SNP capture sequence data from coyotes and kit foxes for individual identification and sexing

We designed and validated a set of probes targeting SNP loci that are polymorphic in coyotes (Canis latrans) and kit foxes (Vulpes macrotis). We tested the ability of the probes to enrich highly degraded DNA from scat samples and we used the data to identify individuals and determine their sex.First, we enriched and sequenced ~20,000 SNP loci that were previously found to be polymorphic in African wild dogs, using DNA extracted from coyote and kit fox tissues. Then, using these data as references, we selected a subset of loci (835) that were polymorphic in either coyotes or kit foxes and were capable of differentiating individuals. Using the program BaitsTools, we designed probe sequences with ~4X tiling around each SNP of interest. We also included probes to enrich for the ZFX/ZFY genes. We found that the capture probes allowed us to genotype individual canids using even very low concentration, degraded DNA from scat samples.