Combining surveillance data from, and comparing the relative utility of wildlife sentinels for detecting bovine tuberculosis in New Zealand

Brushtail possums (Trichosurus vulpecula) are the main wildlife host of bovine tuberculosis in New Zealand. The disease cycle can be broken by intensive large-scale reduction of possum populations to low levels. That strategy has been successfully applied over much of New Zealand, to the point that a key question now is whether the disease has indeed been locally eliminated, so that the expensive disease control programme can be stopped. However, it is usually too expensive to survey the few possums left. We have therefore developed a new approach to characterising the Tb detection capabilities of any wild animal species that can host the disease. The approach assigns each individual animal and spatially-explicit “detection kernel” that combines data on average range utilisation with probabilities of becoming infected when Tb is present in possums at the lowest sustainable level. We describe the principles involved, and compare the detection capabilities and cost-effectiveness across the species that are commonly being used for this purpose – wild pigs (Sus scrofa), ferrets (Mustela furo), and deer (Cervus spp.).     

Spatially-explicit wildlife surveillance to prove freedom from diseases or pests

Surveillance undertaken to prove freedom from a disease has traditionally focussed on sampling a specified proportion of the population to determine the presence of the infective agent. Based on a sample of individuals testing negative for disease, standard probability theory using the binomial or hypergeometric distribution can be used to make inference about the probability of disease being absent. However, if the disease agent involves a wildlife host, then determining what proportion of the population was sampled becomes problematic as it requires an estimate of population abundance, which may be difficult and expensive to obtain. Surveillance during the eradication of pests such as feral ungulates often make use of the Judas technique, whereby radio-collared individuals are released and followed in the hope that the sociality of the individuals will betray the locations of conspecifics, which can then be dispatched. Data collected during such surveillance is explicitly spatial, containing information about the ‘search area’ of the Judas animal. However, there has been no attempt to use such data to make inference about the probability of the area being free of the pest, given Judas animals fail to detect any conspecifics. We present a framework for making specific use of the spatial nature of such wildlife surveillance data to make inference about the probability of freedom from the disease or pest. Underlying the sampling framework is a model of the detection process by sampled individuals. Estimates of individual detection probability are spatially smoothed using the extent of individual movements to produce a spatially- explicit detection surface. Bayes theorem is then used to combine this 2-dimensional surface with prior information on the probability of pest or disease presence, prior to sampling, to estimate the probability that the area is free from the disease or pest, given surveillance fails to detect evidence of their presence. We illustrate the method with examples of the detection of bovine Tb in wildlife in New Zealand and the detection of pigs (Sus scrofa) using the Judas technique during the feral pig eradication programme on Santa Cruz Island, California.     

New approaches to tuberculosis surveillance in nonhuman primates

Despite significant progress in reducing the incidence of tuberculosis in nonhuman primates (NHPs) maintained in captivity, outbreaks continue to occur in established colonies, with potential serious consequences in human exposures, animal losses, disruption of research, and costs related to disease control efforts. The intradermal tuberculin skin test (TST) using mammalian old tuberculin (MOT) has been the mainstay of NHP tuberculosis surveillance and antemortem diagnosis for more than 60 years. But limitations of the TST, particularly its inability to reliably identify animals with latent TB infections, make it unsuitable for use as a single, standalone test for TB surveillance in nonhuman primates in the 21st century. Advances in technology and the availability of Mycobacterium spp. genomic sequence data have facilitated the development and evaluation of new immune-based screening assays as possible adjuncts and alternatives to the TST, including in vitro whole blood assays that measure the release of interferon gamma in response to stimulation with tuberculin or specific mycobacterial antigens, and assays that detect antibodies to highly immunogenic secreted proteins unique to M. tuberculosis, M. bovis, and other species belonging to the M. tuberculosis complex. It is becoming apparent that no single screening test will meet all the requirements for surveillance and diagnosis of tuberculosis in nonhuman primates. Instead, the use of several tests in combination can increase the overall sensitivity and specificity of screening and surveillance programs and likely represents the future of TB testing in nonhuman primates. In this article we describe the characteristics of these newer screening tests and discuss their potential contributions to NHP tuberculosis surveillance programs.     

