Overwhelming evidence for senescence, the within-individual decline in performance at advanced age, has now been documented in the natural populations of many taxa. As such, the focus of senescence research is shifting from simply documenting its existence, towards understanding the fundamental mechanisms underpinning it and determining which environmental factors give rise to the considerable variation in senescence rates observed in nature. In this thesis I use a wild population of European badgers (Meles meles) to investigate three important traits implicated in, or arising as a direct product of, senescence; immune cell telomere length, pro-inflammatory cytokine response and body mass declines in late life. My work reveals rare longitudinal evidence for the existence of senescence in immune traits in a wild mammal. First, I show that within-individual declines in immune cell telomere length occur with increasing age (Chapter 2). Second, after demonstrating that immune cell telomere length displays repeatable between-individual differences in adulthood, I show that the environmental conditions experienced in early-life contribute to such between-individual variation. Individuals that experienced harsh early-life environmental conditions had shorter immune cell telomere lengths than those that experienced favourable conditions (Chapter 3). Third, I show that within-individual declines in a second immune trait, pro-inflammatory cytokine response, also occur with age (Chapter 4). However, the declines in immune cell telomere length and pro-inflammatory cytokine response occur independently of one another (Chapter 4). Finally I take advantage of a 37 year longitudinal dataset to reveal that sex differences in body mass senescence arise as a consequence of the scale of intra-sexual competition experienced in early adulthood (Chapter 5). Taken together this work provides novel evidence suggesting that age-related declines in immunocompetence can contribute to whole organism senescence in the wild. Furthermore, evidence that early life environmental and social conditions can markedly influence senescence rates has important implications for our understanding of the drivers of variation in senescence rates observed within natural populations.

Auf der Ostseeinsel Rügen wurde eine 3-jährige Untersuchung zur Siedlungsstruktur, Raum- und Habitatnutzung des Dachses (Meles meles L., 1758) unter besonderer Berücksichtigung der Landschaftszerschneidung und des Landnutzungsmusters durchgeführt. Über 70 % der Inselfläche ist landwirtschaftlich, überwiegend ackerbaulich, genutzt und nur knapp ein Fünftel wird von Wald bedeckt. Während die Zersiedelung und Zerschneidung der Landschaft durch Siedlungs- und Verkehrsfläche im bundesdeutschen Vergleich als sehr gering einzustufen war, ist nach der ?Wende? eine stete Verdichtung des Straßennetzes zu beobachten, die von einem enormen Anstieg der Verkehrsdichte begleitet wird. Die Auswirkungen dieser Rahmenbedingungen wurden anhand von Nahrungsanalysen, eines inselweiten Baukatasters, Fang und Telemetrie einiger Dachse sowie einer Erfassung verkehrstoter Dachse untersucht. Die erfassten Totfunde dienten einer Abschätzung des Gefährdungspotentials unterschiedlicher Straßentypen (Bundesstraße, Landesstraße usw.). Zusätzlich wurde auf Grundlage des Baukatasters, des Totfundkatasters und von Verkehrszählungen der Zusammenhang zwischen Verkehrslast, Siedlungsdichte (des Dachses) und Verkehrsmortalität des Dachses mit Hilfe eines einfachen Modells ermittelt. / On the baltic island of Rügen investigations had been carried for 3 years with regard to distribution, space use and habitat utilization of the European badger (Meles meles L., 1758). Special attention was focused on landscape fragmentation and patterns of land use. More than 70 % of the island is agricultural, almost arable land and just under a fifth is woodland. Before 1990, fragmentation and dessection of the landscape due to housing and roads was low compared with the german average, but after the political "turn" the road system has increased constantly combined with an enormous increase in traffic density. The effect of these conditions on badgers was investigated studying diet composition, surveying and registrating badger setts all over the island, badger-watching and trapping, radio-tracking some badgers and collecting all reported badgers fallen victim to traffic accidents. Relating the road-killed badgers to the length and traffic density of the different road categories, potential danger to be killed by car was estimated. Relating the density of traffic, the density of the badger's local population and its road-mortality was done by simply using data of the sett survey, the road-killed badgers and traffic census.

