Abstract
Practical tools to quantify range-wide dietary choices of the polar bear have not been well developed, thus impeding the monitoring of this species in a changing climate. Here we describe our steps toward non-invasive polar bear diet determination with the optimization of 454 pyrosequencing of a 136 base pair (bp) mitochondrial cytochrome b (cytb) fragment amplified from the extracts of captive and wild polar bear faeces. We first determine the efficacy, reliability, and accuracy of our method using five faecal samples from a captive polar bear fed a known diet at the Canadian Polar Bear Habitat in Cochrane, Ontario, Canada; 19 samples from three polar bears at the Metro Toronto Zoo, Toronto, Ontario, Canada; and seven samples from seven wild (unfed) polar bears from a holding facility in Churchill, Manitoba, Canada. We report 91% overall success in amplifying a 136 bp cytb amplicon from the faeces of polar bears. Our DNA analyses accurately recovered the vertebrate diet profiles of captive bears fed known diets. We then characterized multiyear vertebrate prey diet choices from free-ranging polar bears from the sea ice of the M’Clintock Channel polar bear management unit, Nunavut, Canada (n = 117 from an unknown number of bears). These data point to a diet unsurprisingly dominated by ringed seal (Pusa hispida) while including evidence of bearded seal (Erignathus barbatus), harbour seal (Phoca vitulina), muskox (Ovibos moschatus ssp.), Arctic fox (Vulpes lagopus), wolf (Canis lupus), Herring Gull (Larus argentatus), and Willow Ptarmigan (Lagopus lagopus). We found low levels of contamination (< 3% of sequences when present) and suggest specific process improvements to reduce contamination in range-wide studies. Together, these findings indicate that next-generation sequencing-based diet assessments show great promise in monitoring free-ranging polar bears in this time of climate change. 
Highlights
The anticipated changes in the Arctic climate and concomitant reduction in sea-ice quantity and quality is hypothesized to affect polar bear diet (Derocher et al 2004)
Polar bear diet determination from Next Generation Sequencing (NGS) assays of their faeces – initial evidence from a single captive bear: Our pilot study of 454 diet determination from a 136 bp cytochrome b (cytB) sequence amplified from extracts of 5 polar bear faeces from a single bear (PBH) fed three different diets for three weeks over 9 weeks – suggests that our molecular diagnoses are accurate to vertebrate genus level (Table 1)
Three out of 5 Polar Bear Habitat (PBH) faecals (A, B, & F) samples worked across both dilutions in the initial cytB PCR. [Neither extract for PBH D &E amplified across both dilutions and unlike the process followed for all other initial FAIL or WEAK PCRS, they were not reextracted nor were PCRs repeated in this pilot]
Summary
The anticipated changes in the Arctic climate and concomitant reduction in sea-ice quantity and quality is hypothesized to affect polar bear diet (Derocher et al 2004). Polar bear diet investigations have been largely based on direct observation (Dyck& Romberg 2007), morphological identification of prey remains from their scats (Iversen 2011; Gormezano and Rockewell 2013), biochemical analyses of fatty acids (FA) and or stable isotopes profiles from harvested tissue or biopsy plugs Those requiring tissue from biopsy studies such as FA analyses or direct observations are labour intensive, costly, and can be stressful for the animal
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