Diverse factors, including environmental features and cognitive processes, can drive animals' movements and space use, with far-reaching implications. For example, repeated use of individual-level travel routeways (directionally constrained but imperfectly aligned routes), which results in spatial concentration of activity, can shape encounter-based processes including predation, mate finding, and disease transmission. However, how much variation in routeway usage exists across species remains unknown. By analyzing GPS movement tracks for 1,239 range-resident mammalian carnivores-representing 16 canid and 18 felid species from six continents-we found strong evidence of a clade-level difference in species' reliance on repeatedly used travel routeways. Across the global dataset, tracked canids had a 15% (±7 CI) greater density of routeways within their home ranges than did felids, rising to 33% (±16 CI) greater in landscapes shared with tracked felids. Moreover, comparisons within species across landscapes revealed broadly similar home range routeway densities despite habitat differences. On average, canids also reused their travel routeways more intensively than did felids, with hunting strategies and spatial contexts also contributing to the intensity of routeway usage. Collectively, our results suggest that key aspects of carnivore routeway-usage have an evolutionary component. Striking interspecific and clade-level differences in carnivores' reliance on reused travel routeways within home ranges identify important ways in which the movement patterns of real-world predators depart from classical assumptions of predator-prey theory. Because such departures can drive key aspects of human-wildlife interactions and other encounter-based processes, continued investigations of the relationships between movement mechanisms and space use are critical.

Due to increasing anthropogenic impacts, many species survive only in small and isolated populations. Active conservation management to reduce extinction risk includes increasing habitat connectivity, translocations from captive populations, or intensive surveillance of highly protected closed populations. Advances in sequencing technology mean that it is now possible to consider the genomic impacts of such strategies, as a proxy for variation in individual fitness. Using whole genome sequences from critically endangered eastern black rhinoceros (Diceros bicornis michaeli), we compare the consequences of different types of conservation efforts, based on cohorts of offspring resulting from parents from different sources. Based on the fraction of the genome in runs of homozygosity (ROH) of different lengths, we found lower inbreeding in offspring of individuals that had either been translocated from ex-situ populations (FROH>1Mb = 0.047) or dispersed between proximate native populations (FROH>1Mb = 0.065) compared to the intensively managed closed population from which the migrant moved (FROH>1Mb = 0.112). However, the benefit of such movement was removed after only a few generations of closed breeding (FROH>1Mb = 0.149). Although sample size restricted power to detect significance of differences, the relative abundance of highly deleterious mutations was higher for offspring resulting from translocation compared to the other cohorts and this load was sheltered by higher heterozygosity, which could increase risks of inbreeding depression if inbreeding subsequently occurs. In contrast, native dispersers reduced the negative effects of inbreeding without compromising the benefits of past purging of deleterious mutations. Our study highlights the importance of natural dispersal and reiterates the importance of maintaining habitat corridors between populations.

To conserve wide-ranging species in degraded landscapes, it is essential to understand how the behavior of animals changes in relation to the degree and composition of modification. Evidence suggests that large inter-individual variation exists in the propensity for use of degraded areas and may be driven by both behavioral and landscape factors. The use of cultivated lands by wildlife is of particular interest, given the importance of reducing human-wildlife conflicts and understanding how such areas can function as biodiversity buffers. African elephant space use can be highly influenced by human activity and the degree to which individuals crop-raid. We analyzed GPS data from 56 free-ranging elephants in the Serengeti-Mara Ecosystem using resource selection functions (RSFs) to assess how crop use may drive patterns of resource selection and space use within a population. We quantified drivers of similarity in resource selection across individuals using proximity analysis of individual RSF coefficients derived from random forest models. We found wide variation in RSF coefficient values between individuals indicating strongly differentiated resource selection strategies. Proximity assessment indicated the degree of crop use in the dry season, individual repeatability, and time spent in unprotected areas drove similarity in resource selection patterns. Crop selection was also spatially structured in relation to agricultural fragmentation. In areas with low fragmentation, elephants spent less time in crops and selected most strongly for crops further from protected area boundaries, but in areas of high fragmentation, elephants spent twice as much time in crops and selected most strongly for crops closer to the protected area boundary. Our results highlight how individual differences and landscape structure can shape use of agricultural landscapes. We discuss our findings in respect to the conservation challenges of human-elephant conflict and incorporating behavioral variation into human-wildlife coexistence efforts.