Auf der Ostseeinsel Rügen wurde eine 3-jährige Untersuchung zur Siedlungsstruktur, Raum- und Habitatnutzung des Dachses (Meles meles L., 1758) unter besonderer Berücksichtigung der Landschaftszerschneidung und des Landnutzungsmusters durchgeführt. Über 70 % der Inselfläche ist landwirtschaftlich, überwiegend ackerbaulich, genutzt und nur knapp ein Fünftel wird von Wald bedeckt. Während die Zersiedelung und Zerschneidung der Landschaft durch Siedlungs- und Verkehrsfläche im bundesdeutschen Vergleich als sehr gering einzustufen war, ist nach der ?Wende? eine stete Verdichtung des Straßennetzes zu beobachten, die von einem enormen Anstieg der Verkehrsdichte begleitet wird. Die Auswirkungen dieser Rahmenbedingungen wurden anhand von Nahrungsanalysen, eines inselweiten Baukatasters, Fang und Telemetrie einiger Dachse sowie einer Erfassung verkehrstoter Dachse untersucht. Die erfassten Totfunde dienten einer Abschätzung des Gefährdungspotentials unterschiedlicher Straßentypen (Bundesstraße, Landesstraße usw.). Zusätzlich wurde auf Grundlage des Baukatasters, des Totfundkatasters und von Verkehrszählungen der Zusammenhang zwischen Verkehrslast, Siedlungsdichte (des Dachses) und Verkehrsmortalität des Dachses mit Hilfe eines einfachen Modells ermittelt. / On the baltic island of Rügen investigations had been carried for 3 years with regard to distribution, space use and habitat utilization of the European badger (Meles meles L., 1758). Special attention was focused on landscape fragmentation and patterns of land use. More than 70 % of the island is agricultural, almost arable land and just under a fifth is woodland. Before 1990, fragmentation and dessection of the landscape due to housing and roads was low compared with the german average, but after the political "turn" the road system has increased constantly combined with an enormous increase in traffic density. The effect of these conditions on badgers was investigated studying diet composition, surveying and registrating badger setts all over the island, badger-watching and trapping, radio-tracking some badgers and collecting all reported badgers fallen victim to traffic accidents. Relating the road-killed badgers to the length and traffic density of the different road categories, potential danger to be killed by car was estimated. Relating the density of traffic, the density of the badger's local population and its road-mortality was done by simply using data of the sett survey, the road-killed badgers and traffic census.

This thesis examines the space use, movement and contact rate patterns of a high- density, group-living, Eurasian badger (Meles meles) population in the UK naturally infected with bovine tuberculosis (bTB). Recently developed proximity logging devices were deployed on a representative sample of 51 badgers from eight different social groups to track their movements using radio-telemetry and to quantify their within- and between-group contact rates. Whilst interactions within social groups accounted for more than 90% of contacts, the entire study population was ultimately connected through interactions among individuals from neighbouring groups. Both within and between-group contacts, and also the use of denning sites, were heavily influenced by seasonal and demographic factors, which appear to be motivated to a large extent by reproductive behaviours. Nevertheless, by using social network analysis I found that badgers that tested positive for bTB were found to interact with fewer of their group members and for a shorter amount of time. Specifically these test-positive individuals were found to associate with test-negative group members significantly less than would be expected by chance. Those animals testing positive for bTB were also found to use outlying setts significantly more frequently than those that tested negative. The within and between-group contact rates of individuals were found to correlate with their sett use patterns. Those animals that spent less time interacting with group members and those that spent more time interacting with members of foreign social groups, were found to spend a greater proportion of their time at outlier setts. The findings in this thesis suggest a link between wider roaming behaviour and the disease status of an individual. This adds support to the argument that the social disruption of badger populations, for example through culling, may promote rather than alleviate the spread of bTB as a result of increased movement and contacts between groups. State-of-the-art technology has enabled me to demonstrate the strong influence that badger social organisation may have on the transmission of an economically significant infectious disease. My findings suggest that disease control measures might be enhanced by taking into account seasonal and individual-level variation in ranging behaviour and use of outlier setts, for example, by identifying and targeting functional groups of individuals, specific areas, or times of the year that contribute disproportionately to disease spread.

