Deciphering patterns of genetic variation within a species is essential for understanding population structure, local adaptation and differences in diversity between populations. Whilst neutrally evolving genetic markers can be used to elucidate demographic processes and genetic structure, they are not subject to selection and therefore are not informative about patterns of adaptive variation. As such, assessments of pertinent adaptive loci, such as the immunity genes of the major histocompatibility complex (MHC), are increasingly being incorporated into genetic studies. In this study, we combined neutral (microsatellite, mtDNA) and adaptive (MHC class II DLA-DRB1 locus) markers to elucidate the factors influencing patterns of genetic variation in the African wild dog (Lycaon pictus); an endangered canid that has suffered extensive declines in distribution and abundance. Our genetic analyses found all extant wild dog populations to be relatively small (N(e) < 30). Furthermore, through coalescent modelling, we detected a genetic signature of a recent and substantial demographic decline, which correlates with human expansion, but contrasts with findings in some other African mammals. We found strong structuring of wild dog populations, indicating the negative influence of extensive habitat fragmentation and loss of gene flow between habitat patches. Across populations, we found that the spatial and temporal structure of microsatellite diversity and MHC diversity were correlated and strongly influenced by demographic stability and population size, indicating the effects of genetic drift in these small populations. Despite this correlation, we detected signatures of selection at the MHC, implying that selection has not been completely overwhelmed by genetic drift.

Legislative changes during the 1960s-1970s granted user rights over wildlife to landowners in southern Africa, resulting in a shift from livestock farming to wildlifebased land uses. Few comprehensive assessments of such land uses on private land in southern Africa have been conducted and the associated benefits are not always acknowledged by politicians. Nonetheless, wildlife-based land uses are growing in prevalence on private land. In Namibia wildlife-based land use occurs over c. 287,000 km 2 . Employment is positively related to income from ecotourism and negatively related to income from livestock. While 87% of meat from livestock is exported $ 95% of venison from wildlife-based land uses remains within the country, contributing to food security. Wildlife populations are increasing with expansion of wildlife-based land uses, and private farms contain 21-33 times more wildlife than in protected areas. Because of the popularity of wildlife-based land uses among younger farmers, increasing tourist arrivals and projected impacts of climate change on livestock production, the economic output of wildlife-based land uses will probably soon exceed that of livestock. However, existing policies favour livestock production and are prejudiced against wildlife-based land uses by prohibiting reintroductions of buffalo Syncerus caffer, a key species for tourism and safari hunting, and through subsidies that artificially inflate the profitability of livestock production. Returns from wildlife-based land uses are also limited by the failure to reintroduce other charismatic species, failure to develop fully-integrated conservancies and to integrate black farmers sufficiently.

Changing land use patterns in southern Africa have potential to dramatically alter the prospects for carnivore conservation. Understanding these influences is essential for conservation planning. We interviewed 250 ranchers in Namibia to assess human tolerance towards and the distribution of large carnivores. Cheetahs (Acinonyx jubatus), leopards (Panthera pardus) and brown hyaenas (Hyaena brunnea) were widely distributed on Namibian farmlands, spotted hyaenas (Crocuta crocuta) had a narrower distribution, and wild dogs (Lycaon pictus) and lions (Panthera leo) are largely limited to areas near source populations. Farmers were most tolerant of leopards and least tolerant of lions, wild dogs and spotted hyaenas. Several factors relating to land use correlated consistently with carnivore-presence and landowner tolerance. Carnivores were more commonly present and/or tolerated where; wildlife diversity and biomass were higher; income from wildlife was higher; income from livestock was lower; livestock biomass was lower; in conservancies; game fencing was absent; and financial losses from livestock depredation were lower. Efforts to create conditions whereby the costs associated with carnivores are lowest, and which confer financial value to them are likely to be the most effective means of promoting carnivore conservation. Such conditions are achieved where land owners pool land to create conservancies where livestock are replaced with wildlife (or where livestock husbandry is improved) and where wildlife generates a significant proportion of ranch income. Additional measures, such as promoting improved livestock husbandry and educational outreach efforts may also help achieve coexistence with carnivores. Our findings provide insights into conditions more conducive to the persistence of and tolerance towards large carnivores might be increased on private (and even communal) lands in Namibia, elsewhere in southern and East Africa and other parts of the world where carnivore conservation is being attempted on private lands.

a b s t r a c tInfectious diseases impact African wild dogs (Lycaon pictus), but the nature and magnitude of this threat likely varies among populations according to different factors, such as the presence and prevalence of pathogens and land-use characteristics. We systematically evaluated these factors to assist development of locally appropriate strategies to mitigate disease risk. Wild dogs from 16 sites representing five unconnected populations were examined for rabies virus, canine distemper virus (CDV), canine parvovirus, canine coronavirus, and Babesia spp. exposure. Analyses revealed widespread exposure to viral pathogens, but Babesia was never detected. Exposure to CDV was associated with unprotected and protected-unfenced areas where wild dogs likely have a high probability of domestic dog contact and, in the case of protected-unfenced areas, likely reside amongst high wildlife densities. Our findings also suggest that domestic dog contact may increase rabies and coronavirus exposure risk. Therefore, domestic dogs may be a source of CDV, rabies and coronavirus, while wildlife may also play an important role in CDV transmission dynamics. Relatively high parvovirus seroprevalence across land-use types suggests that it might persist in the absence of spillover from domestic dogs. Should intervention be needed to control pathogens in wild dogs, efforts to prevent rabies and coronavirus exposure might be directed at reducing infection in the presumed domestic dog reservoir through vaccination. If prevention of CDV and parvovirus infections were deemed a management necessity, control of disease in domestic dogs may be insufficient to reduce transmission risks, and vaccination of wild dogs themselves may be the optimal strategy.

The Kavango–Zambezi Transfrontier Conservation Area Programme promotes landscape-level connectivity between clusters of wildlife management areas in five neighbouring countries. However, declining regional biodiversity can undermine efforts to maintain, expand and link wildlife populations. Narratives promoting species connectivity should thus be founded on studies of system and state changes in key resources. By integrating and augmenting multiple data sources throughout eight wildlife management areas, covering 1.7 million ha, we report changes during 1978–2015 in the occurrence and distribution of 31 mammal species throughout a landscape linking the Greater Kafue System to adjacent wildlife management areas in Namibia and Botswana. Results indicate species diversity is largely unchanged in Kafue National Park and Mulobezi and Sichifulo Game Management Areas. However, 100% of large carnivore and 64% of prey diversity have been lost in the Simalaha areas, and there is no evidence of migrational behaviour or species recolonization from adjacent wildlife areas. Although temporal sampling scales influence the definition of species occupancy and distribution, and data cannot elucidate population size or trends, our findings indicate an emerging connectivity bottleneck within Simalaha. Evidence suggests that at current disturbance levels the Greater Kafue System, Zambia's majority component in the Kavango–Zambezi Transfrontier Conservation Area, is becoming increasingly isolated at the trophic scale of large mammals. Further investigations of the site-specific, interacting drivers influencing wildlife distribution and occurrence are required to inform appropriate conservation interventions for wildlife recovery in key areas identified to promote transboundary connectivity in the Kavango–Zambezi Transfrontier Conservation Area.