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Conservation Genetics and Ecology of the Hazel

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Conservation Genetics and Ecology of the Hazel CONSERVATION GENETICS AND ECOLOGY OF THE HAZEL DORMOUSE Fraser Combe Department of Natural Sciences Manchester Metropolitan University A thesis submitted in partial fulfilment of the requirements of Manchester Metropolitan University for the degree of Doctor of Philosophy 2018 i Declaration This dissertation is the result of my own work and includes nothing, which is the outcome of work done in collaboration except where specifically indicated in the text. It has not been previously submitted, in part or whole, to any university of institution for any degree, diploma, or other qualification. Signed:__Fraser Combe___________________________________________________ Date:__________28/11/2018_______________________________________________________ ii Abstract Woodland species face a challenging future because of human activity and global climate change, as such it is vital to understand the ecology of species that inhabit these habitats in order to conduct effective conservation management. I describe the phylogeographic structure of the hazel dormouse within the UK, to identify post-glacial dispersal routes and to describe population units for conservation. I provide evidence for a single post-glacial colonization coincident with the start of the Holocene period, 7.5-11 Kya. I also demonstrate the utility of novel occupancy modelling techniques to determine dormouse presence with high probability of detection. I provide optimal survey guidelines for ecological practitioners to conduct rigorous statistically significant surveys. This species is known to be susceptible to habitat loss and fragmentation limiting dispersal and functional connectivity. I use a landscape genetics approach to characterize the genetic structure of populations of dormice from seven regions around the UK to explicitly test for the role of landscape heterogeneity and barriers to dispersal. The results suggests build- up of genetic structure amongst islands of fragmented habitat that is explained in part due to isolation-by-distance, and in part due to specific landscape features between different regions. The isolation-by-resistance analysis allows us to identify the landscape features, such as land cover, hedgerows and roads that facilitate or inhibit gene flow. Results suggest that dispersal in hazel dormice is strongly influenced by barriers in the landscape, with our main findings being that urban areas and roads are associated with decreased gene flow while habitat features such as hedgerows and forest cover are associated with increased gene flow. Finally, I investigated the effect of density dependence and climatic factors on the population demography of five marked hazel dormice populations in Europe (four in the UK and one in Lithuania). The results from the chapter have identified the environmental drivers of these population parameters on hibernating mammals whilst providing evidence that density dependence has the greatest effect on population dynamics in this species. The results provide information that variability in winter conditions can have serious consequences for individual fitness, decreasing the dormancy season and leading to an increased extinction risk in this species. I discuss the implications for hazel dormouse conservation in the UK, and make recommendations for conservation practitioners to ensure the future persistence of this species. iii Acknowledgements Firstly, thanks go to my supervisor, Ed Harris, you have been an extremely supportive mentor on this journey, it truly has been one of the most enjoyable periods in my life you have guided and encouraged me throughout always having my best interests in mind. Your scientific knowledge and patience has helped me turn in to a more confident researcher. Thank you my other supervisors, Jonathan Ellis for your guidance, knowledge and most importantly your patience whilst offering me encouragement whenever I needed it and Phil Wheater for helping me make new contacts and always offering to read a manuscript at the last minute. I particularly thank Neil Cresswell, who ensured I was not only able to earn an income during my PhD, but for also acting as a mentor, encouraging me to move into the world of teaching. Your enthusiasm was something I learnt greatly from, whilst your guidance and encouragement was a nudge to take myself out of my comfort zone and take on new challanges. I greatly thank my colleagues in the School of Science and the Environment, for their helpful insight, lab assistance, and the beers that helped distract or offer guidance and advice whenever I needed it. I am especially grateful to Danny Norrey, Rosie Stanbrook and Tom Higginbottom, that not only offered scientific support and knowledge but for the entertaining conversations and rants. Thanks to Francesca Preston and Eve Taylor-Cox for their assistance in the lab, putting up with my complete lack of organisation and being there for the excitement of when experiments do actually work, I hope I at least taught you a few things in molecular biology. Outside of MMU, many members of the dormouse research community have offered me valuable feedback and discussions about my results, for which I am incredibly grateful. Collecting samples from so many locations around the UK and Europe would not have been possible without the assistance of a number of individuals that generously spent their time to carefully collect samples for me. I could not mention all your names but I admire how everyone was always keen help, increase knowledge and go out of their way. I am eternally grateful to Simone Bullion for not only sharing her vast knowledge of ecology and dormice but also for her generosity in putting us up in her house or all the times you put a good word in for me to help make more contacts. Thanks to Sarah, Roger and Rimvydas for allowing me to analyse their microchipping data, such long- term studies are unique but most importantly you also offered time to go through and organise data. Thank you to the People’s Trust for Endangered species for funding this work and to Nida and Ian for always offering to help interpret the results for dormice conservation. 4 My brothers and friends have been a support network throughout my PhD studies. It’s not possible to name all, but you know who you are – thanks for the distractions, the beers and moral support even when you had no idea what I was talking about. Special thanks to Peter Lawrence, not just a close friend for so many years but someone to bounce scientific ideas off, proof-reader or fieldwork assistant, it has always been a pleasure to do a PhD alongside you. Finally thank you to my parents Brian and Sheena Combe, you have always been a source of strength with not only love but also the encouragement to follow my passions with unwavering belief. 5 Contents 1 Chapter 1: General Introduction ..................................................................................................... 9 1.1 Introduction: Habitat fragmentation and genetic diversity in natural populations ............... 9 1.2 Habitat fragmentation and conservation genetics ................................................................. 9 1.3 Conservation units or ESU’s for species management ......................................................... 11 1.4 Detection of species using presence/absence ...................................................................... 12 1.5 Landscape genetics ............................................................................................................... 13 1.6 The hazel dormouse: current status and conservation ........................................................ 15 1.7 Conservation status and management ................................................................................. 17 1.8 Thesis Aims ............................................................................................................................ 18 1.9 References ............................................................................................................................ 20 2 Chapter 2: After the ice age: the impact of post-glacial dispersal on the phylogeography of a small mammal, Muscardinus avellanarius. ........................................................................................... 26 2.1 Abstract ................................................................................................................................. 26 2.2 Introduction .......................................................................................................................... 26 2.3 Material and methods .......................................................................................................... 29 2.4 Results ................................................................................................................................... 33 2.4.1 Phylogenetic analysis and genetic diversity .................................................................. 33 2.4.2 Divergence Time calculation and demographics .......................................................... 39 2.5 Discussion .............................................................................................................................. 42 2.5.1 Genetic structure between UK and continental Europe ............................................... 42 2.5.2 Genetic structure within the UK ................................................................................... 42 2.5.3 Colonization of mainland UK- Land bridge hypothesis ................................................
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