Abstract
Black bears (Ursus americanus) are an ecologically and economically important species requiring protection from the threats of illegal wildlife trade. DNA analysis techniques such as genotyping by sequencing can reveal allele sequence variation (also referred to as novel alleles). These novel alleles can identify genetic distinctions among populations and improve our ability to determine the location of origin of evidence seized in poaching and wildlife trafficking cases. This can aid in locating poaching hotspots, identifying criminal networks, and preventing illegal take of wildlife. The objectives of this research were to 1) identify novel alleles in U. americanus populations in California and 2) identify all genetically distinct populations of U. americanus populations in California to better determine an individual black bear’s location of origin. To accomplish these objectives, 1,544 black bear DNA samples were sequenced at nine microsatellite loci and three sex markers using the Illumina MiSeq high-throughput sequencing (HTS) platform. Allele counts and a genotype concordance for samples with allele calls at a minimum of six of the nine microsatellite loci (n = 635) were performed to compare 1) the total number of alleles identified and 2) the genotype assignments made through HTS vs. those previously assigned through capillary electrophoresis (CE), a genotyping method commonly used in wildlife forensics. Novel allele variants were detected at eight of the nine loci in the analysis panel and 29.9% of alleles identified through HTS were novel variants. HTS methods detected a total of 137 alleles across all loci while CE detected 96, a 42.7% increase in known alleles. An analysis of the genetic population structure using genotypes assigned through HTS identified seven genetic clusters (populations) of black bears in California, an increase compared to the six identified using CE genotyping for the same sample set. This population structure analysis may serve as a reference for future method development to match black bear DNA samples to their region of origin. The HTS methods developed for black bears through this research will serve as a reference for method development and optimization for other species, such as deer and mountain lion, commonly analyzed in wildlife forensics.