An Optimised Method to Identify Reintroduced Swift Foxes (Vulpes velox) Through SNP Genotyping of Non-Invasively Collected Scat Samples Using In-Solution Hybridisation Capture.

Abstract

Genomic methods have become increasingly common in wildlife population studies over the past two decades. While noninvasive genetic sampling has been prevalent since the 1990s, the field has lagged in the adoption of high-throughput sequencing methods. In-solution hybridisation capture offers an efficient way to enrich and sequence degraded, low-quantity DNA with a large percentage of exogenous content (e.g., scat samples) for specific targets of interest. Despite their frequent use in ancient and historical DNA applications, hybridisation capture techniques have not been widely adopted for noninvasive genetic samples. Previous studies demonstrated that capture enrichment of single-nucleotide polymorphism (SNP) loci enables genotyping of field-collected kit fox and coyote scats to effectively identify species, individuals and sex. Here, we expanded on this work by (1) investigating whether probes designed for kit foxes can generate multi-locus SNP genotypes and identify sex in closely related swift foxes (Vulpes velox), (2) assessing the capability of the resulting genotypes to differentiate among swift foxes by calculating identity-by-state values between samples from the same individual, (3) exploring the impact of replicate index polymerase chain reactions (PCRs) on genotyping success, and (4) exploring the performance of the marker set for inference of population genetic structure. We applied these methods to samples from swift foxes reintroduced to the Fort Belknap Indian Reservation, Montana, and showed a success rate of 85%. Our developed methodology can be applied to monitor the success of swift fox reintroduction efforts by estimating dispersal, survival, and reproduction. We also showed that probes designed and optimised for one species can produce informative genotypes from closely related species, highlighting their versatility for broader applications in wildlife population studies.