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.

作为一门学科的入侵遗传学（invasion genetics）所聚焦的入侵事件遗传基础相关知识，在南美巴塔哥尼亚地区非本土物种对当地生态系统造成的已被充分记录的生态影响背景下，仍然十分匮乏。在巴塔哥尼亚及其他地区的淡水生态系统中，虹鳟（Oncorhynchus mykiss）是入侵性最强的物种之一。该物种于20世纪早期被引入智利，用于增殖放流并推动休闲渔业发展；20世纪晚期又因养殖需求被引入，目前已在当地建立种群或实现归化。本研究借助基于种群和个体的单核苷酸多态性（single nucleotide polymorphisms, SNPs）推断分析，针对受虹鳟养殖影响严重的巴塔哥尼亚湖泊兰基胡埃湖（Lake Llanquihue）中虹鳟的种群建立与归化过程，设置了三项研究目标，采样工作于两个季节（冬季与春季）在五条入湖溪流中开展。其一，研究发现种群内（时间尺度）的遗传变异可能比种群间（空间尺度）的遗传变异发挥了更显著的作用。春季与冬季采样的鱼群间等位基因频率存在差异，这与两季采样个体的体长差异相符，或可解释时间尺度上的遗传分化。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受春季在耶尔巴斯布埃纳斯（Yerbas Buenas, YER）采样到的推测养殖来源繁殖体驱动，冬季则无此特征，这表明养殖亲鱼会在春季向上游该溪流中迁徙产卵。目前尚不清楚在该溪流与其他溪流中，"pure"归化虹鳟与养殖虹鳟之间是否发生了基因交流。其三，半数采样批次的年度有效繁殖个体数（Nb）估计值低于73，这表明该种群规模在遗传层面较小且为新近建立，可能经历了显著的遗传漂变。本研究结果进一步证实，归化虹鳟新近起源于一个规模较小但遗传多样性丰富的源种群，且在该高密度虹鳟养殖的单一湖泊中，养殖来源繁殖体可能对虹鳟的入侵过程发挥了重要作用。研究结果同时呼吁完善防控措施，包括加强养殖逃逸个体管理，以及制定策略以最大程度降低养殖设施的无意放生风险。