Data from: Parallel evolution and adaptation to environmental factors in a marine flatfish: implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus)

Unraveling adaptive genetic variation represents, in addition to the estimate of population demographic parameters, a cornerstone for the management of aquatic natural living resources, which in turn, represent the raw material for breeding programs. The turbot (Scophthalmus maximus) is a marine flatfish of high commercial value living on the European continental shelf. While wild populations are declining, aquaculture is flourishing in Southern Europe. We evaluated the genetic structure of turbot throughout its natural distribution range (672 individuals; 20 populations) by analyzing allele frequency data from 755 Single Nucleotide Polymorphism discovered and genotyped by Double Digest RAD Sequencing. The species was structured into four main regions: Baltic Sea, Atlantic Ocean, Adriatic Sea and Black Sea, with subtle differentiation apparent at the distribution margins of the Atlantic region. Genetic diversity and effective population size estimates were highest in the Atlantic populations, the area of greatest occurrence, while turbot from other regions showed lower levels, reflecting geographical isolation and reduced abundance. Divergent selection was detected within and between the Atlantic Ocean and Baltic Sea regions, and also when comparing these two regions with the Black Sea. Evidence of parallel evolution was detected between the two low salinity regions, the Baltic and Black seas. Correlation between genetic and environmental variation indicated that temperature and salinity were probably the main environmental drivers of selection. Mining around the four genomic regions consistently inferred to be under selection identified candidate genes related to osmoregulation, growth and resistance to diseases. The new insights are useful for the management of turbot fisheries and aquaculture by providing the baseline for evaluating the consequences of turbot releases from restocking and farming.

解析适应性遗传变异，结合种群人口统计参数估算，乃是水生野生生物资源管理的核心支柱；而该类资源同时也是育种项目的核心原料。大菱鲆（Scophthalmus maximus）是栖息于欧洲大陆架的高商业价值海生比目鱼。当前其野生种群数量持续下降，但南欧的大菱鲆养殖业正蓬勃发展。本研究通过分析基于双酶切限制性位点相关DNA测序（Double Digest RAD Sequencing, ddRAD-seq）发掘并分型得到的755个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点的等位基因频率数据，对其自然分布范围内（20个种群共672个个体）的大菱鲆遗传结构进行了评估。该物种的遗传结构可划分为四个主要区域：波罗的海、大西洋、亚得里亚海以及黑海；大西洋区域的分布边缘地带则呈现出细微的遗传分化。大西洋种群的分布范围最广，其遗传多样性与有效种群大小估算值均为最高；其余区域的大菱鲆种群则表现出较低水平的相关参数，这反映了地理隔离与种群丰度下降的现状。研究在大西洋与波罗的海区域内部及二者之间，以及将这两个区域与黑海进行对比时，均检测到了歧化选择信号。在波罗的海与黑海这两个低盐度区域之间，检测到了平行演化的证据。遗传变异与环境变异的相关性分析表明，水温与盐度可能是驱动选择的主要环境因子。对这四个持续受到选择作用的基因组区域进行挖掘，鉴定出了与渗透压调节、生长以及疾病抗性相关的候选基因。本研究获得的新认知可为大菱鲆渔业与养殖业管理提供助力，为评估增殖放流及养殖过程中的大菱鲆释放所带来的影响提供基准参考。