Determination of polar bear (Ursus maritimus) individual genotype and sex based on DNA extracted from paw-prints in snow

Abstract

Polar bears rely upon sea ice to hunt, travel, and reproduce. Declining sea ice extent and duration has led polar bears to be designated as “threatened” (ESA). Population monitoring is vital to polar bear conservation; but recently, poor sea ice has made traditional aircraft-based methods less viable. These methods largely rely upon the capture and handling of polar bears, and have been criticized over animal welfare concerns. Monitoring polar bears via DNA sampling is a promising option. One common method utilizes biopsy darts delivered from a helicopter to collect DNA, a method that faces similar ice associated challenges to those described above. However, epidermal cells shed from the foot pads of a polar bear into its paw-prints in snow are a source of “environmental DNA” (e-DNA) that can be collected non-invasively on the sea ice or on land for potential use in population monitoring. Mitochondrial DNA (mt-DNA) is used to assess whether polar bear DNA is present within a snow sample, and nuclear DNA (n-DNA) can identify individuals and their sex. The goal of this investigation was to assess the viability of using e-DNA collected from paw-prints in the snow to identify individual polar bears and their sex. Snow was sampled from 13 polar bear trails (10 paw-prints per trail) on the sea ice in the Chukchi and Beaufort seas along the North Slope of Alaska. Species verification was based on a mt-DNA PCR fragment analysis test. Identification of individuals was accomplished by amplifying a multiplex of seven n-DNA microsatellite loci, and sex was determined by the amelogenin gene sex ID marker. Six of the 13 bear trails sampled (46%) yielded consensus genotypes for five unique males and one female. To our knowledge, this is the first time that polar bears have been individually identified by genotype and sex using e-DNA collected from snow. This method is non-invasive, could be integrated into genetic mark-recapture sampling designs, and addresses some of the current challenges arising from poor sea ice conditions. It also can involve, engage, and empower Indigenous communities in the Arctic, which are greatly affected by polar bear management decisions.

Individual genotypes from environmental DNA: Fingerprinting snow tracks of three large carnivore species

“…Beside the sampling conditions discussed above, laboratory protocols, from DNA extraction and amplification to the genotyping approach, differed compared to previous snow track genotyping studies (Barber‐Meyer et al., 2020, 2022; Hellström et al., 2019; Von Duyke et al., 2023) and may have contributed to genotyping success. A major difference was the adoption of an HTS approach for amplicon sequencing of STRs.…”

“…Markers analysed are short (<120 bp) tetranucleotides, selected for optimal multiplexing, to facilitate amplification of degraded DNA and multilocus allele scoring from HTS data. While there is evidence that reliable genotypes can be obtained analysing dinucleotide STRs on capillary electrophoresis (Von Duyke et al., 2023; personal data not shown), HTS sequencing of tetranucleotides, provided appropriate sequencing coverage, allows for greater sensitivity and clearer allele calling that may have enabled genotyping even with limited DNA quantities (Fordyce et al., 2015). In our study, sequencing conditions differed between brown bear samples and wolf/lynx samples, and a higher number of sequence reads was available for genotyping brown bear samples.…”

“…The species that will benefit the most are those of conservation concern that are extremely elusive and/or difficult to study. Examples include secretive felid species such snow leopard or Siberian tiger (Rodgers & Janečka, 2013) and the polar bear ( Ursus maritimus ) (Von Duyke et al., 2023) among other species for which population data are lacking. In addition, species commonly monitored through non‐invasive genetic sampling, such as wolves, brown and black bears and mesocarnivores (Kelly et al., 2012; Mumma et al., 2015), will also profit from genotype data collected through snow tracking.…”

“…Snow track eDNA has already been used for species detection of several predators through mtDNA analysis (Barber‐Meyer et al., 2020; Dalén et al., 2007; Franklin et al., 2019; Kinoshita et al., 2019). A number of published studies have attempted to analyse nDNA with varying results for lynx (Hellström et al., 2019), wolf (Barber‐Meyer et al., 2020, 2022) and polar bear (Von Duyke et al., 2023) with only this latter recent study being successful in achieving reliable multilocus genotyping for individual identification in a single species. However, individual genotyping from snow track eDNA as a wildlife non‐invasive genetic method still remains elusive.…”

“…The low level of reads observed in the controls indicates that spurious sequences, including tag-jumps, were not a problem with both protocols and were actually negligible with the Tagsteady protocol used for lynx and wolf samples. Sequencing coverage was, on average, higher for brown than for Janečka, 2013) and the polar bear (Ursus maritimus)(Von Duyke et al, 2023) among other species for which population data are lacking. In addition, species commonly monitored through noninvasive genetic sampling, such as wolves, brown and black bears and mesocarnivores…”