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).