There has been a drastic decline in the number of eastern black rhinoceros ( Diceros bicornis michaeli ) across Africa, leaving individuals restricted to small, isolated populations that are vulnerable to extinction. Focusing on highly threatened populations in Tanzania, this study investigated the genetic impacts of past management interventions on mitochondrial control region diversity in extant subpopulations, assessed whether there has been evidence of dispersal of females between populations based on haplotype sharing, and related current haplotype diversity to historical patterns. Across extant subpopulations in Tanzania, six maternal haplotypes were identified, with an overall haplotype diversity of h = 0.72 but lower overall nucleotide diversity within populations (π = 0.017) compared to historical populations (π = 0.021). Translocated populations did not share haplotypes with native populations, even though all haplotypes from translocated individuals had been found among historic samples from Kenya. This suggests that translocations have been successful at restoring previous diversity to the region but that the current Intensive Protection Zone (IPZ) management practices have restricted the movement of females between subpopulations. Extant haplotypes were distributed among three East African haplogroups described in previous studies, suggesting that multiple lineages have been preserved despite the loss of historical haplotypes. Our recommendation is to enhance the utilisation of previous translocations by enabling the natural movements of individuals between subpopulations. Such a change in management strategy could be less costly both economically and in terms of animal welfare than the alternative of using genetic data to target specific animals for translocation in order to supplement diversity.

Habitat conversion to farmland has increased human-wildlife interactions, which often lead to conflict, injury or death for people and animals. Understanding the behavioural and landscape drivers of human-wildlife conflict is critical for managing wildlife populations. Staging behaviour prior to crop incursions has been described across multiple taxa and offers potential utility in managing conflict, but few quantitative assessments of staging have been undertaken. Animal movement data can provide valuable, fine-scale information on such behaviour with opportunities for application to real-time management for conflict prediction.We developed an approach to assess the efficacy of six widely used metrics of animal movement to identify staging behaviour prior to agricultural incursions. We applied this approach to GPS data from 55 African elephants in the Serengeti-Mara ecosystem and found tortuosity and HMM-derived behavioural states to be the most effective for identifying staging events. We then assessed temporal patterns of defined staging at daily and seasonal scales and explored environmental and anthropogenic drivers of staging from spatial generalized logistic mixed models. Finally, we tested the viability of combining movement and simple spatial metrics to predict crop incursions based on GPS data.Our approach identified staging behaviour that appeared to be driven largely by human activity and diurnal availability of protective cover from forest, riverine vegetation, and topography. Staging also varied substantially by season. Tortuosity and behavioural state metrics identified different staging strategies with distinct spatial distributions and anthropogenic drivers, and appeared to be linked to the juxtaposition between protected and cultivated lands. Tortuosity-based staging combined with distance-to-agriculture produced promising results for pre-event prediction of crop incursion.Synthesis and applications. Our study found staging by elephants prior to crop use could be identified from GPS tracking data, indicating that a better understanding of movement behaviour can inform targeted and proactive human-wildlife conflict management and inform spatial planning efforts. Our approach is extendable to other conflict-prone species to assess pre-conflict behaviours and space use and demonstrates some of the challenges and advantages of using animal behaviour to assess temporal and spatial heterogeneity in human-wildlife conflict.

