Browsing by Author "Clark, Allan E"

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    Open Access
    Characteristics, determinants and management of farmer-predator conflict in a multi-use dryland system, South Africa
    (2019) Drouilly, Marine Justine; O'riain, Mannus; Nattrass Nicoli; Clark, Allan E
    Extensive livestock farming provides an important source of food and fibre for humans and is often the only commercially viable land use in the more arid regions of the globe. Pastoralism can however lead to natural habitat degradation, fragmentation of landscape by fencing and conflict between livestock farmers and predators. Collectively these impacts have been identified as major threats to biodiversity in general and predators in particular. In the semi-arid Central Karoo region of South Africa, extensive small-livestock farming is the primary use of land and provides local predators with a plentiful supply of unguarded, easy-to-catch sheep in addition to permanent artificial water sources. The result is a widespread and pervasive conflict between farmers and predators and amongst diverse stakeholders on how to best manage both livestock and predators to reduce such conflict. A major impediment to understanding human-predator conflict on farmland and its impacts on biodiversity is the paucity of relevant applied research. Most research on mesopredators in South Africa has been conducted in protected areas (PA) or at the level of a single farm, precluding the generalisation of results to broader regions, and therefore limiting our understanding of the conflict on farmlands more generally. In this thesis I sought to better understand farmer-predator conflict in the Karoo region of South Africa with an emphasis on measuring the impacts of livestock farming on wildlife in general and how predators in particular impact livestock. I hypothesized that ecological, environmental and socio-economic factors would all contribute to the negative interactions between predators and small-livestock farmers, and to the persistence of the two most prevalent predators in the region, the black-backed jackal (Canis mesomelas) and the caracal (Caracal caracal), despite sustained lethal control. I addressed this hypothesis by first using camera trapping surveys to compare wildlife species richness on farmland with a nearby and similar-sized PA to assess the impacts of small-livestock farming on wildlife diversity and occupancy, notably predators. I then used scat analysis to compare the diet of jackal and caracal with those of conspecifics living in the PA to understand whether predators on farmland are targeting livestock or simply including them opportunistically in their diet. I also used Global Positioning System (GPS) clusters from collars affixed to mesopredators to determine whether jackal and caracal actively kill versus scavenge on livestock. Finally, I performed spatially-explicit interviews using semistructured questionnaires with farmers to assess the distribution and severity of the conflict with jackal, caracal and chacma baboon (Papio ursinus), to explore the potential environmental and socio-economic drivers of reported livestock losses, the attitudes to predators and the use of lethal methods to control predators. Contrary to predictions, species richness was similar on farmland and the PA while community structure, diversity and composition all differed with land use. Species richness and probability of use both varied with environmental factors but not with human disturbance. Diet differed markedly for jackal and caracal between the two land uses, with micromammals and plants dominating mesopredator diet in the PA and livestock on farmland. By combining the results of the biodiversity surveys with the diet analysis, I was able to assess prey preference by predators on medium and large iv vertebrates. The results revealed that while both jackal and caracal consumed more livestock on farmland than wild prey, only jackal showed a preference for livestock. The results of scat and GPS cluster analyses were consistent reinforcing the findings that mesopredators actively killed livestock on farmland but not from within the PA, even when individuals crossed onto neighbouring farms. Survey results showed that farmers perceive the severity of the conflict with jackal, caracal and baboon to be increasing, especially since the 2000s. There was a positive relationship between perceived livestock losses and both environmental (e.g. terrain ruggedness) and socio-economic (e.g. decrease in farm worker numbers) factors. Surprisingly, negative attitudes towards jackal and caracal were not significantly linked to the percentage of lamb losses but rather to their belief that predators should be confined to PAs. Tolerance was best explained by the perceived aesthetic appeal of both jackal and caracal. Finally, I showed that farmers preferred to use lethal versus non-lethal control methods to manage predation, including poison, because non-lethal methods were considered to be expensive, unpractical, labour intensive and less effective. The use of poison was driven by ecological (e.g. having jackal, caracal