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).