Radionuclide concentration ratios in Australian terrestrial wildlife and livestock: data compilation and analysis

Radionuclide concentrations in Australian terrestrial fauna, including indigenous kangaroos and lizards, as well as introduced sheep and water buffalo, are of interest when considering doses to human receptors and doses to the biota itself. Here, concentration ratio (CR) values for a variety of endemic and introduced Australian animals with a focus on wildlife and livestock inhabiting open rangeland are derived and reported. The CR values are based on U- and Th-series concentration data obtained from previous studies at mining sites and ²⁴¹Am and ^239/240Pu data from a former weapons testing site. Soil-to-muscle CR values of key natural-series radionuclides for grazing Australian kangaroo and sheep are one to two orders of magnitude higher than those of grazing cattle in North and South America, and for ²¹⁰Po, ²³⁰Th, and ²³⁸U are one to two orders of magnitude higher than the ERICA tool reference values. When comparing paired kangaroo and sheep CR values, results are linearly correlated (r = 0.81) for all tissue types. However, kidney and liver CR values for kangaroo are typically higher than those of sheep, particularly for ²¹⁰Pb, and ²¹⁰Po, with values in kangaroo liver more than an order of magnitude higher than those in sheep liver. Concentration ratios for organs are typically higher than those for muscle including those for ²⁴¹Am and ^239/240Pu in cooked kangaroo and rabbit samples. This study provides CR values for Australian terrestrial wildlife and livestock and suggests higher accumulation rates for select radionuclides in semi-arid Australian conditions compared with those associated with temperate conditions.     

Combining genetic and ecological data to assess the conservation status of the endangered Ethiopian walia ibex

Knowledge about the phylogenetic history, genetic variation and ecological requirements of a species is important for its conservation and management. Unfortunately, for many species this information is lacking. Here we use multiple approaches (phylogenetics, population genetics and ecological modelling) to evaluate the evolutionary history and conservation status of Capra walie , an endangered flagship species of wild goat endemic to Ethiopia. The analysis of mitochondrial cytochrome b and Y-chromosome DNA sequences suggests that C. walie forms a monophyletic clade with Capra nubiana , but potentially has been isolated for up to 0.8 million years from this closely related species. Microsatellite DNA analyses show that C. walie has very low genetic variation (mean heterozygosity=0.35) compared with other endangered mammals. This reduced variation likely derives from a prolonged demographic decline and small effective population size. Ecological niche modelling using the bioclimatic features of habitats occupied by C. walie , suggests ecological differences between C. walie and C. nubiana , and identifies the areas most suitable for future reintroductions of C. walie . The genetic and bioclimatic data suggest that C. walie is distinct and requires immediate conservation actions including genetic monitoring and reintroductions to establish independent populations. This study illustrates how combining noninvasive sampling along with genetic and ecological (bioclimatic) approaches can help assess conservation status of poorly known species.     

Combining immunological and molecular data to assess phylogenetic relations of some Greek Podarcis species

Most recent molecular studies revealed the phylogeny of Greek Podarcis species, which for years remained elusive, due to discordant data produced from various chromosomal, complement fixation and protein studies. In this report, we analyzed cellular immune responses of spleen-derived lymphocytes from six allopatric Podarcis species encountered in Greece, by assessing two-way mixed lymphocyte reaction (MLR)-induced proliferation. On the basis of stimulation indices (S.I.) as determined from cultures set up from xenogeneic splenocytes coincubated in pairs, we generated a phylogenetic tree, fully consistent with the phylogenetic relationships of Podarcis as determined by parallel analyses based on partial mitochondrial (mt) DNA sequences. Although the exact mechanisms triggering lymphocyte responses in lizard two-way xenogeneic MLR are not fully understood, our results show the potential use of cell-mediated immune responses as an additional approach to mtDNA analysis, for species delimitation within specific lizard taxa.     

Protected species and predator detection dog use in New Zealand wildlife conservation projects

In many New Zealand threatened species (birds, lizards, frogs, invertebrates) recovery programmes dogs are a significant conservation management tool. Protected species detection dogs have regularly been used to locate rare birds since the 1970’s and more recently lizards. They have been used to detect, but not capture, kakapo, takahe, kiwi, whio, pateke, taiko, skinks and geckos, for monitoring and translocation purposes. Kakapo would possibly be extinct today if dogs had not been used to locate birds on Stewart Island and Fiordland for translocation to predator-free islands before predators and old age eliminated these original remnant populations. Use of these dogs on the kiwi recovery projects has advanced the progress of these projects by about ten years. Predator detection dogs support threatened species recovery programmes and their role is to enhance other predator control methods. They have been regularly used since 2002 following a successful three-year pilot project to prove their usefulness. These dogs are used to detect the presence of mammalian predators including rodents, mustelids, cat and hedgehog. They are particularly useful when predator numbers are low when other predator detection methods (tracking tunnels, traps, gnaw sticks) have difficulty confirming their presence. Once detected by the dogs the predators are killed using toxins, traps or shooting. Dogs are used for: surveillance of supposedly predator-free sites; as a tool to focus predator a process of handler application and interview, and a two-step assessment and certification system for dogs and handlers guide these Department of Conservation dog programmes. There are currently 11 predator dog handlers and 26 protected species dog handlers in the programmes.     

