New insights on polar bear (Ursus maritimus) diet from faeces based on Next Generation Sequencing technologies

Practical tools to quantify range-wide dietary choices on the polar bear have not been well developed 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 polar bear faeces from captive polar bears fed known diets at the Cochrane Polar Bear Habitat (Canada, n = 5 faeces from 1 bear) and Metro Toronto Zoo (Canada, n =19 from 3 polar bears); and from wild (unfed) polar bears from a holding facility in Churchill (Canada; n=7 from 7 polar bears). 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 (MC) polar bear Management Unit (Canada) (n =117 from an unknown number of bears). These data point to a diet unsurprisingly dominated by ringed seal (Phoca hispidia) while including evidence of bearded seal (Erignathus barbatus), harbor seal (Phoca vitulina), muskox (Ovibos spp.), Arctic foxes (Alopex lagopus), wolves (Canis lupus), herring gull (Larus argentatus) and willow ptarmigan (Lagopus lagopus). We found low levels pf contamination (<3% of sequences when present), suggesting 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