Studies of the evolution of the major histocompatibility complex (MHC) have been central to the understanding sexual selection and pathogen-mediated selection. The European badger Meles meles is well suited for exploring such questions because of its life history characteristics, reproductive biology and mating system. In this thesis, I examined both MHC class I and class II genes. Seven putatively functional sequences were found for class I genes and four for class II DRB genes. Evidence of past balancing selection of both genes was demonstrated by the d_Nd_S ratio, by positive selection at the antigen-binding site (ABS) and by trans-species polymorphism of alleles within other mustelids and carnivores. MHC class I genes also showed evidence of concerted evolution, but domains showed different evolutionary histories. MHC genes may influence microbiota and odour of an individual and influence mating preferences. I examined the bacterial community of the subcaudal gland secretion and demonstrated a high number of bacterial species (56 operational taxonomic units), which cubs exhibited a higher diversity than adults. The microbiota may lead to an individual-specific odour as a cue signaling the MHC genotype of potential mating partners. I report the first evidence for a MHC- based mating preference in carnivores. Female badgers showed a MHC-assortative mate choice towards breeding with males that had functionally similar MHC genes, for MHC class II DRB genes. This applied to neighbouring-group matings. I also found considerable annual fluctuation in the occurrence of MHC-based mate choice. Based on genome-wide background in the same mating randomizations I found no evidence of inbreeding, which indicated that MHC similarity was apparently the actual target of mate choice. In line with MHC-assortative mate choice, MHC heterozygosity had no influence on the co-infection status. Individual MHC alleles did, however, associate with resistance and susceptibility to specific pathogens, suggesting that MHC diversity may be driven and maintained by pathogen-mediated selection through rare-allele advantages and/or fluctuating selection. My study of genetic characteristics, mate choice and pathogen pressures in a wild population revealed past and contemporary evolutionary process of the MHC genes. This increases knowledge of how the MHC may affect mating behaviour and sexual selection, ultimately influencing population processes.

Diseases that infect wildlife populations pose a significant threat to public health, agriculture, and conservation efforts. The spread of these diseases can be influenced by the social structure of the population, and therefore often need to be accounted for in disease models. In this thesis I use high-resolution contact data to explore the social structure of a high-density population of European badgers (Meles meles). I explore how this structure might influence the spread of bovine tuberculosis (bTB), a debilitating disease of cattle for which badgers are a wildlife reservoir. Denning and home range data collected using radio tracking is also used to determine how this social structure is related to badger space use. I use social network analysis to identify the community structure of the badger population, revealing that badgers interact in fewer, more distinct groups than previously assumed. This is likely to inhibit the spread of disease through the population, given that the probability of infection entering a new social group will be reduced. However, among-group contact is still found to occur even between the most isolated groups. I show that this among-group contact is more likely to occur between less related individuals, possibly suggesting that breeding behaviour may drive among-group contact as a mechanism for inbreeding avoidance. To gain additional insight into this among-group contact, I determine how badger spatial behaviours are related. I show that the use of dens (setts) away from the social group’s main sett (outlier setts) in the spring is associated with extra-territorial ranging. I also show that this extra-territorial ranging is associated with more central network positions. The seasonality of this behaviour further suggests that this may be related to breeding activity. These findings suggest that behaviours associated with extra-group ranging may increase the risk of acquiring and transmitting infection. Therefore, use of outlier setts in the spring could act as a spatial proxy to identify high-risk individuals for disease spread, offering potential targets for disease control. Finally, I discuss the implications of these findings in regard to what they reveal about badger behaviour, disease transmission, and the design of effective disease control strategies. The importance of understanding population social structure for the study of wildlife disease in general is also discussed.

