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Rabies is a lethal zoonotic disease mainly transmitted to humans by dog bites. The purpose of this study was to assess the efficacy of rabies control policies in Japan, which resulted in the elimination of the disease from the country in 1957. Using historical records from the Kanto region (Chiba, Kanagawa, Saitama and Tokyo Prefectures) between 1947 and 1956 where the final canine cases were recorded, we undertook a descriptive epidemiological study, applying spatio-temporal scan statistics using SaTScan and estimating the effective reproduction number (Rt) for the clusters and each prefecture using the growth rates. There were 1,567 dog rabies and 161 human rabies cases recorded during this period. Vaccination coverage in registered dogs was over 70% after 1951, with much lower coverage in free-roaming and unregistered dogs. Eight clusters of dog rabies cases were identified: the first appeared in 1947 in Tokyo and was linked to three further clusters in peripheral prefectures between 1947 and 1951. Three more clusters occurred in Tokyo again between 1952 and 1954, and the last cluster was in Tokyo and Kanagawa between 1955 and 1956. Rt in the first cluster was 1.68, and Rt values in the others ranged between 1.18 and 1.86, with an exception of 4.05 in the smallest cluster in Tokyo in 1952 (10 cases). The moving average of Rt coincided with the clusters. As dog vaccination and dog management progressed, and the number of dog rabies cases declined, the moving average of Rt declined to below 1. Delays in the implementation of dog management policies in Kanagawa may have prolonged this last outbreak. These results demonstrate the effectiveness of coordinated control policy involving dog vaccination and management of free-roaming dog populations for rabies elimination.

1. Understanding the role of different species in the transmission of multi-host pathogens, such as rabies virus, is vital for effective control strategies. Across most of sub-Saharan Africa domestic dogs Canis familiaris are considered the reservoir for rabies, but the role of wildlife has been long debated. Here we explore the multi-host transmission dynamics of rabies across south-east Tanzania. 2. Between January 2011 and July 2019, data on probable rabies cases were collected in the regions of Lindi and Mtwara. Hospital records of animal-bite patients presenting to healthcare facilities were used as sentinels for animal contact tracing. The timing, location and species of probable rabid animals were used to reconstruct transmission trees to infer who infected whom and the relative frequencies of within- and between-species transmission. 3. During the study, 688 probable human rabies exposures were identified, resulting in 47 deaths. Of these exposures, 389 were from domestic dogs (56.5%) and 262 from jackals (38.1%). Over the same period, 549 probable animal rabies cases were traced: 303 in domestic dogs (55.2%) and 221 in jackals (40.3%), with the remainder in domestic cats and other wildlife species. 4. Although dog-to-dog transmission was most commonly inferred (40.5% of transmission events), a third of inferred events involved wildlife-to-wildlife transmission (32.6%), and evidence suggested some sustained transmission chains within jackal populations. 5. A steady decline in probable rabies cases in both humans and animals coincided with the implementation of widespread domestic dog vaccination during the first 6 years of the study. Following the lapse of this program, dog rabies cases began to increase in one of the northernmost districts. 6. Synthesis and applications. In south-east Tanzania, despite a relatively high incidence of rabies in wildlife and evidence of wildlife-to-wildlife transmission, domestic dogs remain essential to the reservoir of infection. Continued dog vaccination alongside improved surveillance would allow a fuller understanding of the role of wildlife in maintaining transmission in this area. Nonetheless, dog vaccination clearly suppressed rabies in both domestic dog and wildlife populations, reducing both public health and conservation risks and, if sustained, has potential to eliminate rabies from this region.

