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.