Abstract Objective Rainbow Trout Oncorhynchus mykiss were originally stocked in Missouri streams in the late 1800s, and several spring-fed streams retain self-sustaining populations, presumably derived from the original stocking events. The phylogenetic and geographic origins of Missouri Rainbow Trout are unclear and based on historical records that have not been substantiated by genetic techniques. Methods Fin clips were collected from Rainbow Trout in 10 Missouri streams, eight of which contain self-sustaining wild stocks. Single-nucleotide polymorphisms (SNPs) and microsatellites were used to compare the wild-caught fish with hatchery strains from Missouri as well as hatchery and wild populations of Rainbow Trout from California. Results Phylogenetic analyses, which included Golden Trout O. aguabonita and Coastal Cutthroat Trout O. clarkii as outgroups, indicated that Missouri Rainbow Trout were most similar to Coastal Rainbow Trout O. m. irideus from California’s Sacramento River drainage, with perhaps some introgression from other stocks. Wild and hatchery populations from Missouri were all more similar to each other than to any sampled population outside the state, indicating mixing of stocks among Missouri streams and hatcheries since the original stocking events, coupled with genetic drift between founder and source populations over the past century. At the population level, STRUCTURE analysis of SNPs and microsatellites found Mill Creek to be most distinct, but all wild populations were distinct from each other and from hatchery strains at higher levels of resolution. The SNPs associated with anadromy and the ancestral form of the Omy05 and Omy20 chromosomal inversions were at high frequencies in Missouri streams, indicating that the original source contained offspring of steelhead (anadromous Rainbow Trout). Effective population sizes in the largest stream populations were small, but we recommend that stocking should cease, thereby allowing local adaptation to continue shaping their evolutionary trajectory. Conclusions Missouri Rainbow Trout of both wild-caught and hatchery-propagated lines are most closely related to each other in this study. Overall, they are similar to the populations of the Coastal Rainbow Trout subspecies from the Sacramento River drainage, supporting their origin from California in the 1800s. Since that time, they have maintained polymorphisms relating to either temperature variation or migration tendency in the form of chromosomal inversion variations on Omy05 and Omy20. The genetic background of these fish is distinctive, probably representing both a sampling of unique genetic variation from the original source population and the effects of isolation in Missouri since the founding of populations in that state.
Heist et al. (Tue,) studied this question.