1. Understanding the demography of domestic dog populations is essential for effective disease control, particularly of canine-mediated rabies. Demographic data are also needed to plan effective population management. However, no study has comprehensively evaluated the contribution of demographic processes (i.e. births, deaths and movement) to variations in dog population size or density, or determined the factors that regulate these processes, including human factors. 2. We report the results of a 3-year cohort study of domestic dogs, which is the first to generate detailed data on the temporal variation of these demographic characteristics. The study was undertaken in two communities in each of Bali, Indonesia and Johannesburg, South Africa, in rabies-endemic areas and where the majority of dogs were free-roaming. None of the four communities had been engaged in any dog population management interventions by local authorities or animal welfare organizations. All identified dogs in the four communities were monitored individually throughout the study. 3. We observed either no population growth or a progressive decline in population size during the study period. There was no clear evidence that population size was regulated through environmental resource constraints. Rather, almost all of the identified dogs were owned and fed regularly by their owners, consistent with population size regulated by human demand. Finally, a substantial fraction of the dogs originated from outside the population, entirely through the translocation of dogs by people, rather than from local births. These findings demonstrate that previously reported growth of dog populations is not a general phenomenon and challenge the widely held view that free-roaming dogs are unowned and form closed populations. 4. Synthesis and applications. These observations have broad implications for disease and population control. The accessibility of dogs for vaccination and evaluation through owners and the movement of dogs (some of them infected) by people will determine the viable options for disease control strategies. The impact of human factors on population dynamics will also influence the feasibility of annual vaccination campaigns to control rabies and population control through culling or sterilization. The complex relationship between dogs and people is critically important in the transmission and control of canine-mediated rabies. For effective management, human factors must be considered in the development of disease and population control programmes.

Little is known about the dynamics of small mammals in tropical savanna: a critical gap in our understanding of Africa's best known ecosystems. Historical evidence suggested small mammals peak in abundance (outbreak) in Serengeti National Park (SNP), as in agricultural systems. We asked 1) what are bottom–up drivers of small mammals and 2) do predators have top–down effects? We documented dynamics of small mammals, birds of prey, and mammalian carnivores in SNP and agricultural areas. We used climatic fluctuations and differences between unmodified and agricultural systems as perturbations to examine trophic processes, key to understanding responses to climate change and increasing human pressures. Data were derived from intermittent measures of abundance collected 1968–1999, combined with systematic sampling 2000–2010 to construct a 42-year time series. Data on abundance of black-shouldered kites (1968–2010), eight other species of rodent-eating birds (1997–2010), and 10 carnivore species (1993–2010) were also collated. Outbreaks occurred every 3–5 years in SNP, with low or zero abundance between peaks. There was a positive relationship between rainfall in the wet season and 1) small mammal abundance and 2) the probability of an outbreak, both of which increased with negative Southern Oscillation Index values. Rodent-eating birds and carnivores peaked 6–12 months after small mammals. In agricultural areas, abundance remained higher than in natural habitats. Abundances of birds of prey and mammalian carnivores were extremely low in these areas and not related to small mammal abundance. Small mammals are an important food resource for higher trophic levels in the Serengeti ecosystem. Changes in climate and land use may alter their future dynamics, with cascading consequences for higher trophic levels, including threatened carnivores. Although outbreaks cause substantial damage to crops in agricultural areas, small mammals also play a vital role in maintaining some of the diversity and complexity found in African savanna ecosystems.

Understanding how entire ecosystems maintain stability in the face of climatic and human disturbance is one of the most fundamental challenges in ecology. Theory suggests that a crucial factor determining the degree of ecosystem stability is simply the degree of synchrony with which different species in ecological food webs respond to environmental stochasticity. Ecosystems in which all food-web pathways are affected similarly by external disturbance should amplify variability in top carnivore abundance over time due to population interactions, whereas ecosystems in which a large fraction of pathways are nonresponsive or even inversely responsive to external disturbance will have more constant levels of abundance at upper trophic levels. To test the mechanism underlying this hypothesis, we used over half a century of demographic data for multiple species in the Serengeti (Tanzania) ecosystem to measure the degree of synchrony to variation imposed by an external environmental driver, the El Niño Southern Oscillation (ENSO). ENSO effects were mediated largely via changes in dry-season vs. wet-season rainfall and consequent changes in vegetation availability, propagating via bottom-up effects to higher levels of the Serengeti food web to influence herbivores, predators and parasites. Some species in the Serengeti food web responded to the influence of ENSO in opposite ways, whereas other species were insensitive to variation in ENSO. Although far from conclusive, our results suggest that a diffuse mixture of herbivore responses could help buffer top carnivores, such as Serengeti lions, from variability in climate. Future global climate changes that favor some pathways over others, however, could alter the effectiveness of such processes in the future.

