Phenotypic plasticity and population genetic structure in a wild vertebrate population Daniel H. Nussey Submitted for the degree of Doctor of Philosophy University of Edinburgh October 2005 Declaration: I have composed this thesis. All analyses presented this thesis are my own work, with the exception of the spatial autocorrelation analysis presented in Figure 5.3 and discussed through Chapter 5, which was performed by Dr Dave Coltman. This work has not been submitted for any other degree or professional qualification. Acknowledgements: I'll begin by expressing my immense thanks to Loeske Kruuk, my supervisor, for her instruction, support and encouragement throughout my Ph.D. Loeske somehow managed to balance insightful and careful commentary on all the work I've done with genuine kindness and support whenever it was needed. I cannot imagine how I could possibly have been supervised better. I'm also extremely grateful to have had the support of Josephine Pemberton, as a second supervisor, and Steve Albon, as a CASE supervisor. Josephine's academic support has been much appreciated, particularly during Loeske's maternity leave. Steve's contribution to the plasticity work has improved the quality and rigour of the analyses presented here immensely. I've learnt a great deal from both of you. Thanks also to NERC for funding my time in Edinburgh, and to CEH Banchory and the Macaulay Institute which have provided CASE funding. None of the work presented here would be possible without the vision of Tim Clutton-Brock in Cambridge, in starting up and managing the Kilmory deer project, or without the hard work and skill of Fiona Guinness and all the Kilmory field research assistants. I am especially grateful to Ali Donald and Sean Morris, the present and previous field researchers for the deer project on Rum, for everything they've taught me about deer and how to go about doing fieldwork properly, and for all the great times I've had on Rum during these three years. Comments and support from Tim Clutton-Brock, Tim Coulson and Dave Coltman have been instrumental in much of the work presented in this thesis. Ian Stevenson's remarkable red deer database has almost certainly shaved months off the date of this thesis' submission. I owe a great many people in Josephine's lab thanks too: Kate Byrne helped me find my feet in the lab when I first arrived, and Barbara Wimmer, Floss Jones, Silvia Perez-Espona and Dario Bernaldi have always been on hand whenever my ignorance of all things molecular has become too apparent. I have to thank Key Connaghan, Keith Allan and Jon Slate for red deer DNA extractions which I managed to steal over the course of my PhD. The work in this thesis has also benefited immensely from discussion with David Elston, Dany Garant, Jon Brommer, Anne Charmantier, and Alastair Wilson. And thanks to everyone at the Netherlands Institute of Ecology, particularly Erik Postma, Phillip Gienapp, Kate Lessels and Marcel Visser, for putting up with me for a month and for many stimulating discussions about my work. On a more personal note, I'd like to thank my parents for their unwavering support. I've had an incredible time during my three years in Edinburgh, and that's really down to the fantastic bunch of people I've spent that time with. First, to Eva Jacobs: thanks for all your kindness and support in the two-and-a-half years we shared in Edinburgh. And a huge thank you to Ron Nussey, Sapna Patel, Steve Roe, Key Connaghan, Kate Henderson, Becky Coe, Helen Simcox, Floss Jones, Culum Brown, Alastair Wilson, Arnie Fulton, Darren Obbard, Jamie Moore, Tracey Reynolds, Kath Baldock, Kathy Foerster, Chloe Scott, and Louisa Tempest for their valued friendship and the great times shared over the last three years. And finally, thanks to Sarah Reece for making these last few weeks of thesis writing - my PhD's "death zone" supposedly - some of the best I can remember. Abstract: My thesis focuses on maternal phenotypic plasticity in two neonatal traits and population genetic structure at different spatial scales in a wild red deer (Cervus elaphus) population on the Isle of Rum, Scotland. Life history plasticity represents a vital mechanism allowing populations to respond rapidly to environmental change, yet it is rarely examined in natural settings. At the same time, fine-scale genetic structure may lead to spatial variation in evolutionary potential or kin selection within natural populations. Empirical exploration of the presumably dynamic relationship between ecological or demographic processes and spatial genetic patterns in wild vertebrates is lacking. In the five data chapters comprising my thesis I present analyses and discussion of life-history plasticity in female red deer on Rum; I also document fine-scale spatial genetic patterns across the population and link these to ecology, demography and recent human management practices. Specifically, I present: An analysis of offspring birth weight - spring temperature plasticity in female red deer using linear regression to measure individual reaction norms. I found evidence of variation in plasticity between females and show that early experiences of high population density reduce female plasticity. The description of a mixed-effects linear model approach to analysing phenotypic plasticity from a reaction norm perspective, and application of this model to birth date in the Rum deer population. I use the model to examine variation in phenotypic plasticity between females and selection on plasticity at different population density levels. An examination of population history and structure in red deer from across the Isle of Rum using mitochondrial DNA and microsatellite markers. Analysis revealed that deer in this introduced population came from geographically isolated ancestral populations, and there was genetic evidence for strongly male-biased dispersal. Recent management practices on the island may have led to spatial variation in effective male dispersal on Rum. A comparison of fine-scale spatial genetic structure between male and female deer in the North Block study area using microsatellite markers and census data. There was evidence of structure at extremely fine spatial scales amongst females but not males, and a decline in the structure amongst females over time. I relate this change in female spatial genetic structure to concurrent changes in population size and mating system. An analysis of the spatial distribution of different mtDNA haplotypes in male and female red deer across the North Block. There was evidence for spatial structuring of haplotypes in both sexes. Table of Contents: 1 General Introduction 1 1.1 The evolutionary ecology of phenotypic plasticity 2 1.2 Spatial genetic structure in wild mammal populations 11 1.3 The study population 16 1.4 The objectives of this thesis 22 2 Constraints on plastic responses to climate 24 variation in red deer 2.1 Summary 24 2.2 Introduction 25 2.3 Methods 27 2.4 Results 29 2.5 Discussion 31 3 Phenotypic plasticity in a maternal trait in red 34 deer 3.1 Summary 34 3.2 Introduction 35 3.3 Methods 43 3.4 Results 49 3.5 Discussion 54 3.6 Conclusions 59 4 The genetic consequences of human 60 management in an introduced island population of red deer 4.1 Summary 60 4.2 Introduction 61 4.3 Methods 67 4.4 Results 75 4.5 Discussion 83 5 Rapidly declining fine-scale spatial genetic 89 structure in female red deer 5.1 Summary 89 5.2 Introduction 90 5.3 Methods 94 5.4 Results 102 5.5 Discussion 110 5.6 Conclusions 113 6 Fine-scale spatial structuring of mtDNA variation 115 in a wild red deer population: the role of ecological conditions and selection on haplotype 6.1 Summary 115 6.2 Introduction 116 6.3 Methods 120 6.4 Results 127 6.5 Discussion 138 6.6 Conclusions 143 7 General Discussion 144 7.1 Maternal life history plasticity in the wild 144 7.2 Spatial genetic structure in a wild mammal population 152 7.3 Final thoughts 159 References 161 184 Appendices 0 A Red deer microsatellite markers 184 B Alignment of red deer mitochondrial control region 186 sequences C Generalised linear mixed effects models for individual 191 fitness traits in red deer D Publications arising from this thesis 195 GENERAL INTRODUCTION CHAPTER 1 Chapter 1: General Introduction The dependence of micro-evolutionary dynamics on the environmental conditions experienced by a population is becoming increasing clear from empirical research (Hoffmann and Merila, 1999, Charmantier and Garant, 2005). Long-term individual based studies of wild vertebrate populations have provided an excellent means of assessing the impact of the environment on natural selection and levels of additive genetic variation in a variety of traits (e.g. Coulson et al, 2003, McAdam and Boutin, 2003, Charmantier et al, 2004, Garant et al, 2004, Garant et al, 2005, Wilson et al, 2005c). In this thesis, I use data collected during a long-term study of red deer (Cervus elaphus) on the Isle of Rum, Scotland, to address two important aspects of any vertebrate species' evolutionary ecology: phenotypic plasticity in life history traits and fine-scale spatial genetic structure. Phenotypic plasticity, defined as the ability of a single genotype to express different phenotypes in different environments, represents an important mechanism by which populations can respond rapidly to changes in ecological conditions. Fine scale spatial genetic structure, the non-random distribution of alleles across relatively short geographic distances, can dictate the spatial scale on which selection can act and underpins a population's evolutionary potential. Life history plasticity and fine-scale spatial genetic structure are expected in many vertebrate systems, and recent research interest in these topics has improved 1 GENERAL INTRODUCTION CHAPTER 1 our understanding of when and why they might vary between populations and species (Sugg et al, 1996, Pigliucci, 2001).