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Europe’s largest population of wild red deer (Cervus elaphus) resides in the British Isles and has been present since the end of the last ice age, c. 11,000BP. Since the mid-19th century, multiple introductions of Japanese sika (Cervus nippon) and wapiti (Cervus canadensis) have taken place across the British Isles. While wapiti introductions have generally gone extinct, sika have thrived and expanded and now often live in sympatry with red deer. Hybridisation between these species has been demonstrated in captivity and in the wild. This study sought to determine the extent of hybridisation and introgression between red and sika across large parts of the British Isles and elucidate some of its potential consequences. Chapter 2 addresses the extent of hybridisation and introgression across Scotland and NW England. A total of 2984 samples from the North Highlands, the central Highlands, the Hebrides, Kintyre and the English Lake District were genotyped at 22 microsatellite loci, which are highly diagnostic for red and sika and strongly diagnostic for red and wapiti and a mitochondrial marker that is diagnostic for red and sika, alongside 49 wapiti samples from Canada. Microsatellite data was analysed using the Bayesian clustering program Structure 2.3 to determine the extent of admixture between species. There was some evidence for very low-level introgression by wapiti into a small number of Scottish red deer (<0.2% of total). Only two areas (both in Kintyre, Argyll) showed extensive introgression with collapse of assortative mating between red and sika (50.4% and 61.8% of sampled individuals were hybrid in West Loch Awe and South Kintyre, respectively). However, rare and widely scattered individuals with low-level sika introgression or cytonuclear disequilibrium suggest hybridisation has occurred in several other places in mainland Scotland and Cumbria in the past without subsequent loss of assortative mating. Chapter 3 addresses the extent of hybridisation in Ireland. There are now an estimated 4,000 red deer in Ireland and their numbers are increasing. It has recently been determined that the red deer in Killarney, County Kerry are descended from an ancient (c. 5,000BP) introduction and therefore merit genetic conservation. Introduction of exotic species, including Japanese sika and North America wapiti, since the 19th century have primarily occurred via the now defunct Powerscourt Park, County Wicklow, which was the source of many translocations to the rest of Ireland as well as to the UK. 374 deer samples from across Ireland were analysed as in Chapter 2. Wapiti introgression was again very low, with trace amounts of introgression detected in a small proportion of samples (0.53%), whilst 41% of 197 deer sampled in Co. Wicklow and 47% of 15 deer sampled in Co. Cork were red-sika hybrids according to either their nuclear genome or mitochondrial haplotype. No pure red deer were detected in Co. Wicklow, suggesting that in this region the red deer has disappeared following hybridisation. Whilst no hybrids were detected among 37 red samples and 77 sika samples in Co. Kerry, the Co. Cork hybrids pose a threat to the Killarney populations due to their proximity. Chapter 4 investigates population genetic structure within red and sika populations across the British Isles and investigates whether low-level introgression by the other species influences the resolved population structure. Structure analysis was conducted separately using 2307 ‘pure’ red deer individuals and 752 ‘pure’ sika animals from the British Isles (defined as Q > 0.95 for red and Q < 0.05 for sika) and then on reduced sample sizes using more stringent purity criteria (Q ≥ 0.99 and Q ≤ 0.01). As might be predicted, the more stringent criteria removed individuals in areas known to contain advanced backcrosses. In red deer, there was some evidence for a loss of within-species population structure under the more stringent criteria, while for sika there was not. Datasets were also analysed using Discriminate Analysis of Principal Components; a multivariate method designed to infer and describe genetic population structure. In red deer, both analytical approaches confirmed the strong separation of the deer on Harris and Lewis from others, and there is support for clusters typified by the other Hebridean islands, Kintyre, central and North Scotland and the English sites. Among sika, both approaches supported the likelihood of three clusters which are presumably the result of bottleneck events as each introduction was made. Chapter 5 investigates the phenotypic consequences of hybridisation by three approaches. Firstly, carcass weight was regressed against genetically-determined hybrid scores (at two stringency levels, see Chapter 4) and heterozygosity (in terms of red and sika alleles). Among hybrids, carcass weight is linearly related to hybrid score (Q) and there is some evidence for a positive relationship with heterozygosity. This suggests that additive genetic variation explains variation in carcass weight to a greater extent than heterosis. Secondly, analysis of five case studies representing individual putative hybrids submitted by stalkers from areas without known hybridisation, two proved to be hybrids, while the other three were pure sika. Lastly, in regions known to contain hybrids, the accuracy of ranger-assigned phenotype averaged 78% and revealed that in Scotland accuracy tends to decline as an individual becomes more genetically intermediate; whilst in Co. Wicklow it is the identification of pure parental animals that is more challenging. In conclusion, the existence of rare and widely scattered advanced red-sika backcrosses with low-level nuclear introgression and/or mitochondrial introgression (e.g. in North of Scotland, Cumbria) highlight that some hybridisation events are followed by extensive backcrossing without the breakdown of assortative mating, while others are followed by the generation of a hybrid swarm (e.g. in South Kintyre, West Loch Awe, Co. Wicklow, Co. Cork). Phenotypic traits can become intermediate due to hybridisation and this may facilitate further gene flow and hybridisation. New molecular tools including next generation sequencing (NGS) will enable better understanding the hybridisation process and its phenotypic consequences in this and other systems.

