Data from: Population genomic evidence for adaptive differentiation in the Baltic Sea herring

Detecting and estimating the degree of genetic differentiation among populations of highly mobile marine fish having pelagic larval stages is challenging because their effective population sizes can be large, and thus, little genetic drift and differentiation is expected in neutral genomic sites. However, genomic sites subject to directional selection stemming from variation in local environmental conditions can still show substantial genetic differentiation, yet these signatures can be hard to detect with low-throughput approaches. Using a pooled RAD-seq approach we investigated genome-wide patterns of genetic variability and differentiation within and among 20 populations of Atlantic herring in the Baltic Sea (and adjacent Atlantic sites), where previous low-throughput studies and/or studies based on few populations have found limited evidence for genetic differentiation. Stringent quality control was applied in the filtering of 1 791 254 SNPs, resulting in a final dataset of 68 182 polymorphic loci. Clear differentiation was identified between Atlantic and Baltic populations in many genomic sites, while differentiation within the Baltic Sea area was weaker and geographically less structured. However, outlier analyses – whether including all populations or only those within the Baltic Sea – uncovered hundreds of directionally selected loci in which variability was associated with either salinity, temperature, or both. Hence, our results support the view that although the degree of genetic differentiation among Baltic Sea herring populations is low, there are many genomic regions showing elevated divergence, apparently as a response to temperature- and salinity-related natural selection. As such, the results add to the increasing evidence of local adaptation in highly mobile marine organisms, and those in the young Baltic Sea in particular.

对于具有浮游幼体阶段的高度洄游海洋鱼类而言，检测并估算其种群间遗传分化程度颇具挑战：这类物种的有效种群规模（effective population size）往往较大，因此中性基因组位点（neutral genomic sites）的遗传漂变（genetic drift）与遗传分化水平通常较低。不过，受局部环境条件差异驱动的定向选择（directional selection）所作用的基因组位点，仍可呈现显著的遗传分化，但这类分化信号通过低通量技术难以捕捉。本研究采用混合RAD测序（RAD-seq）方法，对波罗的海及其邻近大西洋海域的20个大西洋鲱（Atlantic herring）种群的遗传变异与分化的全基因组模式展开分析——此前针对该物种的低通量研究或基于少量种群的研究，仅发现了有限的遗传分化证据。研究人员对1791254个单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）位点进行严格质控过滤，最终得到包含68182个多态性位点的最终数据集。在众多基因组位点中，研究人员明确检测到大西洋种群与波罗的海种群间存在显著遗传分化；而波罗的海海域内部的种群分化程度较弱，且地理结构相对不明显。不过，无论是纳入全部种群还是仅纳入波罗的海内部种群开展离群位点分析，均发现了数百个受定向选择的位点，这些位点的遗传变异与盐度（salinity）、温度（temperature）或二者共同作用显著相关。综上，本研究结果支持这一学术观点：尽管波罗的海鲱种群间的遗传分化程度较低，但存在众多呈现出升高分化水平的基因组区域，这显然是对与温度、盐度相关的自然选择（natural selection）的适应性响应。由此，本研究结果进一步补充了日益增多的证据，表明高度洄游的海洋生物（尤其是形成时间较晚的年轻波罗的海海域生物）普遍存在局部适应性演化现象。