Abstract
Accurate dietary inference of wild carnivores is essential to understand their impacts on the ecosystem and manage carnivore-livestock conflicts. Diet analysis with fecal DNA metabarcoding technology can help deliver valuable insights with fine-grained resolution. The recovery of wolves in Washington, USA offers an excellent opportunity to study the diet of this iconic carnivore species and explore prey partitioning between sympatric wolves and coyotes. We characterized the diet composition and spatiotemporal dietary variations in each species using fecal DNA metabarcoding technology on 202 fecal samples from wolves (N = 99) and coyotes (N = 103) collected across three wolf pack ranges and two seasons in northeastern Washington. We also quantified the diet niche overlap between these two canid species. In total, 19 different prey items were detected, with most assigned at the species level. Frequency of occurrence (FOO) data showed that wolves primarily preyed upon deer (Odocoileus sp.; 47.5%) and moose (Alces alces; 42.4%). Coyotes also consumed moose (30.1%) and deer (21.4%), but snowshoe hares (Lepus americanus) were the most common prey (61.2%) in the coyote diet. Multiple samples were found to contain DNA from domestic animals, including pig, rabbit, and cow. Results on diet composition using FOO and relative read abundance were qualitatively similar, indicating a strong biological pattern. We found significant spatial variations in the wolf diet composition (p = 0.001) and significant spatio temporal variations in the coyote diet (pack range: p = 0.003; season: p = 0.023). Dietary overlap between these two canid species varied with pack ranges and seasons (\(O\) = 0.08–0.74). Our study demonstrates that fecal DNA metabarcoding is an efficient non-invasive tool to characterize high-resolution diet profiles of carnivores and monitor their dietary changes over space and time. Limitations of fecal DNA metabarcoding are also discussed.
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Data availability
Raw sequence reads (fastq.gz) from 202 samples used in this research along with corresponding metadata were archived in the NCBI Sequence Read Archive with BioProject ID PRJNA675955. The following data files were deposited on Github (https://github.com/melodysyue/CanidPrey_MBC): (1) raw sequence reads (fastq.gz) from negative controls (extraction and PCR negative controls); (2) initial MOTU table of 374 MOTUs (.tab) after the obitools pipeline along with their sequences (.fasta); (3) taxonomy classification of 348 MOTUs with a minimum identity of 0.98 (.csv); (4) meta information for 202 samples in the study; (5) final MOTU table of 332 MOTUs; (6) presence and absence data of 19 identified prey items across samples. (.csv).
Code availability
Scripts used in this study were deposited on Github (https://github.com/melodysyue/CanidPrey_MBC).
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Acknowledgements
We thank all the conservation canines and dog handlers for their great efforts in sample collection, including Heath Smith, Jennifer Hartman, Suzie Marlow, Will Chrisman, Caleb Stanek, Justin Broderick, Casey McCormack, Mairi Poisson, Collette Yee, Rachel Katz, Jake Lammi, Peter Dubyoski, Marlen Richmond and Julianne Ubigau. We thank Burke Museum of Natural History for providing specimens during the initial testing phase. We thank Noah Synder-Mackler, India Schneider-Crease, and Sierra Sams for advice on library prep and MiSeq sequencing. The MiSeq sequencing platform is funded by the Student Technology Fee at the University of Washington. We thank Pierre Taberlet for advice on experimental design and Susanne Butschkau for help with bioinformatic data analysis. We thank the editor and two anonymous reviewers for their constructive comments, which greatly improved the manuscript.
Funding
The study was funded by the Johnson Foundation, the Dawkins Trust and the Maritz Family foundation. YS was funded by WRF Hall Fellowship from the University of Washington.
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YS and SKW conceived the project. YS designed the experiments. YS, YH and ER performed the experiments. YS conducted the analyses and wrote the manuscript. SKW guided analyses and edited the manuscript. SKW, YH and ER commented on the manuscript.
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Fecal samples were collected using the detection dogs from the Conservation Canine Program at the University of Washington under IACUC protocol #2850-08.
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Shi, Y., Hoareau, Y., Reese, E.M. et al. Prey partitioning between sympatric wild carnivores revealed by DNA metabarcoding: a case study on wolf (Canis lupus) and coyote (Canis latrans) in northeastern Washington. Conserv Genet 22, 293–305 (2021). https://doi.org/10.1007/s10592-021-01337-2
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DOI: https://doi.org/10.1007/s10592-021-01337-2