Use of SNPs in a low diversity system for genetic monitoring and identifying a successful translocation event in the Paiute Cutthroat Trout ( O. henshawi seleniris )

Abstract Objective Maintaining genetic diversity in small, isolated populations is a key goal in conservation genetics. Genetic monitoring can guide management decisions, but comparisons across studies and time points are often complicated by differences in genetic markers and data sets. We aimed to develop a consistent, replicable set of genetic markers to support long-term monitoring of Paiute Cutthroat Trout ( Oncorhynchus henshawi seleniris ), a federally threatened subspecies persisting in a network of isolated refuge populations in California, USA. Methods We used RAD (Restriction site-associated DNA) sequencing to identify single nucleotide polymorphisms (SNPs) from 476 individuals representing eight extant refuge populations. Filtering steps included the removal of paralogous loci and exclusion of F ST outliers associated with sequencing batch effects. We selected a panel of 1,114 SNPs that were shared across all populations and validated the panel in silico by comparing population structure and genetic diversity estimates to those derived from the full RAD sequencing dataset. Results The candidate panel SNPs captured key patterns of genetic differentiation and diversity consistent with previous studies and the larger RAD dataset. We present updated baseline genetic metrics for each refuge population, providing a consistent reference point for future monitoring efforts. We also demonstrate the ability of our candidate panel SNPs to detect successful spawning after a translocation event. Conclusion This study provides a set of SNPs tailored for monitoring genetic diversity and structure in Paiute Cutthroat Trout refuge populations. Future work should include development of a high-throughput genotyping assay to implement these candidate panel SNPs for ongoing management. This would enable consistency over time with genetic studies and be a foundational tool for repeated evaluation of conservation actions such as reintroductions and augmentations. Lay Summary We identified genetic markers to help track and protect one of the rarest trout in the United States. This work supports long-term conservation by making it easier to monitor isolated populations and measure the success of efforts to restore the species.