Data from: Temporal genetic variance and propagule-driven genetic structure characterize naturalized rainbow trout (Oncorhynchus mykiss) from a Patagonian lake impacted by trout farming

Knowledge about the genetic underpinnings of invasions—a theme addressed by invasion genetics as a discipline—is still scarce amid well documented ecological impacts of non-native species on ecosystems of Patagonia in South America. One of the most invasive species in Patagonia’s freshwater systems and elsewhere is rainbow trout (Oncorhynchus mykiss). The species was introduced in Chile during the early twentieth century for stocking and promoting recreational fishing and, during the late twentieth century, for farming purposes and is now established or naturalized. We used population- and individual-based inference from single nucleotide polymorphisms (SNPs) to illuminate three objectives related to the establishment and naturalization of rainbow trout in Lake Llanquihue, a Patagonian lake heavily affected by trout farming, by sampling five inlet streams over two seasons (winter and spring). First, we found that significant intra- population (temporal) genetic variance might have played a more significant role than inter-population (spatial) genetic variance. Allele frequency differences between cohorts, consistent with variation in fish length between spring and winter collections, might explain temporal genetic differences. Second, individual-based Bayesian clustering suggested that genetic structure within Lake Llanquihue was largely driven by putative farm propagules found at Yerbas Buenas (YER) during spring, but not in winter, suggesting farm broodstock migrate upstream to breed during spring at that particular stream. It is unclear whether interbreeding has occurred between “pure” naturalized and farm trout in this and other streams. Third, estimates of the annual number of breeders (Nb) were below 73 in half of the collections, suggestive of genetically small and recently founded populations that might experience substantial genetic drift. Our results reinforce the notion that naturalized trout originated recently from a small yet genetically diverse source and that farm propagules might have played a significant role in the invasion of rainbow trout within a single lake with intensive trout farming. They also argue for better mitigation measures, including management of escapes and strategies to minimize unintentional releases from farm facilities.

入侵遗传学（invasion genetics）作为一门学科，其核心主题是阐明生物入侵的遗传基础，但目前针对南美洲巴塔哥尼亚地区非本土物种对当地生态系统造成的已有详实记录的生态影响，相关的入侵遗传机制研究仍较为匮乏。虹鳟（Oncorhynchus mykiss）是巴塔哥尼亚淡水生态系统乃至全球范围内入侵性最强的物种之一。该物种于20世纪早期被引入智利，用于人工放流以发展休闲垂钓产业；20世纪后期又被引入用于水产养殖，目前已在当地建立野生种群或实现归化。本研究基于单核苷酸多态性（single nucleotide polymorphisms, SNPs）的种群与个体水平推断方法，针对受水产养殖严重影响的巴塔哥尼亚兰基胡埃湖（Lake Llanquihue）内虹鳟的定殖与归化过程，通过在两个季节（冬季与春季）对五条入湖溪流开展采样，实现了三项研究目标。其一，研究发现种群内（时间维度）的遗传变异相较于种群间（空间维度）的遗传变异，可能发挥了更为关键的作用。不同世代间的等位基因频率差异，与春季与冬季采样个体的体长差异相契合，可解释该时间维度上的遗传分化。其二，基于个体的贝叶斯聚类分析显示，兰基胡埃湖内的遗传结构主要由春季（而非冬季）在耶尔瓦斯布埃纳斯（Yerbas Buenas, YER）采样到的疑似水产养殖来源的繁殖体所驱动，这表明养殖亲鱼会在春季向上游该溪流迁徙产卵。目前尚不清楚该溪流与其他溪流内的"纯种"归化虹鳟与养殖虹鳟之间是否发生了基因交流。其三，半数采样组的年度繁殖个体数（Nb）估计值低于73，提示这些种群为近期建立的小型遗传种群，可能经历了显著的遗传漂变。本研究结果进一步佐证了两个观点：一是归化虹鳟近期起源于一个规模较小但遗传多样性丰富的源种群；二是在该高密度虹鳟养殖的单一湖泊中，养殖来源的繁殖体可能在虹鳟入侵过程中发挥了重要作用。本研究同时呼吁完善相关防控措施，包括养殖逃逸个体的管理，以及制定策略以最大限度降低水产养殖设施的无意放生风险。