In the late 1800’s, steelhead trout (Oncorhynchus mykiss) were introduced successfully into Lake Michigan and have had self-sustaining populations ever since. Throughout their native range, which includes the Pacific Northwest, steelhead migrate to sea and return to their natal rivers to spawn as adults. However, while the steelhead populations in Lake Michigan continue to spawn in rivers, they now treat the freshwater environment of the Great Lakes as a surrogate ocean. In addition to salinity, there are many additional differences between the two environments including predators, forage species, spawning habitat, and climate. To examine how this species has adapted to this novel environment, we obtained 40x genome-wide coverage of individuals from both their native and introduced ranges. We were also able to identify the progenitor population of the fish that were introduced into Lake Michigan in the late 1800’s (a population near Mt. Shasta, California), such that candidate outliers can be inferred to have arisen in response to natural selection in the novel environment as opposed to local adaptation in a native, but non-progenitor population.
Results/Conclusions
Using a sliding window of 200kb with 100kb steps, we identified a total of 105 FST outliers, 12 of which had correspondingly low levels of homozygosity. These outliers were distributed across all 29 chromosomes, with chromosome 1 having the most outliers (n = 7) and chromosomes 22 and 28 having the fewest (n = 1). Annotation of these regions indicated genes associated with transposable elements (TEs) and hemoglobin. TEs, which are mobile genes that have an inherent ability to move within the genome, tend to proliferate when populations are stressed and have been implicated in adaptation to novel regions. Changes in hemoglobin suggests adaptation to an environment with different dissolved oxygen regimes. Genetic diversity in both native and introduced populations was high, indicating little evidence of a founder effect. Overall, these results provide large-scale genomic evidence of rapid adaptation to a novel freshwater environment provides key insights into identifying how species can adapt to changing environmental conditions (e.g., global climate change).