Sample collection
Our work draws upon multiple sample sources, including archived harvest
tissue samples (HV; n = 38) from bears taken by Inuit hunters, and
biopsy samples (BP; n = 138) that are housed in collections by the
Nunavut and Northwest Territories governments in accordance with
Government of the Northwest Territories and Government of Nunavut
research permits. We also received “sample sets” from hunted bears,
which contained fat, tissue, liver, and lower intestine with feces, and
were collected in accordance with wildlife research permits ARI #WL
500540 to MB and WL-2019-061 to SCL. These were used to estimate fecal
genotyping error by comparing genotypes from set tissue (MS; n = 108)
and feces from the colon (CF; n = 78). Non-invasive, field-collected
fecal samples (FF; n = 72) were also located and collected by Inuit
hunters in accordance with wildlife research permit WL-2018-006 to SCL.
All sample types were stored in -20°C or -80°C at Queen’s university
until subsampling. Many of these samples were too degraded for use in
previous NGS-based studies and thus, represent opportunities to expand
sampling coverage and draw new inferences regarding population
structure. As the ultimate goal is to use our GT-seq method on
field-collected scat samples, we took duplicate subsamples from 21 FF
samples to assess within-sample genotyping error and variation in
genotype quality. Subsamples of MS, HV, and BP were stored in 100%
ethanol at -20°C or -80°C and CF and FF subsamples were stored without
ethanol at -20°C until DNA extraction.
All samples were collected across 11 of the 13 Canadian subpopulations
between 1998 and 2019, with mean year of sample collection ranging from
1999 (M’Clintock Channel) to 2018 (Southern Hudson Bay). For 9
subpopulations, we had at least 10 sampled individuals (range: 10-95).
However, there were only 4 samples from Davis Strait and 3 samples from
Western Hudson Bay, and no samples from either Norwegian Bay or Kane
Basin. While this represents a sampling limitation, we supplement our
GT-seq data with ddRADseq data (Jensen et al., 2020) for our final
assessment of Canadian polar bear structure and diversity, and note that
census population size estimates for the two subpopulations for which we
have no samples are small (KB = 357 individuals, NW = 203 individuals;
Hamilton & Derocher, 2019).