After-action review uses experiences gained from past events to adopt best practices, thereby improving future interventions. In December 2016 and late 2018, the government of Tanzania with support from partners responded to anthrax and rabies outbreaks in Arusha and Morogoro regions respectively. The One Health Coordination Desk (OHCD) of the Prime Minister’s Office (PMO) later coordinated after-action reviews to review the multi-sectoral preparedness and response to the outbreaks. To establish and describe actions undertaken by the multi-sectoral investigation and response teams during planning and deployment, execution of field activities, and outbreak investigation and response, system best practices and deficiencies. These were cross-sectional surveys. Semi-structured, open and closed-ended questionnaire and focus group discussions were administered to collect information from responders at the national and subnational levels. It was found that the surveillance and response systems were weak at community level, lack of enforcement of public health laws including vaccination of livestock and domestic animals and joint preparedness efforts were generally undermined by differential disease surveillance capacities among sectors. Lack of resources in particular funds for supplies, transport and deployment of response teams contributed to many shortfalls. The findings underpin the importance of after-action reviews in identifying critical areas for improvement in multi-sectoral prevention and control of disease outbreaks. Main sectors under the coordination of the OHCD should include after action reviews in their plans and budget it as a tool to continuously assess and improve multi-sectoral preparedness and response to public health emergencies.

During serological surveillance of peste des petits ruminants (PPR) disease, it required capture of randomly selected herds of gazelles as part of a study to determine the epidemiological role of these species in the circulation of peste des petits ruminants virus (PPRV). The study targeted capturing 135 Grant's gazelles (Gazella granti) from the Serengeti ecosystem, Tanzania. A modified netting technique was used aiming at providing safe, efficient and cost-effective method for capture of gazelles. Locally available materials were used, and wildlife professionals guided the process of manufacturing supporting frame for the nets. Twenty (20) black metal pipes, 20 metal bars, four nets and three vehicles were used in the procedure. A total of 136 Grant's gazelles and nine Thomson's gazelles were captured in three missions. The Grant's gazelles were captured as per sample size calculated in all locations: Loliondo (n = 25), Serengeti National Park (n = 44) and Ngorongoro Conservation Area (NCA) (n = 67) using less time and minimum cost than estimated. Injuries of three fawns (2%) inadvertently captured with the groups of adults and sub-adult animals were recorded. Comparing with 2014 and other studies, modified netting technique showed high animal and operator safety levels with minimal injuries. With this technique, it was possible to capture even flighty animals that behave nervously because of hunting and other human activities, including Thomson's gazelles, a species previously found to be difficult to capture by netting.

Meat from wildlife species (bushmeat) represents a major source of dietary protein in low- and middle-income countries where humans and wildlife live in close proximity. Despite the occurrence of zoonotic pathogens in wildlife, their prevalence in bushmeat remains unknown. To assess the risk of exposure to major pathogens in bushmeat, a total of 3784 samples, both fresh and processed, were collected from three major regions in Tanzania during both rainy and dry seasons, and were screened by real-time PCR for the presence of DNA signatures of Bacillus anthracis (B. anthracis), Brucella spp. (Brucella) and Coxiella burnetii (Coxiella). The analysis identified DNA signatures of B. anthracis (0.48%), Brucella (0.9%), and Coxiella (0.66%) in a total of 77 samples. Highest prevalence rates of B. anthracis, Brucella, and Coxiella were observed in wildebeest (56%), dik-dik (50%), and impala (24%), respectively. Fresh samples, those collected during the rainy season, and samples from Selous or Serengeti had a greater relative risk of being positive. Microbiome characterization identified Firmicutes and Proteobacteria as the most abundant phyla. The results highlight and define potential risks of exposure to endemic wildlife diseases from bushmeat and the need for future investigations to address the public health and emerging infectious disease risks associated with bushmeat harvesting, trade, and consumption.

