Data from: Genomewide introgressive hybridization patterns in wild Atlantic salmon influenced by inadvertent gene flow from hatchery releases

Many salmonid fish populations are threatened by genetic homogenization, primarily due to introgressive hybridization with hatchery-reared conspecifics. By applying genomewide analysis using two molecular marker types (1986 SNPs and 17 microsatellites), we assessed the genetic impacts of inadvertent gene flow via straying from hatchery releases on wild populations of Atlantic salmon in the Gulf of Finland, Baltic Sea, over 16 years (1996–2012). Both microsatellites and SNPs revealed congruent population genetic structuring, indicating that introgression changed the genetic make-up of wild populations by increasing genetic diversity and reducing genetic divergence. However, the degree of genetic introgression varied among studied populations, being higher in the eastern part and lower in the western part of Estonia, which most likely reflects the history of past stocking activities. Using kernel smoothing and permutation testing, we detected considerable heterogeneity in introgression patterns across the genome, with a large number of regions exhibiting nonrandom introgression widely dispersed across the genome. We also observed substantial variation in nonrandom introgression patterns within populations, as the majority of genomic regions showing elevated or reduced introgression were not consistently detected among temporal samples. This suggests that recombination, selection and stochastic processes may contribute to complex nonrandom introgression patterns. Our results suggest that (i) some genomic regions in Atlantic salmon are more vulnerable to introgressive hybridization, while others show greater resistance to unidirectional gene flow; and (ii) the hybridization of previously separated populations leads to complex and dynamic nonrandom introgression patterns that most likely have functional consequences for indigenous populations.

许多鲑科鱼类种群正面临遗传同质化的威胁，其主要成因是与养殖繁育的同种个体发生渐渗杂交（introgressive hybridization）。本研究采用两种分子标记类型——1986个单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）与17个微卫星标记（microsatellites）开展全基因组分析，对1996至2012年这16年研究周期内，波罗的海芬兰湾海域大西洋鲑（Atlantic salmon）野生种群因养殖放流个体洄游扩散引发的意外基因流所带来的遗传影响进行了评估。

微卫星标记与SNPs均揭示出一致的种群遗传结构，表明渐渗杂交通过提升遗传多样性、降低遗传分化，改变了野生种群的遗传组成。但不同研究种群间的遗传渐渗程度存在显著差异：爱沙尼亚东部种群的渐渗水平更高，西部种群则相对更低，这一分布格局大概率反映了过往的水产放流活动历史。

通过核平滑法（kernel smoothing）与置换检验（permutation testing），本研究检测到基因组内的渐渗模式存在显著异质性，大量呈现非随机渐渗的基因组区域广泛分布于整个基因组中。此外，种群内部的非随机渐渗模式也存在显著变异，多数表现出渐渗水平升高或降低的基因组区域，并未在各时间采样批次中被一致检测到。这提示重组、选择与随机过程可能共同塑造了复杂的非随机渐渗模式。

本研究结果表明：其一，大西洋鲑的部分基因组区域更易受到渐渗杂交的侵扰，而另一些区域则对单向基因流表现出更强的抗性；其二，此前相互隔离的种群发生杂交，会形成复杂且动态的非随机渐渗模式，这大概率会对土著种群产生功能性影响。