Combining capture–recapture data and pedigree information to assess heritability of demographic parameters in the wild

Quantitative genetic analyses have been increasingly used to estimate the genetic basis of life‐history traits in natural populations. Imperfect detection of individuals is inherent to studies that monitor populations in the wild, yet it is seldom accounted for by quantitative genetic studies, perhaps leading to flawed inference. To facilitate the inclusion of imperfect detection of individuals in such studies, we develop a method to estimate additive genetic variance and assess heritability for binary traits such as survival, using capture–recapture (CR) data. Our approach combines mixed‐effects CR models with a threshold model to incorporate discrete data in a standard ‘animal model’ approach. We employ Markov chain Monte Carlo sampling in a Bayesian framework to estimate model parameters. We illustrate our approach using data from a wild population of blue tits (Cyanistes caeruleus) and present the first estimate of heritability of adult survival in the wild. In agreement with the prediction that selection should deplete additive genetic variance in fitness, we found that survival had low heritability. Because the detection process is incorporated, capture–recapture animal models (CRAM) provide unbiased quantitative genetics analyses of longitudinal data collected in the wild.     

Control of bovine tuberculosis in British livestock: there is no 'silver bullet'

Bovine tuberculosis (bTB; Mycobacterium bovis) is a bacterial infection of cattle that also affects certain wildlife species. Culling badgers (Meles meles), the principal wildlife host, results in perturbation of the badger population and an increased level of disease in cattle. Therefore, the priority for future management must be to minimize the risk of disease transmission by finding new ways to reduce the contact rate among the host community. At the farm level, targeting those individuals that represent an elevated risk of transmission might prove to be effective. At the landscape level, risk mapping can provide the basis for targeted surveillance of the host community. Here, we review the current evidence for bTB persistence in Britain and make recommendations for future management and research.     

Reconstructing demographic events from population genetic data: the introduction of bumblebees to New Zealand

Four British bumblebee species (Bombus terrestris, Bombus hortorum, Bombus ruderatus and Bombus subterraneus) became established in New Zealand following their introduction at the turn of the last century. Of these, two remain common in the United Kingdom (B. terrestris and B. hortorum), whilst two (B. ruderatus and B. subterraneus) have undergone marked declines, the latter being declared extinct in 2000. The presence of these bumblebees in New Zealand provides an unique system in which four related species have been isolated from their source population for over 100 years, providing a rare opportunity to examine the impacts of an initial bottleneck and introduction to a novel environment on their population genetics. We used microsatellite markers to compare modern populations of B. terrestris, B. hortorum and B. ruderatus in the United Kingdom and New Zealand and to compare museum specimens of British B. subterraneus with the current New Zealand population. We used approximate Bayesian computation to estimate demographic parameters of the introduction history, notably to estimate the number of founders involved in the initial introduction. Species-specific patterns derived from genetic analysis were consistent with the predictions based on the presumed history of these populations; demographic events have left a marked genetic signature on all four species. Approximate Bayesian analyses suggest that the New Zealand population of B. subterraneus may have been founded by as few as two individuals, giving rise to low genetic diversity and marked genetic divergence from the (now extinct) UK population.     

Combining fossil and molecular data to date the diversification of New World Primates

Recent methodological advances in molecular dating associated with the growing availability of sequence data have prompted the study of the evolution of New World Anthropoidea in recent years. Motivated by questions regarding historical biogeography or the mode of evolution, these works aimed to obtain a clearer scenario of Platyrrhini origins and diversification. Although some consensus was found, disputed issues, especially those relating to the evolutionary affinities of fossil taxa, remain. The use of fossil taxa for divergence time analysis is traditionally restricted to the provision of calibration priors. However, new analytical approaches have been developed that incorporate fossils as terminals and, thus, directly assign ages to the fossil tips. In this study, we conducted a combined analysis of molecular and morphological data, including fossils, to derive the timescale of New World anthropoids. Differently from previous studies that conducted total‐evidence analysis of molecules and morphology, our approach investigated the morphological clock alone. Our results corroborate the hypothesis that living platyrrhines diversified in the last 20 Ma and that Miocene Patagonian fossils compose an independent evolutionary radiation that diversified in the late Oligocene. When compared to the node ages inferred from the molecular timescale, the inclusion of fossils augmented the precision of the estimates for nodes constrained by the fossil tips. We show that morphological data can be analysed using the same methodological framework applied in relaxed molecular clock studies.     