Anthrax is endemic throughout Africa, causing considerable livestock and wildlife losses and severe, sometimes fatal, infection in humans. Predicting the risk of infection is therefore important for public health, wildlife conservation and livestock economies. However, because of the intermittent and variable nature of anthrax outbreaks, associated environmental and climatic conditions, and diversity of species affected, the ecology of this multihost pathogen is poorly understood. We explored records of anthrax from the Serengeti ecosystem in north-west Tanzania where the disease has been documented in humans, domestic animals and a range of wildlife. Using spatial and temporal case-detection and seroprevalence data from wild and domestic animals, we investigated spatial, environmental, climatic and species-specific associations in exposure and disease. Anthrax was detected annually in numerous species, but large outbreaks were spatially localized, mostly affecting a few focal herbivores. Soil alkalinity and cumulative weather extremes were identified as useful spatial and temporal predictors of exposure and infection risk, and for triggering the onset of large outbreaks. Interacting ecological and behavioural factors, specifically functional groups and spatiotemporal overlap, helped to explain the variable patterns of infection and exposure among species. Synthesis and applications. Our results shed light on ecological drivers of anthrax infection and suggest that soil alkalinity and prolonged droughts or rains are useful predictors of disease occurrence that could guide risk-based surveillance. These insights should inform strategies for managing anthrax including prophylactic livestock vaccination, timing of public health warnings and antibiotic provision in high-risk areas. However, this research highlights the need for greater surveillance (environmental, serological and case-detection-orientated) to determine the mechanisms underlying anthrax dynamics. Keywords: Bacillus anthracis, disease ecology, exposure, infectious disease, multihost, serology, surveillance, susceptibility, zoonosis Introduction Bacillus anthracis (Cohn), the causative agent of anthrax, is a multihost pathogen affecting human, livestock and wildlife populations. The disease has a world-wide distribution, but has declined in many developed countries because of the implementation of livestock vaccination programmes and sanitary measures. However, anthrax is still endemic in Africa, with severe outbreaks causing significant losses in domestic and wild animal populations (Prins & Weyerhaeuser 1987; Shiferaw et al. 2002; Siamudaala 2006; Clegg et al. 2007; Wafula, Patrick & Charles 2008). Non-fatal cutaneous anthrax acquired through contact with infected carcasses or animal products accounts for >95% of all reported human cases globally (World Health Organization 2008). More severe forms, particularly gastrointestinal anthrax because of handling and consumption of inadequately cooked products from infected animals, may also exert a substantial burden that is both underreported and under-diagnosed (Sirisanthana & Brown 2002). Predicting the risk of infection is therefore important from the perspectives of public health, wildlife conservation and livestock economies. Despite the infamous reputation of anthrax, the ecology and transmission of the disease under natural conditions are not well understood (Hugh-Jones & de Vos 2002). The difficulty lies in the intermittent and variable nature of outbreaks, with considerable variation in the species affected, and associated environmental and climatic conditions (Table 1). Table 1 Anthrax outbreaks in Eastern and Southern Africa for which details were available. Predominant species are emboldened, followed by species in which > 5 cases were documented The life cycle of B. anthracis comprises a multiplication phase in the mammalian host and a persistence phase of spores in the soil. Transmission to herbivores largely occurs indirectly, so risk factors are usually associated with exposure to spores, rather than direct animal-to-animal transmission. Survival mechanisms of the pathogen outside the host remain unclear. Bacillus anthracis has been shown to be associated with plant roots (Saile & Koehler 2006), and this is suggested to be an adaptation that increases the likelihood of infecting ungulate hosts (Raymond et al. 2010). Certain environmental factors affect long-term spore survival and thus increase the risk of anthrax (Blackburn et al. 2007). For example, the endemicity of B. anthracis in some areas has been associated with calcium-rich and neutral-to-alkaline soils (van Ness 1971; Dragon et al. 2005; Hugh-Jones & Blackburn 2009), although strain differences exist in soil chemistry preferences (Smith et al. 2000). Strain differences, in fact, may also govern spread in anthrax epidemics (Blackburn et al. 2007; Garofolo et al. 2010). Seasonal incidence patterns