This study builds on a previous study that demonstrates the existence of deep mitochondrial lineages in the gecko Tarentola boettgeri within Gran Canaria (Gubitz et al. 2005). Here, I identified and analyzed the area where the two most divergent mitochondrial •lineages meet. The primary aim was to examine how geographical structuring of mtDNA has been maintained after secondary contact. MtDNA analyses used a 608 basepair fragment of the cytochrome b (cyt b) gene from 389 individuals sampled from 14 populations along a 32 km southeast (SE) transect across Gran Canaria. It revealed a low degree of mtDNA admixture and negligible gene flow across the contact zone. This led to the hypothesis that reproductive barriers may have formed between populations from different mtDNA lineages. Analyses of seven body dimension and scalation characters revealed that spatial patterns of morphological changes were not associated with the transition in mtDNA lineage frequency across the transect. This contrasted with another lizard species on the same island, Chalcides sexlineatus, in which phylogeography and morphology are highly correlated. This study identified ten unique microsatellite markers in T. boettgeri. Like morphology, analyses of these microsatellites did not reveal a pronounced spatial pattern of differentiation in the nuclear genome. These results appear to reject the hypothesis of a physical or genetic barrier to reproduction. Studies of micro satellites also suggested that T. boettgeri is a low dispersal species and this might explain the persistence of mtDNA contact zone. However, evidence of concordant spatial patterns between divergence in the nuclear genome and morphology was detected. The discordant spatial patterns of mitochondrial and nuclear genotype frequencies do not appear to be explained by sex-biased gene flow, and are difficult to understand because of expected interactions between the two genomes. Thus, further investigation is suggested to allow clarification of the causes of mito-nuclear discordance in T. boettgeri.

In Guinea-Bissau (GB) the Guinea baboon (Papio hamadryas papio) is threatened by hunting pressure. Along with local extinctions, these practices may be inducing long-term genetic changes and disrupting underlying social structure. In this study, the bushmeat trade in GB was evaluated for the first time and the effect of hunting practices on the genetic diversity and population structure was investigated. By following the bushmeat trade at urban markets, we found baboons to be the third most traded primate species. Male baboon carcasses were sold at a price 60% higher than any other primate due to their larger body mass. Semi-structured interviews conducted with hunters revealed a preference towards male baboons and recent difficulty in finding this primates species. Non-invasive DNA sampling in southern GB and two different genetic markers (fourteen microsatellite loci and a fragment of the mitochondrial control region) suggested substantial levels of genetic diversity and recent genetic contact between different populations. However, geographic distances had a weak effect on population structure and the genetic discontinuities found were not related with landscape features. A contact zone was identified. Here, gene flow seems to be unidirectional and admixed individuals were in higher proportion. Hunting pressure may have induced recent contact between genetically differentiated individuals, which now co-exist in the same social unit. Additionally, the sex-specific patterns of gene flow and the composition of social units were compared with a non-hunted Guinea baboon population, using a molecular sex determination protocol and thirteen microsatellite loci. GB displayed a lower ratio of males within social units, which are formed in some cases by unrelated individuals. The clear female-biased dispersal pattern displayed in Senegal was less intense in GB, where gene flow seems to be mediated through both sexes. The aforementioned contact zone resulted from male immigration. Male baboon dispersal in GB could be the result of flight behaviour or a consequence of an altered sex ratio induced by hunting practices. The GB baboons displayed signs of a disrupted population and its future conservation requires specific actions to reduce or eliminate this activity.

The banteng (Bos javanicus lowi) is an endangered wild bovid that is endemic to the island of Borneo. Within their last stronghold, the Malaysian state of Sabah, their population is believed to be less than 500 individuals, which are threatened with extinction by habitat loss and hunting. The banteng is highly elusive and rarely seen, and their preference for dense and remote tropical forest habitat makes them a highly challenging species to study. No extensive quantitative surveys have been undertaken in Sabah, and there is little information available to underpin their conservation and management. This thesis provides the first baseline data on the Bornean banteng in Sabah using ecological and molecular techniques. In Chapter 2, I created the first extensive natural history account of the banteng, which will help further the knowledge of this species. This compilation helped identify gaps in the knowledge, which were then addressed by this thesis. In Chapter 3, I test non-invasive survey techniques and individual identification, and estimate the population size in two forest reserves. In Chapter 4, I demonstrate that logged forests undergo dramatic changes in structure and ambient temperature, and that banteng mitigate these changes by altering their behaviour to avoid thermal-stress. Chapter 5 presents new information of the population genetic structure of banteng in four forest reserves in Sabah. Using mitochondrial markers I show that the ancestral lineage of the Bornean banteng reinforces the suggestion that they should be recognised as a separate subspecies to the Burmese and Javan banteng. I also show that the banteng experienced a population expansion following their colonisation of Borneo, and that the present genetic diversity indicates the population may be managed as two geographically-distinct units. Chapter 6 summarises the main findings of this thesis and the implications for the conservation of the Bornean banteng in Sabah.

The endangered population of Amur tigers (Panthera tigris altaica) in the Russian Far East (RFE) faces an increasing risk of extinction due to infection with canine distemper virus (CDV). Short-lasting CDV infections are unlikely to be maintained in small populations of species with limited connectivity like tigers, where viruses fade out as susceptible hosts are depleted. Multi-host pathogens can persist in more abundant host species that can act as reservoirs of infection for threatened populations. This study combines assessments of host demography, serology and viral phylogeny to establish the relative contribution of domestic dogs and small bodied wild mesocarnivores to the maintenance of CDV, and as sources of infection for tigers. No antibodies were detected among tigers sampled prior to 2000 (n=19), but were measured in 35.7% of tigers in subsequent years (n=56), with at least five discrete transmission events occurring in one well-monitored population. Viral sequences from three tigers and one Far Eastern leopard (P. pardus orientalis) aligned within the Arctic-like clade of CDV, and shared recent common ancestry with viruses from 22 other wild carnivores from the region. Extensive spatial mixing of wild carnivore lineages suggested long chains of transmission consistent with a maintenance population. The exposure of tigers following 2000 coincides with increases in sable (Martes zibellina) numbers and hunting pressure, which could lead to greater pathogen prevalence and potential for spill over from a wild reservoir. The ratio of humans to dogs in rural areas in the RFE are among the lowest in the world (1.73), but the overall number of dogs has been stable during the period of increased CDV exposure in tigers. The only CDV sequence obtained from dogs shared high identity with Asia-4 clade viruses from dogs in Thailand, and was distantly related to wildlife sequences from the RFE. Serum antibodies were detected in dogs in all 26 communities where households were surveyed, but seroprevalence was higher in remote, less densely populated areas, suggesting possible transmission from wildlife. Although the maintenance of CDV in Russian dogs remains unconfirmed, the strong support for a wildlife reservoir limits options for managing the impact of CDV on tiger populations. The high turnover of large and often inaccessible populations of mesocarnivores combines with limitations in vaccine safety, efficacy and delivery, to render the control of CDV in a wildlife reservoir untenable. Managing the impact of CDV on Amur tigers must therefore focus on restoring the size and integrity of remaining tiger populations to withstand future outbreaks. The safety and efficacy of vaccine products for tigers should also be investigated, for use in low coverage vaccination strategies that could enhance the long-term persistence of tiger populations.