Development of a genotyping-in-thousands by sequencing (GT-seq) panel for identifying individuals and estimating relatedness among Alaska black bears (Ursus americanus)

Abstract

The management and conservation of large mammals, such as black bears ( Ursus americanus ), have long been informed by genetic estimates of population size and individual dispersal. Amplicon sequencing methods, also known as ‘genotyping-in-thousands-by sequencing’ (GT-seq), now enable the efficient and cost-effective genotyping of hundreds of loci and individuals in the same sequencing run. Here, we develop a GT-seq panel for individual identification and kinship inference in Alaska black bears. Using genomic data from restriction site-associated DNA sequencing of hunter-harvested bears from Southcentral Alaska ( n = 85), we identified 170 microhaplotype and single nucleotide polymorphism (SNP) loci that were highly heterozygous in local populations. To enable sexing of individuals, we also included a previously published sex-linked locus in the GT-seq panel. We empirically validated the GT-seq panel using samples collected at different spatial scales. These samples included tissues ( n = 82) obtained from bears within a small geographic area in Anchorage, Alaska, which were likely to be relatives as well as the hunter-harvested samples collected from geographically widespread locations throughout Southcentral Alaska. Empirical validation indicated high genotyping success and genotype reproducibility across replicate subsamples. Computer simulations demonstrated that the GT-seq panel had ample statistical power for distinguishing distinct individuals and first-order relatives (parent-offspring and full-sibling pairs) from unrelated individuals. As a final proof of concept, the panel was used to identify individual bears and close kin sampled from urban and wild habitats in Anchorage, Alaska. We anticipate that the GT-seq panel will be a useful genomic resource for the monitoring and management of Alaska black bear populations. ons.