neutral and outlier SNPs, respectively. Bayesian computation estimated a concurrent and historical divergence among these three ecotypes and evidence of local adaptation was found in the S. mentella genome. Overall, these findings imply that the depth-defined habitat divergence of S. mentella has led to reproductive isolation and possibly adaptive radiation among these ecotypes. Additional sub-structuring was detected within the 'shallow' and 'deep' pelagic ecotypes. Population assignment of individual fish showed more than 94% agreement between results based on SNP and previously generated microsatellite data, but the SNP data provided a lower estimate of hybridization among the ecotypes than that by microsatellite data. We identified a SNP panel with only 21 loci to discriminate populations in mixed samples based on a machine-learning algorithm. This first SNP based investigation clarifies the population structure of S. mentella, and provides novel and high-resolution genomic tools for future investigations. The insights and tools provided here can readily be incorporated into the management of S. mentella and serve as a template for other exploited marine species exhibiting similar complex life history traits.
海洋生物的生物学和生态学具有多样性，这可能导致同种内遗传变异的中性和适应性遗传变异呈现出复杂的模式。拟沙丁鱼表现出一种特殊的生活史，即胎生，这使得该物种的遗传种群结构可能因多种生态型的存在而变得复杂。使用双酶切限制位点相关 DNA 技术研究了拟沙丁鱼的遗传种群结构，并扫描了选择的证据。在 277 条鱼中检测到了 42288 个 SNP，经过严格过滤，选择了 1943 个中性和 97 个暂定适应性基因座。在先前定义的“浅海层”、“深海层”和“深海坡”生态型之间发现了前所未有的遗传分化水平，中性和外显子 SNP 的总体平均 FST 值分别为 0.05 和 0.24。贝叶斯计算估计了这三个生态型之间的同时和历史分化，并在拟沙丁鱼基因组中发现了局部适应的证据。总的来说，这些发现表明，拟沙丁鱼的深度定义的栖息地分化导致了这些生态型之间的生殖隔离和可能的适应性辐射。在“浅”和“深”海洋生态型中还检测到了额外的亚结构。个体鱼的种群分配显示，基于 SNP 和先前生成的微卫星数据的结果之间有超过 94%的一致性，但 SNP 数据提供的生态型间杂交程度低于微卫星数据。我们基于机器学习算法，确定了一个由 21 个基因座组成的 SNP 面板，用于在混合样本中区分种群。这是首次基于 SNP 的调查，阐明了拟沙丁鱼的种群结构，并为未来的研究提供了新颖且高分辨率的基因组工具。这里提供的见解和工具可以很容易地纳入拟沙丁鱼的管理中，并为其他表现出类似复杂生活史特征的受捕捞海洋物种提供模板。