Peste des petits ruminants (PPR) is a viral disease of goats and sheep that occurs in Africa, the Middle East and Asia with a severe impact on livelihoods and livestock trade. Many wild artiodactyls are susceptible to PPR virus (PPRV) infection, and some outbreaks have threatened endangered wild populations. The role of wild species in PPRV epidemiology is unclear, which is a knowledge gap for the Global Strategy for the Control and Eradication of PPR. These studies aimed to investigate PPRV infection in wild artiodactyls in the Greater Serengeti and Amboseli ecosystems of Kenya and Tanzania. Out of 132 animals purposively sampled in 2015–2016, 19.7% were PPRV seropositive by ID Screen PPR competition enzyme-linked immunosorbent assay (cELISA; IDvet, France) from the following species: African buffalo, wildebeest, topi, kongoni, Grant’s gazelle, impala, Thomson’s gazelle, warthog and gerenuk, while waterbuck and lesser kudu were seronegative. In 2018–2019, a cross-sectional survey of randomly selected African buffalo and Grant’s gazelle herds was conducted. The weighted estimate of PPRV seroprevalence was 12.0% out of 191 African buffalo and 1.1% out of 139 Grant’s gazelles. All ocular and nasal swabs and faeces were negative by PPRV real-time reverse transcription-polymerase chain reaction (RT-qPCR). Investigations of a PPR-like disease in sheep and goats confirmed PPRV circulation in the area by rapid detection test and/or RT-qPCR. These results demonstrated serological evidence of PPRV infection in wild artiodactyl species at the wildlife–livestock interface in this ecosystem where PPRV is endemic in domestic small ruminants. Exposure to PPRV could be via spillover from infected small ruminants or from transmission between wild animals, while the relatively low seroprevalence suggests that sustained transmission is unlikely. Further studies of other major wild artiodactyls in this ecosystem are required, such as impala, Thomson’s gazelle and wildebeest.

Bushmeat harvesting and consumption represents a potential risk for the spillover of endemic zoonotic pathogens, yet remains a common practice in many parts of the world. Given that the harvesting and selling of bushmeat is illegal in Tanzania and other parts of Africa, the supply chain is informal and may include hunters, whole-sellers, retailers, and individual resellers who typically sell bushmeat in small pieces. These pieces are often further processed, obscuring species-identifying morphological characteristics, contributing to incomplete or mistaken knowledge of species of origin and potentially confounding assessments of pathogen spillover risk and bushmeat offtake. The current investigation sought to identify the species of origin and assess the concordance between seller-reported and laboratory-confirmed species of origin of bushmeat harvested from in and around the Serengeti National Park in Tanzania. After obtaining necessary permits, the species of origin of a total of 151 bushmeat samples purchased from known intermediaries from 2016 to 2018 were characterized by PCR and sequence analysis of the cytochrome B (CytB) gene. Based on these sequence analyses, 30%, 95% Confidence Interval (CI: 24.4-38.6) of bushmeat samples were misidentified by sellers. Misreporting amongst the top five source species (wildebeest, buffalo, impala, zebra, and giraffe) ranged from 20% (CI: 11.4-33.2) for samples reported as wildebeest to 47% (CI: 22.2-72.7) for samples reported as zebra although there was no systematic bias in reporting. Our findings suggest that while misreporting errors are unlikely to confound wildlife offtake estimates for bushmeat consumption within the Serengeti ecosystem, the role of misreporting bias on the risk of spillover events of endemic zoonotic infections from bushmeat requires further investigation.

Canine distemper virus (CDV) is a multi-host pathogen with variable clinical outcomes of infection across and within species. We used whole-genome sequencing (WGS) to search for viral markers correlated with clinical distemper in African lions. To identify candidate markers, we first documented single-nucleotide polymorphisms (SNPs) differentiating CDV strains associated with different clinical outcomes in lions in East Africa. We then conducted evolutionary analyses on WGS from all global CDV lineages to identify loci subject to selection. SNPs that both differentiated East African strains and were under selection were mapped to a phylogenetic tree representing global CDV diversity to assess if candidate markers correlated with documented outbreaks of clinical distemper in lions (n = 3). Of 54 SNPs differentiating East African strains, ten were under positive or episodic diversifying selection and 20 occurred in the clinical strain despite strong purifying selection at those loci. Candidate markers were in functional domains of the RNP complex (n = 19), the matrix protein (n = 4), on CDV glycoproteins (n = 5), and on the V protein (n = 1). We found mutations at two loci in common between sequences from three CDV outbreaks of clinical distemper in African lions; one in the signaling lymphocytic activation molecule receptor (SLAM)-binding region of the hemagglutinin protein and another in the catalytic center of phosphodiester bond formation on the large polymerase protein. These results suggest convergent evolution at these sites may have a functional role in clinical distemper outbreaks in African lions and uncover potential novel barriers to pathogenicity in this species.

