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