[en] 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
Disciplines :
Zoology
Author, co-author :
Michaux, Johan ; Université de Liège - ULiège > Département des sciences de la vie > Laboratoire de génétique de la conservation
Dyck, Markus
Loughed, Steven
Van coeverden de Groot, Peter
Language :
English
Title :
New insights on polar bear (Ursus maritimus) diet from faeces based on Next Generation Sequencing technologies
Andriollo, T., Gillet, F., Michaux, J.R., and Ruedi, M. 2019. The menu varies with metabarcoding practices: A case study with the bat Plecotus auritus. PLoS ONE 14(7): E0219135. https://doi.org/10.1371/journal.pone.0219135
Bernatchez, L., Glémet, H., Wilson, C.C., and Danzmann, R.G. 1995. Introgression and fixation of Arctic char (Salvelinus alpinus) mitochondrial genome in an allopatric population of brook trout (Salvelinus fontinalis). Canadian Journal of Fisheries and Aquatic Science 52(1):179 – 185. https://doi.org/10.1139/f95-018
Biffi, M., Gillet, F., Laffaille, P., Colas, F., Aulagnier, S., Blanc, F., Galan, M., et al. 2017a. Novel insights into the diet of the Pyrenean desman (Galemys pyrenaicus) using next-generation sequencing molecular analyses. Journal of Mammalogy 98(5):1497 – 1507. https://doi.org/10.1093/jmammal/gyx070
Biffi, M., Lafaille, P., Jabiol, J., André, A., Gillet, F., Lamothe, S., Michaux, J.R., and Buisson, L. 2017b. Comparison of diet and prey selectivity of the Pyrenean desman and the Eurasian water shrew using next-generation sequencing methods. Mammalian Biology 87:176 – 184. https://doi.org/10.1016/j.mambio.2017.09.001
Deagle, B.E., Jarman, S.N., Pemberton, D., and Gales, N.J. 2005. Genetic screening for prey in the gut contents from a giant squid (Architeuthis sp.). Journal of Heredity 96(4):417 – 423. https://doi.org/10.1093/jhered/esi036
Derocher, A.E., Lunn, N.J., and Stirling, I. 2004. Polar bears in a warming climate. Integrative and Comparative Biology 44(2):163 – 176. https://doi.org/10.1093/icb/44.2.163
Dyck, M.G., and Morin, P. 2011. In vivo digestibility trials of a captive polar bear (Ursus maritimus) feeding on harp seal (Pagophilus groenlandicus) and Arctic charr (Salvelinus alpinus). Pakistan Journal of Zoology 43(4):759 – 767.
Dyck, M.G., and Romberg, S. 2007. Observations of a wild polar bear (Ursus maritimus) successfully fishing Arctic charr (Salvelinus alpinus) and fourhorn sculpin (Myoxocephalus quadricornis). Polar Biology 30:1625 – 1628. https://doi.org/10.1007/s00300-007-0338-3
Galan, M., Guivier, E., Caraux, G., Charbonnel, N., and Cosson, J.-F. 2010. A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies. BMC Genomics 11: 296. https://doi.org/10.1186/1471-2164-11-296
Galan, M., Pagès, M., and Cosson, J.-F. 2012. Next-generation sequencing for rodent barcoding: Species identification from fresh, degraded and environmental samples. PLoS ONE 7(11): E48374. https://doi.org/10.1371/journal.pone.0048374
Galan, M., Pons, J.-B., Tournayre, M., Pierre, E., Leuchtmann, P., Pontier, D., and Charbonnel, N. 2018. Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis. Molecular Ecology Resources 18(3):474 – 489. https://doi.org/10.1111/1755-0998.12749
Galicia, M.P., Thiemann, G.W., Dyck, M.G., and Ferguson, S.H. 2015. Characterization of polar bear (Ursus maritimus) diets in the Canadian High Arctic. Polar Biology 38:1983 – 1992. https://doi.org/10.1007/s00300-015-1757-1
Gillet, F., Tiouchichine, M.-L., Galan, M., Blanc, F., Némoz, M., Aulagnier, S., and Michaux, J.R. 2015. A new method to identify the endangered Pyrenean desman (Galemys pyrenaicus) and to study its diet, using next generation sequencing from faeces. Mammalian Biology 80(6):505 – 509. https://doi.org/10.1016/j.mambio.2015.08.002
Gitay, H., Suárez, A., Watson, R.T., and Dokken, D.J., eds. 2002. Climate change and biodiversity. IPCC Technical Paper 5. Geneva, Switzerland: Intergovernmental Panel on Climate Change.