The outcome of pathogen spillover from a reservoir to a novel host population can range from a “dead‐end” when there is no onward transmission in the recipient population, to epidemic spread and even establishment in new hosts. Understanding the evolutionary epidemiology of spillover events leading to discrete outcomes in novel hosts is key to predicting risk and can lead to a better understanding of the mechanisms of emergence. Here we use a Bayesian phylodynamic approach to examine cross‐species transmission and evolutionary dynamics during a canine distemper virus (CDV) spillover event causing clinical disease and population decline in an African lion population (Panthera leo) in the Serengeti Ecological Region between 1993 and 1994. Using 21 near‐complete viral genomes from four species we found that this large‐scale outbreak was likely ignited by a single cross‐species spillover event from a canid reservoir to noncanid hosts <1 year before disease detection and explosive spread of CDV in lions. Cross‐species transmission from other noncanid species probably fuelled the high prevalence of CDV across spatially structured lion prides. Multiple lines of evidence suggest that spotted hyenas (Crocuta crocuta) could have acted as the proximate source of CDV exposure in lions. We report 13 nucleotide substitutions segregating CDV strains found in canids and noncanids. Our results are consistent with the hypothesis that virus evolution played a role in CDV emergence in noncanid hosts following spillover during the outbreak, suggest that host barriers to clinical infection can limit outcomes of CDV spillover in novel host species.

Understanding multi-host pathogen maintenance and transmission dynamics is critical for disease control. However, transmission dynamics remain enigmatic largely because they are difficult to observe directly, particularly in wildlife. Here, we investigate the transmission dynamics of canine parvovirus (CPV) using state–space modelling of 20 years of CPV serology data from domestic dogs and African lions in the Serengeti ecosystem. We show that, although vaccination reduces the probability of infection in dogs, and despite indirect enhancement of population seropositivity as a result of vaccine shedding, the vaccination coverage achieved has been insufficient to prevent CPV from becoming widespread. CPV is maintained by the dog population and has become endemic with approximately 3.5-year cycles and prevalence reaching approximately 80%. While the estimated prevalence in lions is lower, peaks of infection consistently follow those in dogs. Dogs exposed to CPV are also more likely to become infected with a second multi-host pathogen, canine distemper virus. However, vaccination can weaken this coupling, raising questions about the value of monovalent versus polyvalent vaccines against these two pathogens. Our findings highlight the need to consider both pathogen- and host-level community interactions when seeking to understand the dynamics of multi-host pathogens and their implications for conservation, disease surveillance and control programmes.

Bushmeat, the meat and organs derived from wildlife species, is a common source of animal protein in the diets of those living in sub-Saharan Africa and is frequently associated with zoonotic spillover of dangerous pathogens. Given the frequent consumption of bushmeat in this region and the lack of knowledge about the microbial communities associated with this meat, the microbiome of 56 fresh and processed bushmeat samples ascertained from three districts in the Western Serengeti ecosystem in Tanzania was characterized using 16S rRNA metagenomic sequencing. The results show that the most abundant phyla present in bushmeat samples include Firmicutes (67.8%), Proteobacteria (18.4%), Cyanobacteria (8.9%), and Bacteroidetes (3.1%). Regardless of wildlife species, sample condition, season, or region, the microbiome is diverse across all samples, with no significant difference in alpha or beta diversity. The findings also suggest the presence of DNA signatures of potentially dangerous zoonotic pathogens, including those from the genus Bacillus, Brucella, Coxiella, and others, in bushmeat. Together, this investigation provides a better understanding of the microbiome associated with this major food source in samples collected from the Western Serengeti in Tanzania and highlights a need for future investigations on the potential health risks associated with the harvesting, trade, and consumption of bushmeat in Sub-Saharan Africa.

