ESR4: Shotgun sequencing for comparative diet analysis of capercaillies

In short

Do you know that from just a single drop of your faeces, I would be able to tell what you had for dinner last night? For my study, I will be using molecular faecal analysis to study the diet of the western capercaillie. Capercaillies are a type of herbivorous birds that can be found across most of Eurasia. Their fascinating courtship display has captivated the hearts of both the young and the old alike. Sadly, they are threatened by many factors such as habitat destruction. By studying their diet, information about their resource use and habitat requirements can be used to better conserve these magnificent creatures.

Project description

Diet analysis is a prerequisite to fully understand the biology of a species and the functioning of ecosystems. For animals, traditional diet analyses rely mostly on morphological identification of undigested remains in the faeces, but recent advances in metabarcoding have enabled using DNA of ingested foods to reconstruct diets. However, amplicon metabarcoding markers have limited resolution in species identification and the absence of complete sequence reference databases further limit accurate species identification. Recently, national DNA reference database projects have emerged, which create organelle genome reference data for each species: in the Alps (PhyloAlps), Norway (NorBOL) and Denmark (DNAmark). This PhD project will explore the optimal use of these novel and comprehensive reference databases for accurate species-level identification of plants in animal diets through a comparative shotgun sequencing diet study on capercailles (wood grouse) in the Alps and Norway. The project will involve fieldwork, laboratory preparation of collected faecal samples for shotgun sequencing and exploration/development of laboratory and bioinformatics protocols and workflows.

Research output


Towards the extended barcode concept: Generating DNA reference data through genome skimming of danish plants

Physilia Y. S. Chua, Frederik Leerhøi, Emilia M. R. Langkjær, Ashot Margaryan, Christina L. Noer, Stine R. Richter, Marlene E. Restrup, Hans Henrik Bruun, Ida Hartvig, Eric Coissac, Sanne Boessenkool, Inger G. Alsos, Kristine Bohmann

bioRxiv 2021.08.11.456029; 


Chua, P. Y. S., Lammers, Y., Menoni, E., Ekrem, T., Bohmann, K., Boessenkool, S., & Alsos, I. G. (2021). Molecular dietary analyses of western capercaillies (Tetrao urogallus) reveal a diverse diet. Environmental DNA, 00, 1– 16.

Kristine Bohmann, Physilia Chua, Luke E. Holman, Christina Lynggaard. DNAqua-Net conference unites participants from around the world with the quest to standardize and implement DNA-based aquatic biomonitoring. Environmental DNA. 31 May 2021

Physilia Ying Shi Chua, Alex Crampton‐Platt, Youri Lammers, Inger Greve Alsos,Sanne Boessenkool,  Kristine Bohmann. Metagenomics: A viable tool for reconstructing herbivore diet. Molecular Ecology Resources 10 May 2021

Physilia Ying Shi Chua, Youri Lammers, Emmanuel Menoni, Torbjørn Ekrem, Kristine Bohmann, Sanne Boessenkool, Inger Greve Alsos, 2021. Molecular dietary analyses of western capercaillies (Tetrao urogallus) reveal a diverse diet. bioRxiv 2021.03.08.434346.


Chua P, Boessenkool S, Alsos IG, Ekrem T, Crampton-Platt A, Bohmann K, 2019. Use of emerging complete organelle DNA reference database in the diet analysis of the herbivorous wood grouse, western capercaillies. At: 8th International Barcode of Life Conference. Trondheim, Norway. 17-20 June 2019.

Oral presentations

Chua, Physilia . Metabarcoding for hope: A large-scale molecular dietary study of the western capercailles (Tetrao Urogallus). Given at the BRC16/19 SAMBA meet 2021 - Biodiversity monitoring and mapping (hosted by UFPA, Belem, Brazil). 10 September 2021.