Discovery and validation of a SNP panel to identify hybridization and introgression among three trout species

Anthropogenic introductions of non-native trout for recreation has had widespread effects on native ecosystems and their inhabitants. The Lahontan Cutthroat Trout (LCT; Oncorhynchus henshawi ) is native to western North America and is simultaneously experiencing population declines and hybridization due to climate change and non-native trout introductions, respectively. We used restriction site-associated DNA sequencing (RAD-seq) on 3,205 samples from over 120 populations to assess hybridization and develop a panel of single nucleotide polymorphism (SNP) markers to identify hybridization among three taxonomic groups: Lahontan Cutthroat Trout, Rainbow Trout, and Yellowstone Cutthroat Trout. These markers will facilitate ongoing characterization of hybridization status and guide studies on how environmental and anthropogenic factors impact hybridization across this system.