Using regional wildlife surveys to assess the CRP: scale and data-quality issues

ABSTRACT.   Evidence that the Conservation Reserve Program (CRP) has resulted in large-scale increases in populations of grassland birds is limited. Detecting large-scale CRP effects is difficult because agricultural landscapes are complex, dynamic systems where many concurrent changes are occurring across space and time, and CRP is only one of many factors influencing wildlife populations. Trying to isolate and quantify the contribution of CRP to large-scale population changes under these conditions is extremely difficult and tenuous. Data-quality issues affecting many large-scale monitoring programs exacerbate the problem. We use a case study of land-use and pheasant-monitoring data in Minnesota from 1974–1997 to illustrate these problems. In our example, roadside counts of Ring-necked Pheasants ( Phasianus colchicus ) were correlated positively with percent of CRP grasslands within 1.6 km of survey routes, but the predicted change in mean pheasant counts (pre-CRP vs. CRP) was negative in three of five regions despite the addition of up to 8% CRP grasslands. We also documented concurrent losses (1.8%–6.1% per year) of alternative reproductive habitats that apparently counteracted the positive association between pheasant counts and CRP abundance. These results illustrate the need for a more comprehensive evaluation of Farm Bill effects on wildlife, including commodity provisions that lead to conversion of pasture, hayland, and small grains to row crops.     

Sterilization as an alternative strategy to control wildlife diseases: bovine tuberculosis in European badgers as a case study

Sterilization has rarely been considered as an alternative to culling or vaccination to control wildlife diseases. Disease control by sterilization, as by culling, has most promise when the host'ss ability for compensatory growth following the removal of density-dependent inhibitions is limited, and when moderate reductions in population density cause disproportionately large reductions in disease prevalence, or even eliminate the disease. For many host/disease examples this will not be the case and vaccination may have overwhelming advantages or may be the only practical option. The impact of sterilization on host density and disease prevalence will develop relatively slowly because sterilization can prevent the recruitment of only one age-cohort at a time. Moreover, unless there is vertical transmission, this age-cohort will consist only of susceptibles. Culling, on the contrary, removes infected as well as susceptible animals. However, for certain disease/host examples, the r elative effectiveness of the different control strategies may be altered considerably if their variable effects on the probability of disease transmission are taken into account. Social perturbation or stress could render certain culling strategies ineffective or even counter-productive. Depending on how disease dynamics are influenced by the host'ss age-structure and reproductive investment, fertility control could offer epidemiological advantages that have been ignored by most disease/host models. We illustrate some of these principles by investigating the theoretical and practical feasibility of an hypothetical sterilization campaign to control bovine tuberculosis in badgers (and hence cattle) in Britain.     

The cost of livestock lost to lions and other wildlife species in the Amboseli ecosystem,Kenya

Though retaliatory lion (Panthera leo) killing as a result of livestock predation in the Maasai group ranches between the Tsavo NPs and Amboseli is remarkably high, other wildlife species are known to kill livestock. Surprisingly, lions suffer the most from retaliatory killing by the Maasai community for killing livestock. The extent of livestock predation by lions in comparison to other species is unknown. This study was carried out in the Olgulului group ranch (OGR) located adjacent to Amboseli National Park in June 2009. The cost of livestock killed by each of these species including lion, hyena (Crocuta crocuta), cheetah (Acynonyx jubatus), leopard (Panthera pardus), olive baboon (Papio cynocephalus), black-backed jackal (Canis mesomelas), and African elephant (Loxodonta africana) was analyzed. Questionnaires, focus group discussions, and key informant interviews with officials from OGR, Kenya Wildlife Service (KWS), and compensation scheme organizations were the methods used to collect information. Cluster and systematic sampling techniques were used to select a sample of 199 respondents from OGR. Lions were blamed for 40.5% (US$ 374,603) of the value of livestock lost to wildlife. The costs of livestock lost to hyenas and lions were not significantly different (q = 0.24, p = 0.968). Although hyenas killed more livestock compared to lions, the economic damage between the two was not significantly different because lions attacked cattle which had high economic value. Conservation of lions will be increasingly difficult if the current levels of predation are not reduced to economically and socially acceptable levels.     

