Data from: Defining conservation units in a stocking-induced genetic melting pot: unravelling native and multiple exotic genetic imprints of recent and historical secondary contact in Adriatic grayling

The definition of conservation units is crucial for the sustainable management of endangered species, though particularly challenging when recent and past anthropogenic and natural gene flow might have played a role. The conservation of the European grayling, Thymallus thymallus, is particularly complex in its southern distribution area, where the Adriatic evolutionary lineage is endangered by a long history of anthropogenic disturbance, intensive stocking and potentially widespread genetic introgression. We provide mtDNA sequence and microsatellite data of 683 grayling from 30 sites of Adriatic as well as Danubian and Atlantic origin. We apply Bayesian clustering and Approximate Bayesian Computation (ABC) to detect microgeographic population structure and to infer the demographic history of the Adriatic populations, to define appropriate conservation units. Varying frequencies of indigenous genetic signatures of the Adriatic grayling were revealed, spanning from marginal genetic introgression to the collapse of native gene pools. Genetic introgression involved multiple exotic source populations of Danubian and Atlantic origin, thus evidencing the negative impact of few decades of stocking. Within the Adige River system, a contact zone of western Adriatic and eastern Danubian populations was detected, with ABC analyses suggesting a historical anthropogenic origin of eastern Adige populations, most likely founded by medieval translocations. Substantial river-specific population substructure within the Adriatic grayling Evolutionary Significant Unit points to the definition of different conservation units. We finally propose a catalog of management measures, including the legal prohibition of stocking exotic grayling and the use of molecular markers in supportive- and captive-breeding programs.

保护单元（conservation units）的界定对于濒危物种的可持续管理至关重要，但当近期与历史上的人为活动及自然基因流发挥作用时，该工作往往极具挑战性。欧洲茴鱼（Thymallus thymallus）的保护在其分布区南部尤为复杂，该区域的亚得里亚海演化支（Adriatic evolutionary lineage）因长期的人为干扰、高强度的放养以及潜在的广泛遗传渐渗而濒临灭绝。本研究获取了来自亚得里亚海、多瑙河及大西洋起源的30个采样点的683尾茴鱼的线粒体DNA（mitochondrial DNA）序列与微卫星（microsatellite）数据。我们采用贝叶斯聚类与近似贝叶斯计算（ABC）方法，解析微地理尺度下的种群结构、推断亚得里亚海种群的种群历史，进而界定合理的保护单元。研究揭示了亚得里亚海茴鱼本土遗传特征的频率存在显著差异，范围从轻度遗传渐渗到本土基因库的完全崩溃。此次遗传渐渗涉及多瑙河与大西洋起源的多个外来源种群，由此证实了数十年来的放养活动所带来的负面影响。在阿迪杰河（Adige River）水系中，我们检测到了西部亚得里亚海种群与东部多瑙河种群的接触带；ABC分析表明，阿迪杰河东部种群的起源具有历史人为因素，极有可能源自中世纪的种群移植。亚得里亚海茴鱼进化显著单元（Evolutionary Significant Unit）内部存在显著的水系专属种群亚结构，这提示需界定不同的保护单元。本研究最终提出了一套管理措施清单，包括法律上禁止放养外来茴鱼，以及在辅助繁育与圈养繁育项目中应用分子标记。