DNA extraction
Whole genomic DNA was extracted from fecal samples using the QIAamp Fast DNA Stool Mini Kit (Qiagen) according to manufacturer’s protocols. For BP, HV, and MS samples, genomic DNA was extracted using a modified salt extraction protocol (Aljanabi & Martinez, 1997), with an RNaseA (Thermofisher Scientific) step included. Once extracted, DNA extracts from all tissue samples were run on 1.5% agarose gel stained with RedSafeTM Nucleic Acid Staining Solution (iNtRON Biotechnology) to assess quality and quantified using a Nanodrop ND_1000 spectrophotometer (Nanodrop Technologies Inc.). As feces contains DNA from multiple sources, we used a polar bear-specific qPCR assay targeting the F2 gene to quantify polar bear DNA from both CF and FF samples (Hayward et al., 2020). To gauge the value of running fecal samples through this qPCR assay as a screening tool, we devised a small double-blind experiment in which we randomly divided CF and FF samples into two subsets: 1. 55 samples for which we assayed DNA quantity before GT-seq library construction and sequencing; and 2. 116 samples for which we assayed DNA quantity only after sequencing had already been performed (See Supplemental Information: qPCR Experiment for qPCR experiment methods and results).