Strategies to estimate national forest carbon stocks from inventory data: the 1990 New Zealand baseline

An estimate of live tree carbon stored in New Zealand forests at 1990 was made to partially satisfy New Zealand's international obligations under the Framework Convention for Climate Change. A national database was compiled of 4956 forest inventory plots measured as recently as possible to 1990. Plot biomass estimates were obtained by applying species allometric relationships derived from harvested stands. Forest areas and classes were taken from a 1987 national map of vegetation cover. Regularly spaced grids, based on an initial 1 km × 1 km grid, were overlaid on the total forest area and plots were tested for bias against site characteristics at the grid points. As grid point density and sample size increased, bias was minimal in regional sampling intensity and in total annual precipitation. Differences in mean elevation and annual temperature remained stable as grid point density increased, and showed little correlation with stem biomass. This sampling method gave a measure of precision not available from previous estimates. An efficient sample size to estimate the mean within a 5% level of precision (at 95% probability) required a sample of 574 plots selected from a 4‐km grid. This strategy generated a mean estimate for the 1990 New Zealand forest carbon biomass of 179.3 ± 4.9 Mg ha^?1 (± SE), totalling 919.1 ± 25.1 Mt for the 5.1 million ha mapped forest area. The mean was 6–10% lower than previous estimates, and was within the range reported for other countries. Within forest classes, mean carbon biomass ranged from 105 Mg ha^?1 in pure podocarp forest to 215 Mg ha^?1 in mixed lowland podocarp–broadleaved–beech forest. Of the major taxa groups throughout the forest estate, beech (Nothofagus) contributed 60% of the national forest carbon biomass reservoir, 26.7% was in other hardwoods, 13.2% in conifers, and 0.1% in other taxa (e.g. tree ferns).     

Combining species distribution modeling and distance sampling to assess wildlife population size: A case study with the northern yellow-cheeked gibbon (Nomascus annamensis)

Population size and distribution data for wildlife species play an important role in conservation and management, especially for endangered species. However, scientists seriously lack data on the population status of many species. The northern yellow-cheeked gibbon (Nomascus annamensis) is found in southern Lao PDR, central Vietnam, and northeastern Cambodia. The population of the species has significantly declined due to hunting, habitat loss, and the wildlife trade. To examine the population size and distribution of N. annamensis, we conducted a field survey in Song Thanh Nature Reserve, Quang Nam Province, central Vietnam from February to April 2019 using the audio point count method. We combined Distance Sampling and Ecological Niche Modeling to estimate the population of the gibbons. Results showed that the total suitable area for the gibbons was about 302.32 km², with the two most important variables of the habitat model being the distance-to-villages and forest type. We detected 36 gibbon groups through field surveys and estimated 443 (95% CI, 278–707) gibbon groups in Song Thanh Nature Reserve. Our results indicate that the gibbon population in Song Thanh Nature Reserve is the largest known population of N. annamensis in Vietnam. In addition, our study was the first to combine species distribution modeling with distance sampling to estimate gibbon density and population size. This approach might be useful in surveying and monitoring gibbon populations because it takes imperfect detection probability into account in estimating gibbon population density while estimating the area of potential habitat using environmental variables.     

Mammalian wildlife diseases as hazards to man and livestock in an area of the Llanos Orientales of Colombia

Development of the LLanos Orientales of Colombia, and access to underdeveloped areas in the Llanos, may create disease hazards to man and domestic animals or introduce exotic pathogens, creating reservoirs of infection for domestic animals and acting as limiting factors on the native wild species. A survey of wild animals common to the Llanos revealed a number of parasites indigenous to the area. A total total of 59 mammalian species, representing eight orders were examined. Haematozoa were represented by Trypanosoma cruzi, T. evansi and T. rangeli. Eight species of ticks were found: Amblyomma cajennense, A. auricularium, A. rotundatum, A. maculatum, A. longirostre, A. pacae, Ixodes luciae and Boophilus microplus. Four species of fleas were found: Rhopalopsyllus lugubris lugubris, R. australis tupinus, R. cacicus saevus and Polygenis klagesi samuelis. A species of Echinococcus was commonly found in Cuniculus paca. Serologic titers and/or isolations of pathogenic viral and bacterial agents generally indicated that the wildlife population had not been exposed to the diseases common to the domestic population. A low prevalence of titers to Venezuelan equine encephalomyelitis was found in Cebus apella and Proechimys sp. Neutralizing antibodies to Group B viruses were found in Proechimys sp., Coendor sp. and Nectomys squamipes. Antibodies to Group C viruses were found in Proechimys sp. Serologic titers to Leptospira sejroe and L. tarassovi were found in Proechimys sp. and Didelphis marsupialis. L. tarassovi was isolated from Proechimys sp. Titers to Brucella were not found in 1964 animals. The significance of these findings are discussed.