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.

检测并估算具有浮游幼体阶段的高流动性海洋鱼类种群间的遗传分化程度颇具挑战：此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。然而，受局域环境变异驱动的定向选择（directional selection）所作用的基因组位点，仍可表现出显著的遗传分化，但这类分化信号通过低通量（low-throughput）技术往往难以检测。
本研究采用混合RAD-seq（Restriction-site Associated DNA sequencing）技术，对波罗的海（及邻近大西洋海域）的20个大西洋鲱种群内部及种群间的全基因组遗传变异与分化模式展开了研究。此前针对该物种的低通量研究或基于少量种群的研究，均未发现显著的遗传分化证据。研究团队对1791254个单核苷酸多态性位点（Single Nucleotide Polymorphism, SNPs）进行过滤时实施了严格的质量控制，最终得到包含68182个多态性位点的数据集。
众多基因组位点均显示大西洋种群与波罗的海种群间存在清晰的遗传分化，而波罗的海海域内种群间的分化程度则较弱，且地理结构不明显。然而，无论是纳入全部种群还是仅纳入波罗的海海域内种群进行异常位点分析（outlier analyses），均检测到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）或二者均存在关联。
因此，本研究结果支持如下观点：尽管波罗的海鲱种群间的遗传分化程度较低，但存在大量基因组区域呈现出升高的分化水平，这显然是对与温度和盐度相关的自然选择（natural selection）的响应。综上，本研究结果进一步充实了相关证据，证明高流动性海洋生物存在局域适应性（local adaptation），这一点在形成时间较短的波罗的海海域物种中尤为显著。