Whilst individual differences in circulating hormone levels can influence life history traits throughout an animal’s lifetime, this remains a poorly understood area of research, particularly for wild systems where sufficient sets of individual-based data are rare. This thesis aimed to address this dearth of information by identifying key drivers of hormone variation, as well as exploring potential fitness consequences within a single system of wild red deer (Cervus elaphus) on the Isle of Rum National Nature Reserve in Scotland. It focussed on both androgen (e.g. testosterone) and glucocorticoid (e.g. cortisol) levels, and examined among-individual variation in these two hormone groups from samples collected using both traditional (blood: chapters 3 & 4) and non-invasive (faecal: chapters 5 & 6) methods. Results showed both intrinsic and extrinsic factors to influence an individual’s hormone levels. In general, current or recent environment explained the greatest variation, with both hormone groups exhibiting strong temporal trends at multiple scales. Concentrations changed substantially across an individual’s lifetime as they aged (chapters 5 & 6), and calves born in different years differed in their neonatal testosterone levels (chapter 3). Hormone levels also varied across the year, showing clear seasonal cycles which peaked during key reproductive events: the calving season in females (chapter 6) and the rut in males (chapter 5). An individual’s current life history state was also important, particularly a female’s reproductive state (chapter 6). Whilst there was some evidence of maternal effects on neonatal hormone levels (chapter 3) these were not extensive, and maternal hormone concentrations did not appear to influence those in their new-born calves (chapter 6). There was, however, evidence of neonatal circulating testosterone levels being heritable, and despite overall differences between the sexes the underlying genetic architecture of this trait did not differ between male and female calves (chapter 4). Associations were also found between an individual’s hormone levels and their fitness, although these consequences were only apparent in short-term fitness measures or proxies such as reproductive behaviour (e.g. male reproductive effort in chapter 5). Effects were also not ubiquitous within the population. Whilst a calf’s circulating testosterone levels indicated their probability of surviving their first year of life, these effects were only apparent in firstborn males, a group which is particularly vulnerable to mortality (chapter 3). In general, this thesis suggests that the fitness consequences identified by broad-scale hormone manipulation studies can still be found when looking at subtle individual-level differences. The limited evidence of persistent hormone phenotypes (indicated by the lack of among individual variance for most measures, chapter 5 & 6) does, however, emphasise the importance of repeatedly sampling individuals before drawing extensive conclusions about fitness consequences.

Au cours des 60 dernières années le développement des infrastructures de transports (Autoroutes, Lignes Grandes Vitesse, Nationales doubles voies) a fragmenté l'habitat des cerfs élaphe (Cervus elaphus). D'après les observations naturalistes, cette anthropisation a causé la fragmentation de deux populations géographiques existantes en sept dans la partie Sud et d'une en trois dans la partie Nord. Afin d'évaluer l'impact de ces infrastructures sur la structuration génétique de ces populations de cerfs, nous avons échantillonné chacune de ces populations grâce à la coopération de trois fédérations de chasse. Le cours laps de temps écoulé depuis la construction de ces infrastructures nous a conduits à choisir comme marqueurs moléculaires les microsatellites, efficaces dans l'inférence d'évènements récents. Les nouvelles techniques de séquençages (NGS) permettent d'obtenir d'importants jeux de données rapidement, nous avons choisi d'utiliser ces méthodes de séquençage pour obtenir nos données. Aucun logiciel ne permettant de traiter les données de séquençage haut débit des microsatellites pour des espèces dont le génome n'est pas complètement séquencé, nous avons alors réalisé un programme, MicNeSs qui permet de génotyper rapidement et objectivement (sans intervention humaine) un grand nombre d'individus et de locus. Nous avons utilisé MicNeSs pour génotyper 345 individus pour 17 locus microsatellites. A partir de ce jeu de données, nous avons montré l'existence d'une structuration génétique des populations de cerfs élaphe en Île-de-France en liaison avec les infrastructures routières et ferroviaires. Nous avons mis en évidence un effet fort des jumelages autoroutes/LGV et une efficacité différentielle des passages grande faune de 2ème et 3ème génération sur les populations de cerfs élaphe en Île-de-France. / During the last 60 years, the development of urban areas, main roads, highways and railways in Île de France, has fragmented the habitat of the red deer (Cervus elaphus). According to naturalistic observations, it caused the fragmentation of the two existing putative populations in the South in to seven putative populations and one in three in the North.In order to estimate the impact of the infrastructure on the genetic structure of these populations we sampled each of the putative population with the help of three hunting societies. Due to the short time passed since the first highway construction we chose microsatellite loci as molecular markers, efficient in the inference of recent events. The next generation sequencing (NGS) enable to have quickly important data set, we chose to use this technic to obtain our data. No software permits to treat microsatellites data from NGS for the species without complete genome, we made one program, MicNeSs which genotypes quickly and objectively a lot of individuals and loci. We used MicNeSs to genotype 345 individuals for 17 microsatellite loci. With this data set we showed the presence of a genetic structure of the red deer populations in association with the road and rail infrastructure. We highlighted a strong impact of the paired of highway/railway and a differential efficiency of the wildlife passages of the second and third generation on the red deer populations in Île-de-France.