Phylogeny and Ecology of the Himalayan Wolf Thesis for the Degree of Doctor of Philosophy in Zoology Geraldine Werhahn Wildlife Conservation Research Unit Department of Zoology University of Oxford Trinity Term 2019 Lady Margaret Hall Supervised by Professor David W. Macdonald, Professor Claudio Sillero-Zubiri & Doctor Helen Senn Dedicated to my mother Béatrice Werhahn and my father Peter Werhahn. Contents Abstract ..........................................................................................................................................7 Acknowledgements ..............................................................................................................12 List of original publications ...................................................................................................15 Author affiliations ..................................................................................................................19 Chapter 1. General Introduction ...................................................................................................21 Thesis objectives ..................................................................................................................31 Thesis structure ....................................................................................................................32 Study areas ..........................................................................................................................33 References ...........................................................................................................................38 Chapter 2. Phylogenetic evidence for the ancient Himalayan wolf: towards a clarification of its taxonomic status based on genetic sampling from western Nepal ................................45 Abstract ................................................................................................................................46 Introduction ..........................................................................................................................47 Methods ...............................................................................................................................47 Results .................................................................................................................................49 Discussion ...........................................................................................................................54 Acknowledgments ................................................................................................................59 References ...........................................................................................................................59 Chapter 3. The unique genetic adaptation of the Himalayan wolf to high-altitudes and consequences for conservation ...........................................................................................63 Abstract ................................................................................................................................64 Introduction ..........................................................................................................................65 Methods ...............................................................................................................................66 Results .................................................................................................................................69 Discussion ...........................................................................................................................72 Acknowledgments ................................................................................................................78 References ...........................................................................................................................78 Chapter 4. Himalayan wolf distribution and admixture based on multiple genetic markers .............................................................................................................................83 Abstract ................................................................................................................................85 Introduction ..........................................................................................................................86 Methods ...............................................................................................................................88 Results .................................................................................................................................91 Discussion ...........................................................................................................................101 Acknowledgments ................................................................................................................110 References ...........................................................................................................................112 Chapter 5. Himalayan wolf diet and the importance of wild prey .............................................119 Abstract ................................................................................................................................120 Introduction ..........................................................................................................................122 Methods ...............................................................................................................................123 Results .................................................................................................................................130 Discussion ............................................................................................................................137 Acknowledgments ...............................................................................................................142 References ...........................................................................................................................143 Chapter 6. Canids challenge taxonomy: a review of Asian wolves ..........................................149 Abstract ................................................................................................................................150 Introduction ..........................................................................................................................151 Methods ...............................................................................................................................153 Wolf lineages of Asia ...........................................................................................................155 Discussion ...........................................................................................................................171 References ...........................................................................................................................178 Chapter 7. General Discussion ....................................................................................................187 Conclusion ...........................................................................................................................209 References ...........................................................................................................................211 Appendix A. Additional publications and outputs .....................................................................223 From the wild yak rediscovery to the Nepalese five-rupee bank note ..................................224 Short film ..............................................................................................................................225 Book .....................................................................................................................................225 Publication: Werhahn et al. 2017. Conservation implications for the Himalayan wolf based on observations of packs and home sites in Nepal ...................................................226 Publication: Kusi et al. 2019. Perspectives of traditional Himalayan communities on fostering coexistence with Himalayan wolf and snow leopard ...................233 Publication: Werhahn et al. 2018. Eurasian lynx and Pallas’s cat in Dolpa district of Nepal: Insights into genetics, distribution and diet from non-invasive sampling ..............266 Publication: Macdonald and Campbell et al. 2019. Monogamy: Cause, Consequence or Corollary of Success in Wild Canids .........................................................271 Appendix B. Supplementary materials of genetic studies ........................................................343 B-1. Supplementary information for: Werhahn et al. 2017. Phylogenetic evidence for the ancient Himalayan wolf: towards a clarification of its taxonomic status based on genetic sampling from western Nepal ..................................................................344 B-2. Supplementary information for: Werhahn et al. 2018. The unique genetic adaptation of the Himalayan wolf to high-altitudes and the consequences for conservation .................360 B-3. Supplementary information for: Werhahn et al. 2019. Himalayan wolf distribution and admixture based on multiple genetic markers ...............................................................396 Appendix C. Microscopic hair