The evolution of extra-group paternity (EGP) is a contentious issue in evolutionary biology. This thesis examines the factors and adaptive benefits driving EGP in a high-density, group-living population of European badgers (Meles meles). To improve power to assign parentage, I isolated and characterised 21 new polymorphic microsatellite markers. I genotyped 83% of 1410 badger trapped 1987‒2010 using 35 autosomal microsatellite markers. Maternity and paternity were assigned at 80% confidence ca. 82% of individuals. 48% of paternities were extra-group, where 85% were attributable to neighbouring-group males and EGP was detected in 47% of litters; thus badger social group do not correspond with a breeding unit. I tested whether indirect genetic benefits explain these high EGP rates. (1) ‘Good-gene-as-heterozygosity Hypothesis’: Paternal heterozygosity, but not maternal or an individual’s own heterozygosity, associated positively with first-year survival probability. Under benign environmental conditions, cubs fathered by more heterozygous males had a higher first year survival probability. Despite this correlation, the EGP rate per litter correlated with neither average nor maximum within-group heterozygosity of candidate fathers. (2) Fitness benefit Hypothesis: Extra-group offspring (EGO) had lower first-year survival probability and lived 1.3 years less than within-group offspring (WGO). Female WGO produced more litters and offspring over their lifetime than female EGO, whereas male EGO produced more offspring than male WGO. (3) Inbreeding avoidance hypothesis: The EGP rate within a litter increased with greater average pair-wise relatedness between mothers and within-group candidate fathers. No inbreeding depression on first-year survival probability was detected, but small sample sizes limited statistical power. Socio-ecologically, at the litter level, EGP correlated negatively with the number of within-group candidate fathers, and positively with neighbouring-group candidate fathers. In conclusion, EGP in badgers may reduce inbreeding and be maintained in the population through a sex-specific antagonistic selection and indirect genetic benefits may occur when the total fitness benefits of producing extra-group sons outweigh the costs of producing extra-group daughters. These indirect genetic benefits only partially explain the evolution of promiscuity in European badgers, highlighting that evolutionary factors underlying promiscuity remain unclear.

Els treballs realitzats en aquesta tesi tenen com objectius l'aplicació de la sistemàtica molecular i la filogeografia per resoldre relacions filogenètiques, clarificar la taxonomia i descriure la història de les poblacions de les espècies incloses dins de dos grups de mamífers d'elevat interés conservacionista: els mustélids (família Mustelidae) i els macacs (génere Macaca).L'ús de diferents marcadors genétics mitocondrials (el gen citocrom b i la regió control) i un de nuclear (les seqüencies flanquejants d'una regió repetitiva) ha permés reconstruir les relacions filogenètiques entre 33 espècies de mustelids; delimitar quatre grups filogeogràfics en el teixò euroasiàtic (Meles meles); detectar la venta de productes derivats d'aquesta espècie en països on està protegida; i estudiar el procès d'especiació del macac japonès (Macaca fuscata). A partir dels resultats obtinguts també s'han proposat canvis en la taxonomia d'aquests grups. Al final de la tesi es fan reflexions sobre el paper que desenvolupen els marcadors moleculars en la sistemàtica, sobre com classificar aquelles espècies que no ha finalitzat els seus processos d'especiació i sobre les aplicacions de la sistemàtica, la biologia evolutiva i la genètica en la conservació de la biodiversitat. / The objectives of this thesis were the application of molecular systematics and phylogeography to resolve phylogeny, to clarify taxonomy and to study the population history of species included within two groups of mammals of high conservation interest: the mustelids (Family Mustelidae) and the macaques (Genus Macaca).Using different mitochondrial (cytochrome b gene and control region) and nuclear (flanking sequences of a repetitive region) markers, we have been able to reconstruct the phylogeny of 33 mustelid species; to delimit four phylogeographic groups in the Eurasian badger (Meles meles); to detect the trade of Eurasian badger products in countries where this species is protected; and to study the speciation process of the Japanese macaque (Macaca fuscata). According to our results we have also proposed taxonomic changes in these groups.At the end of the thesis, there are also some reflections about the role of genetic markers in systematics; about how to classify the species that have not finished their speciation process; and about the application of systematics, evolutionary biology and genetics in conservation biology.