Gormezano, L.J., and Rockwell, R.F. 2013. Dietary composition and spatial patterns of polar bear foraging on land in western Hudson Bay. BMC Ecology 13: 51. https://doi.org/10.1186/1472-6785-13-51
Hobson, K.A., Stirling, I., and Andriashek, D.S. 2009. Isotopic homogeneity of breath CO2from fasting and berry-eating polar bears: Implications for tracing reliance on terrestrial foods in a changing Arctic. Canadian Journal of Zoology 87:50 – 55. https://doi.org/10.1139/Z08-137
Iversen, M. 2011. The diet of polar bears (Ursus maritimus) from Svalbard, Norway, inferred from scat analysis. MSc thesis, University of Tromsø, Tromsø, Norway.
Iversen, M., Aars, J., Haug, T., Alsos, I.G., Lydersen, C., Bachmann, L., and Kovacs, K.M. 2013. The diet of polar bears (Ursus maritimus) from Svalbard, Norway, inferred from scat analysis. Polar Biology 36:561 – 571. https://doi.org/10.1007/s00300-012-1284-2
McInnes, J.C., Alderman, R., Deagle, B.E., Lea, M.-A., Raymond, B., and Jarman, S.N. 2017. Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates. Methods in Ecology and Evolution 8(2):192 – 202. https://doi.org/10.1111/2041-210X.12677
McKinney, M., Atwood, T.C., Iverson, S.J., and Peacock, E. 2017. Temporal complexity of southern Beaufort Sea polar bear diets during a period of increasing land use. Ecosphere 8(1): E01633. https://doi.org/10.1002/ecs2.1633
Meglécz, E., Piry, S., Desmarais, E., Galan, M., Gilles, A., Guivier, E., Pech, N., and Martin, J.-F. 2010. SESAME (SEquence Sorter & AMplicon Explorer): Genotyping based on high-throughput multiplex amplicon sequencing. Bioinformatics 27(10):277 – 278. https://doi.org/10.1093/bioinformatics/btq641
Murphy, M.A., Waits, L.P., and Kendall, K.C. 2000. Quantitative evaluation of fecal drying methods for brown bear DNA analysis. Wildlife Society Bulletin 28(4):951 – 957.
Pagès, M., Desse-Berset, N., Tougard, C., Brosse, L., Hänni, C., and Berrebi, P. 2009. Historical presence of the sturgeon Acipenser sturio in the Rhône basin determined by the analysis of ancient DNA cytochrome b sequences. Conservation Genetics 10:217 – 224. https://doi.org/10.1007/s10592-008-9549-6
Pagès, M., Chaval, Y., Herbreteau, V., Waengsothorn, S., Cosson, J.-F., Hugot, J.-P., Morand, S., and Michaux, J. 2010. Revisiting the taxonomy of the Rattini tribe: A phylogeny-based delimitation of species boundaries. BMC Evolutionary Biology 10: 184. https://doi.org/10.1186/1471-2148-10-184
Piñol, J., Senar, M.A., and Symondson, W.O.C. 2018. The choice of universal primers and the characteristics of the species mixture determine when DNA metabarcoding can be quantitative. Molecular Ecology 28(2):407 – 419. https://doi.org/10.1111/mec.14776
Polz, M.F., and Cavanaugh, C.M. 1998. Bias in template-to-product ratios in multitemplate PCR. Applied and Environmental Microbiology 64:3724 – 3730. https://doi.org/10.1128/AEM.64.10.3724-3730.1998
Pompanon, F., Deagle, B.E., Symondson, W.O.C., Brown, D.S., Jarman, S.N., and Taberlet, P. 2012. Who is eating what: Diet assessment using next generation sequencing. Molecular Ecology 21(8):1931 – 1950. https://doi.org/10.1111/j.1365-294X.2011.05403.x
Redenbach, Z., and Taylor, E.B. 2002. Evidence for historical introgression along a contact zone between two species of char (Pisces: Salmonidae) in northwestern North America. Evolution 56(5):1021 – 1035. https://doi.org/10.1111/j.0014-3820.2002.tb01413.x
Russell, R.H. 1975. The food habits of polar bears of James Bay and southwest Hudson Bay in summer and autumn. Arctic 28(2):85 – 152. https://doi.org/10.14430/arctic2823
