Retention of ancestral polymorphism, not recent introgression, best explains elevated levels of genetic variation in Gila Trout <i>Oncorhynchus gilae</i>

Introgressive hybridization is widespread in nature, often between native and introduced species. Closely related species also share ancestral genetic variation that mimics introgressive hybridization. In this study, we employed reduced-representation genome sequencing to test whether elevated levels of genetic variation in a protected fish species were best explained by hybridization or shared ancestry with an introduced nonnative fish. Gila Trout Oncorhynchus gilae is endemic to remote headwaters of the Gila River in the southwestern US. Its close relative, Rainbow Trout O. mykiss, was stocked into the Gila River from the late 1890s to the late 1960s. Shortly thereafter, Gila Trout was protected under the US Endangered Species Act. An isozyme study conducted in the late 1990s identified introgressed individuals in Iron Creek, a genetically distinct Gila Trout lineage. This finding was important for conservation because Iron Creek harbors unique genetic variants and is the 'wildest' Gila Trout lineage with no hatchery influence. We reassessed genetic variation in the Iron Creek lineage using nextRAD and contemporary samples and found little evidence of recent introgression with Rainbow Trout. We simulated Wright-Fisher evolution under different scenarios assuming that Iron Creek was previously hybridized to explore potential mechanisms responsible for loss of nonnative alleles. Though not fully conclusive, the preponderance of evidence indicates genetic variation shared with Rainbow Trout arises from retention of ancestral polymorphism in Iron Creek Gila Trout. Recent common ancestry of potentially hybridizing species poses an important challenge to wholesale application of structured decision frameworks to manage putatively introgressed populations.