Reconstructing the Diet of an Elusive Wood Grouse (Western Capercaillies) Using
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RECONSTRUCTING THE DIET OF AN ELUSIVE WOOD GROUSE (WESTERN CAPERCAILLIES) USING METAGENOMICS displaying its magnificent tail feathers male capercaillie A Spotted! Per Gätzschmann CREDIT: PHOTO by PHYSILIA CHUA Department of Biology, University of Copenhagen, Copenhagen, Denmark Environmental DNA provides a non-invasive and simple means of biomonitoring one are the days when researchers needed to samples circumvents some of the challenges of study- spend countless hours observing an animal in ing animals otherwise hard to find. Gthe wild to understand its behaviour and ecol- One such NGS approach is metagenomics shotgun ogy. As we demonstrate with our study, valuable data sequencing (MSS), which determines the nucleotide can be gathered by simply examining faecal samples composition of large amounts of random DNA mole- with powerful metagenomics approaches. cules recovered from complex samples of DNA from The need for data that effectively informs biological various sources. This method makes it possible to conservation is intensifying as the rate of biodiversity simultaneously retrieve information about the host’s loss increases. Traditionally, scientists have endured diet, microbiome, gut parasites, as well as the popula- long hours in the field, often hiding uncomfortably tion structure of the species1. While it has vast poten- in bushes or traversing dangerous and hard-to-reach tial for conservation biology, few studies have utilised places, all for the purpose of observing elusive ani- MSS to reconstruct the diet of animals, and none have mals. done so for herbivorous birds. With the advent of next-generation sequencing The western capercaillie (Tetrao urogallus), or (NGS) technologies – those that effectively provide wood grouse, is an emblematic species which can large amounts of DNA sequence data – it is now pos- be found in the coniferous forest of Eurasia. Highly sible to obtain a wealth of ecological information from susceptible to the increased levels of habitat destruc- just a single faecal sample. The ease of collecting such tion and fragmentation, their declining population has doi: 10.21083/ibol.v9i1.5725 1 iBOL Barcode Bulletin | Nov 12, 2019 placed them on the International Union for Conser- vation of Nature (IUCN) Red-list throughout most of western and central Europe2. By studying the wood grouse’s diet, we could gain clues about the resources it requires and the other species it interacts with in its habitat, informing better conservation strategies. By observing the animal and morphologically identifying plant remains from their faecal samples, it was deter- mined that the capercaillie’s diet consists of mostly pine needles in the winter, and Vaccinium species in the summer3. A typical day out in the fields high above the Arctic Circle in Tromsø, Dividalen National Park, Norway PHOTO CREDIT: Physilia Chua Searching for capercaillies in the midst of a snow storm in the Norwegian boreal forests PHOTO CREDIT: Physilia Chua However, preliminary results from our study show promising signs that the capercaillie’s diet is more di- verse than once thought. Other than plants, we have A pile of capercaillie scat also discovered parasitoid wasps and several species PHOTO CREDIT: Physilia Chua of mites, which could have been accidental ingestion while feeding or preening. And with the use of metag- enomics, there is also the possibility of obtaining more detailed quantitative information about its diet that can be used to inform habitat management choices. Their gut microbiome, intestinal parasites, and population genetics are also currently being analysed. Unexpectedly, we were also able to detect the pres- ence of plant-pathogenic fungus and nematodes from their faecal samples, providing some interesting eco- logical insights about the capercaillie’s habitat. Even though our research is still in its infancy, by using metagenomics shotgun sequencing on faecal samples, our initial study has already yielded a wealth of data. There is truly an untapped potential for its application Capercaillie’s favourite food? Pine needles (left) and Vaccinium in conservation biology and biomonitoring, which sp (right) should be further explored. PHOTO CREDIT: Physilia Chua doi: 10.21083/ibol.v9i1.5725 2 iBOL Barcode Bulletin | Nov 12, 2019 References 1. Srivathsan A, Sha JCM, Vogler A, Meier R (2015) Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf- feeding monkey (Pygathrix nemaeus). Molecular Ecology Resources 15(2): 250–261. https://doi. org/10.1111/1755-0998.12302 2. Storch I (2000) Grouse: status survey and conservation action plan 2000-2004. IUCN/SSC Action Plans for the Conservation of Biological Diversity. Retrieved from http://www.iucn.org/ dbtw-wpd/edocs/2000-031.pdf The road less travelled might lead to unexpected discoveries PHOTO CREDIT: Physilia Chua 3. Picozzi N, Moss R, Catt DC (1996) Capercaillie habitat, diet and management in a Sitka spruce plantation in central Scotland. International Aknowledgements: Journal of Agriculture and Forestry. 69(4): 373 – I thank my supervisors Kristine Bohmann, Sanne 388. https://doi.org/10.1093/forestry/69.4.373 Boessenkool, and Inger Greve Alsos for their guidance in every step of this research, without whom this study would not have been possible. Online: I am deeply grateful to Torbjørn Ekrem for his invaluable support both in and outside of fieldwork. https://ibol.org/barcodebulletin/illuminations/ I am indebted to my collaborators Kat Bruce and reconstructing-the-diet-of-an-elusive-wood-grouse- Alex Crampton-Platt for taking me into their team western-capercaillies-using-metagenomics/ at NatureMetrics and making bioinformatics look so easy. Lastly, my sincere gratitude to the members of the eDNA group at the Section for Evolutionary Genomics, University of Copenhagen, and also to my fellow Plant.ID ESRs for keeping me in the right headspace. This project is part of the H2020 MSCA- ITN-ETN Plant.ID network and has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 765000. doi: 10.21083/ibol.v9i1.5725 3 iBOL Barcode Bulletin | Nov 12, 2019.