suggest climatic factors (precipitation and ambient temperature) play an important role in triggering outbreaks, although these are not consistent between locations (Table 1), and therefore underlying mechanisms are debated. In some African ecosystems, outbreaks have been reported late in the dry season (Prins & Weyerhaeuser 1987; Turnbull et al. 1991; Lindeque & Turnbull 1994; de Vos & Bryden 1996; Shiferaw et al. 2002; Clegg et al. 2007; Muoria et al. 2007), leading to suggestions that transmission may be facilitated by close grazing, nutritional stress and congregation at water holes (Hugh-Jones & de Vos 2002). Elsewhere, outbreaks have been associated with heavy rains (Lindeque & Turnbull 1994; Mlengeya et al. 1998; Wafula, Patrick & Charles 2008; Bellan 2010), which are hypothesized to unearth spores and amplify vector populations (Durrheim et al. 2009; Hugh-Jones & Blackburn 2009; Lewerin et al. 2010). Experimental spore germination and vegetative growth in the rhizosphere provide a mechanism by which bursts of rainfall could spark epidemics (Saile & Koehler 2006). This would parsimoniously explain anthrax occurrences during dry summers in North America and Australia that have been preceded by rains and when animals are often in good body condition (Turner et al. 1999; Hugh-Jones & de Vos 2002; Parkinson, Rajic & Jenson 2003; Hugh-Jones & Blackburn 2009; Epp, Waldner & Argue 2010). Although anthrax infects a wide range of species, outbreaks are typically associated with just a few (Table 1), for example impala Aepyceros melampus, kudu Tragelaphus strepsiceros, buffalo Syncerus caffer and zebra Equus spp. (Prins & Weyerhaeuser 1987; Mlengeya et al. 1998; Clegg et al. 2007; Muoria et al. 2007; Wafula, Patrick & Charles 2008). Even within a single ecosystem, different species may be affected at different times (Lindeque & Turnbull 1994). Reasons for this remain unclear, but could be attributed to host-specific differences in susceptibility and exposure as a result of behavioural and ecological traits as well as differences in pathogen strains. The overall ecological and genetic factors that contribute to environmental persistence of anthrax, and the underlying conditions that initiate outbreaks and underlie patterns of circulation are poorly known. In the Serengeti ecosystem, anthrax has been reported in a variety of species, with sporadic outbreaks occurring in relatively localized endemic foci and mostly affecting a few focal species (Lembo et al. 2011). The ecosystem covers a large area (over 20 000 km2, Sinclair et al. 2008) encompassing a variety of habitats and environmental gradients, which may influence anthrax occurrence. Here, we draw on data gathered opportunistically including serology indicative of exposure and case reports from human, domestic and wild animal populations in the greater Serengeti ecosystem, to explore ecological factors affecting infection patterns in a range of species. Combined, the investigation into environmental and climatic predictors of anthrax and their associations with species-specific patterns of exposure and mortality provides a holistic picture of ecological drivers of anthrax dynamics and identifies priorities for further research in anthrax endemic ecosystems.

1. This study utilizes a unique data set covering over 19 000 georeferenced records of species presence collected between 1993 and 2008, to explore the distribution and habitat selectivity of an assemblage of 26 carnivore species in the Serengeti-Ngorongoro landscape in northern Tanzania. 2. Two species, the large-spotted genet and the bushy-tailed mongoose, were documented for the first time within this landscape. Ecological Niche Factor Analysis (ENFA) was used to examine habitat selectivity for 18 of the 26 carnivore species for which there is sufficient data. Eleven ecogeographical variables (EGVs), such as altitude and habitat type, were used for these analyses. 3. The ENFA demonstrated that species differed in their habitat selectivity, and supported the limited ecological information already available for these species, such as the golden jackals' preference for grassland and the leopards' preference for river valleys. 4. Two aggregate scores, marginality and tolerance, are generated by the ENFA, and describe each species' habitat selectivity in relation to the suite of EGVs. These scores were used to test the hypothesis that smaller species are expected to be more selective than larger species [Science, 1989, 243, 1145]. Two predictions were tested: Marginality should decrease with body mass; and tolerance should increase with body mass. Our study provided no evidence for either prediction. 5. Our results not only support previous analyses of carnivore diet breadth, but also represent a novel approach to the investigation of habitat selection across species assemblages. Our method provides a powerful tool to explore similar questions in other systems and for other taxa.