Whole genome sequencing to characterize Cutthroat Trout populations across the Continental Divide

Abstract

Cutthroat Trout (Oncorhynchus spp.) are a biological icon of western North America with the largest native range and species diversity of all North American trout. Currently, there are six recognized lineages believed to be native to the Southern Rocky Mountains. Despite almost a decade of genetic and morphological studies, clarity on the phylogenetic history and evolutionary differences between all lineages of Colorado's Cutthroat Trout remains to be resolved and has implications for future management of populations in this species group throughout the Southern Rocky Mountains. Previous molecular studies have used genetic markers representing only a small portion of the genome, such as with ND2 mitochondrial DNA haplotypes, microsatellites, and amplified fragment length polymorphisms (AFLPs), and have not included a comprehensive nuclear DNA assessment from all extant lineages of Cutthroat Trout found in Colorado. To address this knowledge gap, we used whole genome sequencing to analyze DNA samples from all extant lineages of Southern Rocky Mountain Cutthroat Trout, as well as from five other Cutthroat Trout lineages across North America. Using whole genomes, we have confirmed the nuclear distinctiveness of the "blue" and "green" lineages of former Colorado River Cutthroat Trout, as well the form from the San Juan basin. We additionally identified the persistence of ancestral and unique spatial genetic diversity despite widespread historic stocking. These findings, along with an analysis of long-term effective population sizes, provide key insights into possible natural and anthropogenic drivers of population migration, separation, and speciation. Taken together, our results inform conservation management of Cutthroat Trout lineages across their native range in the Southern Rocky Mountains.