Non-invasive DNA sampling to identify and enumerate species is critical to population monitoring and for developing effective management strategies. However, individual DNA identification is often limited by degraded and low template DNA (LT-DNA) that routinely yields partial profiles prone to technical artifacts, thus limiting their utility/reliability. Massively parallel, genotyping-by-sequencing (GBS) assays present an opportunity to amplify not only a large suite of molecular markers simultaneously, providing higher resolution to identify individuals, but also higher levels of sequence redundancy to enable quality metric evaluations of profiles from LT-DNA. Taxidea taxus jacksoni is an endangered badger subspecies in Canada, with low levels of genetic diversity, complicating individual identifications from closely related DNA sequences. Challenges arise from the small number of hairs collected from snag traps set in badger burrows that rarely provide full profiles. We designed a GBS assay to obtain microsatellite profiles compatible with pre-existing databases generated with conventional capillary electrophoresis (CE) genotyping. We assessed the assay’s reproducibility via a dilution series to mimic LT-DNA and tested if the assay produced similar CE-generated results. While GBS offers the potential to genotype large numbers of individuals and markers at the same time, we found low concordance between GBS- and CE-based genotypes from DNA templates < 250 pg. We recommend existing wildlife genetic databases focus on tetra-nucleotide microsatellite or SNP markers to reduce or eliminate sequencing artifacts (i.e., stutter) that present challenges for GBS genotypes from degraded and LT-DNA, and the use of sample replicates to form consensus genotypes.

对物种进行识别和枚举的无创DNA采样对于种群监测和制定有效的管理策略至关重要。但是，单个DNA的鉴定通常受到降解的低模板DNA（LT-DNA）的限制，而LT-DNA通常会产生易于产生技术伪像的部分概况，从而限制了其实用性/可靠性。大规模并行测序基因分型（GBS）分析提供了机会，不仅可以同时扩增一大套分子标记，提供了更高的分辨率来鉴定个体，而且还提供了更高水平的序列冗余，从而可以对LT谱进行质量度量评估-脱氧核糖核酸。紫杉是加拿大濒临灭绝的badge亚种，遗传多样性水平低，使来自密切相关的DNA序列的个体鉴定变得复杂。挑战来自badge坑中设置的障碍捕捉器收集到的少量毛发，这些毛发很少能提供完整的轮廓。我们设计了GBS分析方法，以获取与常规毛细管电泳（CE）基因分型产生的现有数据库兼容的微卫星图谱。我们通过模拟LT-DNA的稀释系列评估了测定的可重复性，并测试了测定是否产生了类似的CE生成结果。尽管GBS提供了同时对大量个体和标记进行基因分型的潜力，但我们发现，从<250 pg的DNA模板中，基于GBS和CE的基因型之间的一致性较低。