Shehzad, W., Riaz, T., Nawaz, M.A., Miquel, C., Poillot, C., Shah, S.A., Pompanon, F., Coissac, E., and Taberlet, P. 2012. Carnivore diet analysis based on next-generation sequencing: Application to the leopard cat (Prionailurus bengalensis) in Pakistan. Molecular Ecology 21(8):1951 – 1965. https://doi.org/10.1111/j.1365-294X.2011.05424.x
Stempniewicz, L. 2006. Polar bear predatory behaviour toward molting Barnacle Geese and nesting Glaucous Gulls on Spitsbergen. Arctic 59(3):247 – 251. https://doi.org/10.14430/arctic310
Taberlet, P., Camarra, J.-J., Griffin, S., Uhrès, E., Hanotte, O., Waits, L.P., Dubois-Paganon, C., Burke, T., and Bouvet, J. 1997. Noninvasive genetic tracking of the endangered Pyrenean brown bear population. Molecular Ecology 6(9):869 – 876. https://doi.org/10.1046/j.1365-294X.1997.00251.x
Taberlet, P., Coissac, E., Pompanon, F., Gielly, L., Miquel, C., Valentini, A., Vermat, T., Corthier, G., Brochmann, C., and Willerslev, E. 2007. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Research 35(3): E14. https://doi.org/10.1093/nar/gkl938
Teletchea, F., Bernillon, J., Duffraisse, M., Laudet, V., and Hänni, C. 2008. Molecular identification of vertebrate species by oligonucleotide microarray in food and forensic samples. Journal of Applied Ecology 45(3):967 – 975. https://doi.org/10.1111/j.1365-2664.2007.01415.x
Thiemann, G.W., Budge, S.M., Iverson, S.J., and Stirling, I. 2007. Unusual fatty acid biomarkers reveal age- and sex-specific foraging in polar bears (Ursus maritimus). Canadian Journal of Zoology 85:505 – 517. https://doi.org/10.1139/Z07-028
Van Coeverden de Groot, P. 2019. M’Clintock Channel polar bear health - Baseline estimates from non-invasively collected faeces. https://www.polardata.ca/pdcsearch/PDCSearch.jsp?doi_id=12988
Van Coeverden de Groot, P., Wong, P.B.Y., Harris, C., Dyck, M.G., Kamookak, L., Pagès, M., Michaux, J., and Boag, P.T. 2013. Toward a noninvasive Inuit polar bear survey: Genetic data from polar bear hair snags. Wildlife Society Bulletin 37(2):394 – 401. https://doi.org/10.1002/wsb.283
Vestheim, H., and Jarman, S.N. 2008. Blocking primers to enhance PCR amplification of rare sequences in mixed samples – a case study on prey DNA in Antarctic krill stomachs. Frontiers in Zoology 5: 12. https://doi.org/10.1186/1742-9994-5-12
Vigfúsdóttir, F., Pálsson, S., and Ingólfsson, A. 2008. Hybridization of Glaucous Gull (Larus hyperboreus) and Herring Gull (Larus argentatus) in Iceland: Mitochondrial and microsatellite data. Philosophical Transactions of the Royal Society B: Biological Sciences 363(1505):2851 – 2860. https://doi.org/10.1098/rstb.2008.0042
Vongraven, D., Aars, J., Amstrup, S., Atkinson, S.N., Belikov, S., Born, E.W., DeBruyn, T.D., et al. 2012. A circumpolar monitoring framework for polar bears. Ursus 23(sp2):1 – 66. https://doi.org/10.2192/URSUS-D-11-00026.1
Wilson, C.C., and Bernatchez, L. 1998. The ghost of hybrids past: Fixation of Arctic charr (Salvelinus alpinus) mitochondrial DNA in an introgressed population of lake trout (S. namaycush). Molecular Ecology 7(1):127 – 132. https://doi.org/10.1046/j.1365-294x.1998.00302.x
Wong, P.B.Y., Van Coeverden de Groot, P., Fekken, C., Smith, H., Pagès, M., and Boag, P.T. 2011. Interpretations of polar bear (Ursus maritimus) tracks by Inuit hunters: Inter-rater reliability and inferences concerning accuracy. The Canadian Field-Naturalist 125(2):140 – 153. https://doi.org/10.22621/cfn.v125i2.1197
Zhang, Z., Schwartz, S., Wagner, L., and Miller, W. 2000. A greedy algorithm for aligning DNA sequences. Journal of Computational Biology 7(1-2):203 – 214. https://doi.org/10.1089/10665270050081478