The human use of landscape causes fragmentation and loss of original habitats. Different species vary in their sensitivity to habitat loss. Especially carnivores can be more sensitive to decrease of their habitat because of lower abundance of their prey. On the other hand several opportunistic carnivores can profit in human modified habitats. This study was carried out in the České Budějovice basin, Czech Republic during the years 2008 and 2009 and the aim of this study was to determine carnivore{\crq}s habitat preferences in the fragmented landscape. During these two years were seven carnivore species monitored in forest patches by using scent stations. Records of this monitoring were compared with physiognomy of these patches and structure of surrounding landscape.

Studies of mating systems and social organisation have been central to understanding of the evolution of social behaviour. The European badger Meles meles is a good species in which to study these processes, as its complex social system provides an opportunity to investigate how both natural and kin selection shape the evolution of mating systems and social structure. In this thesis, I use behavioural and genetic data to describe the mating system and social organisation of a high-density badger population and examine the occurrence of cooperative breeding. I genotyped 915 (85%) badgers trapped in Wytham Woods (1987–2005), 630 of which were cubs, and assigned both parents to 331 cubs with 95% confidence. This revealed a polygynandrous mating system, with up to five mothers and five fathers per social group. Mounting behaviour was also polygynandrous and I show the strongest evidence to date for multiple-paternity litters. I demonstrate, for the first time, that groups consisted of close and distant kin: approximately one third of group members were first-order kin, and overall group members had slightly lower relatedness levels than half-siblings. Within groups, adult and yearling females had higher pairwise relatedness than males, and neighbouring groups contained relatives. These findings result from the high level (42%) of extra-group paternities, 86% of which were assigned to neighbouring males. For the first time I show that females avoided inbreeding by mating with extra-group males; however, incestuous matings did occur. Promiscuous and repeated mountings were observed, which may reduce male–male aggression and infanticide, but may also promote sperm competition, genetic diversity, and / or genetic compatibility. Just under a third of adult males and females were assigned parentage each year and I quantify, for the first time, reproductive skew within badger groups. Correlations between relatedness, group productivity, and reproductive skew were not consistent with the predictions of incomplete-control models; rather, resource availability may play a role. Older and younger badgers displayed reduced annual breeding success, with male success increasing initially with experience. The Restraint, Constraint, and Selection Hypotheses did not explain the age-related breeding pattern in females. Variance in lifetime breeding success (LBS) was greater for males. Males that only bred within or only outside of their groups had half the LBS of males that did both. Females that were assigned maternity probably bred cooperatively and allonursed non-offspring, which has not been demonstrated previously. No benefit was established, however, in terms of litter size, probability of offspring breeding, or offspring lifetime breeding success, with more mothers in a group. In conclusion, badger social groups are fostered through kinship ties. Polygynandry and repeated mounting may have evolved originally to reduce male–male aggression and infanticide by males, through paternity masking. Although plural breeding occurs, group living appears to be costly. Motivation to disperse may be reduced through high-levels of extra-group paternities, which may also reduce inbreeding. Cooperative breeding among mothers may represent a low-cost behaviour with indirect benefits due to high levels of relatedness between female group-members. Badger sociality therefore represents an early stage in the evolution of social behaviour.