and baboon as the top three predators on the farm) and socio-economic (e.g. decrease in farm worker numbers) factors. Together, my results suggest that jackal and caracal, like many other mesocarnivores worldwide, display a remarkable ability to adapt to human-modified landscape, using both rangeland and the PA to feed on a diverse range of prey species. Even if small-livestock farms in the Central Karoo still host important components of indigenous biodiversity, the lack of government support and incentives to protect wildlife, the changes in farming practices, the associated increase in natural habitat from which predators can recolonise commercial farmland, and the reduced labour force may together result in farmers increasing their reliance on non-selective lethal control methods to protect their livestock. Of particular concern is the widespread use of illegal poisoning. If we are to find an appropriate balance between farming and conserving biodiversity on farmland, then a new approach will be required to this very old problem. Resource-constrained conservation authorities will need to be backed by multi-stakeholders’ engagements. Farmers will need to be supported through funds to increase farm worker numbers on farms and through improved livestock husbandry measures based on scientific research conducted at the appropriate temporal and spatial scales. The conflict between predators and farmers in the Karoo is complex and multifactorial, involving environmental, ecological, and socioeconomic factors. Finding solutions to limit its impacts is a societal decision at the crux of the debate between conservation and development and requires better use of available funding and multidisciplinary teams to tackle the issue.
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    Open Access
    Efficient Bayesian analysis of occupancy models with logit link functions
    (2018) Clark, Allan E; Altwegg, Res
    Occupancy models (Ecology, 2002; 83: 2248) were developed to infer the probability that a species under investigation occupies a site. Bayesian analysis of these models can be undertaken using statistical packages such as WinBUGS, OpenBUGS, JAGS, and more recently Stan, however, since these packages were not developed specifically to fit occupancy models, one often experiences long run times when undertaking an analysis. Bayesian spatial single‐season occupancy models can also be fit using the R package stocc. The approach assumes that the detection and occupancy regression effects are modeled using probit link functions. The use of the logistic link function, however, is algebraically more tractable and allows one to easily interpret the coef‐ ficient effects of an estimated model by using odds ratios, which is not easily done for a probit link function for models that do not include spatial random effects. We de‐ velop a Gibbs sampler to obtain posterior samples from the posterior distribution of the parameters of various occupancy models (nonspatial and spatial) when logit link functions are used to model the regression effects of the detection and occupancy processes. We apply our methods to data extracted from the 2nd Southern African Bird Atlas Project to produce a species distribution map of the Cape weaver (Ploceus capensis) and helmeted guineafowl (Numida meleagris) for South Africa. We found that the Gibbs sampling algorithm developed produces posterior samples that are identical to those obtained when using JAGS and Stan and that in certain cases the posterior chains mix much faster than those obtained when using JAGS, stocc, and Stan. Our algorithms are implemented in the R package, Rcppocc. The software is freely available and stored on GitHub (https://github.com/AllanClark/Rcppocc).
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    A variational Bayes approach to the analysis of occupancy models
    (Public Library of Science, 2016) Clark, Allan E; Altwegg, Res; Ormerod, John T
    Detection-nondetection data are often used to investigate species range dynamics using Bayesian occupancy models which rely on the use of Markov chain Monte Carlo (MCMC) methods to sample from the posterior distribution of the parameters of the model. In this article we develop two Variational Bayes (VB) approximations to the posterior distribution of the parameters of a single-season site occupancy model which uses logistic link functions to model the probability of species occurrence at sites and of species detection probabilities. This task is accomplished through the development of iterative algorithms that do not use MCMC methods. Simulations and small practical examples demonstrate the effectiveness of the proposed technique. We specifically show that (under certain circumstances) the variational distributions can provide accurate approximations to the true posterior distributions of the parameters of the model when the number of visits per site ( K ) are as low as three and that the accuracy of the approximations improves as K increases. We also show that the methodology can be used to obtain the posterior distribution of the predictive distribution of the proportion of sites occupied (PAO).