Development of a 96 SNP panel for fecal genotyping and individual identification of bobcats (Lynx rufus) in California

Abstract

Spatial mark-recapture abundance estimates obtained from fecal genotyping are becoming an essential component of conservation of carnivores. The bobcat (Lynx rufus) is a widespread carnivore in California, USA, that until recently lacked robust demographic data. To facilitate a statewide abundance study, we created a single nucleotide polymorphism (SNP) genotyping panel for individual identification. For SNP discovery, we performed restriction site-associated DNA sequencing (RADseq) on 78 samples collected throughout California and subsequently designed a panel of 96 SNPs for sequencing on a microfluidic platform. This panel includes loci to identify sex and differentiate bobcats from other common carnivores. The panel reliably differentiates individuals when using DNA extracted from feces, with 89% of samples amplifying at > 90% of SNPs. Importantly, we found autosomal SNPs were monomorphic in the closely related Canada lynx (L. canadensis) suggesting the panel would still be effective for bobcat study in areas of sympatry. Fecal genotyping provides a cost-effective, noninvasive method for population monitoring and detecting individual movement. Our panel generates standardized genotypes that can be analyzed across laboratories and used for continued bobcat monitoring in California and other western states.