Carnivore parvoviruses infect wild and domestic carnivores, and cross-species transmission is believed to occur. However, viral dynamics are not well understood, nor are the consequences for wild carnivore populations of the introduction of new strains into wild ecosystems. To clarify the ecology of these viruses in a multihost system such as the Serengeti ecosystem and identify potential threats for wildlife conservation, we analyzed, through real-time PCR, 152 samples belonging to 14 wild carnivore species and 62 samples from healthy domestic dogs. We detected parvovirus DNA in several wildlife tissues. Of the wild carnivore and domestic dog samples tested, 13% and 43%, respectively, were positive for carnivore parvovirus infection, but little evidence of transmission between the wild and domestic carnivores was detected. Instead, we describe two different epidemiological scenarios with separate routes of transmission: first, an endemic feline parvovirus (FPV) route of transmission maintained by wild carnivores inside the Serengeti National Park (SNP) and, second, a canine parvovirus (CPV) route of transmission among domestic dogs living around the periphery of the SNP. Twelve FPV sequences were characterized; new host-virus associations involving wild dogs, jackals, and hyenas were discovered; and our results suggest that mutations in the fragment of the vp2 gene were not required for infection of different carnivore species. In domestic dogs, 6 sequences belonged to the CPV-2a strain, while 11 belonged to the CPV-2 vaccine-derived strain. This is the first description of a vaccine-derived parvovirus strain being transmitted naturally.IMPORTANCE Carnivore parvoviruses are widespread among wild and domestic carnivores, which are vulnerable to severe disease under certain circumstances. This study furthers the understanding of carnivore parvovirus epidemiology, suggesting that feline parvoviruses are endemic in wild carnivores in the Serengeti National Park (SNP), with new host species identified, and that canine parvoviruses are present in the dog population living around the SNP. Little evidence of transmission of canine parvoviruses into wild carnivore species was found; however, the detection of vaccine-derived virus (described here for the first time to be circulating naturally in domestic dogs) highlights the importance of performing epidemiological research in the region.

A study to estimate population size and distribution of elephants in the Rubondo Island National Park (RINP) was conducted between March and July 2014. It involved elephant dung survey methods. In estimating elephant dung pile density, a total of 217 dung piles were enumerated in 58 transects (each 1 km). The on-site dung decay rate computed from 100 marked fresh dung piles was estimated to be 0.01542 per day. By combining estimated dung pile density, on-site decay rate and defecation rate of 17 dung piles per day, the study found an estimate of about 102 elephants (95% CI, 72-144). Furthermore, results of this study indicate that, elephants were found to be more concentrated on the central and northern zones, which are the areas of the park that have some open glades allowing elephant to access the area easily to lake shores. The information generated from the study can be incorporated into setting up future management strategies for elephant conservation in RINP. Key words: Rubondo Island National Park (RINP), distance sampling, dung pile density, decay rate.

Morbilliviruses cause many diseases of medical and veterinary importance, and although some (e.g., measles and rinderpest) have been controlled successfully, others, such as canine distemper virus (CDV), are a growing concern. A propensity for host-switching has resulted in CDV emergence in new species, including endangered wildlife, posing challenges for controlling disease in multispecies communities. CDV is typically associated with domestic dogs, but little is known about its maintenance and transmission in species-rich areas or about the potential role of domestic dog vaccination as a means of reducing disease threats to wildlife. We address these questions by analyzing a long-term serological dataset of CDV in lions and domestic dogs from Tanzania's Serengeti ecosystem. Using a Bayesian state-space model, we show that dynamics of CDV have changed considerably over the past three decades. Initially, peaks of CDV infection in dogs preceded those in lions, suggesting that spill-over from dogs was the main driver of infection in wildlife. However, despite dog-to-lion transmission dominating cross-species transmission models, infection peaks in lions became more frequent and asynchronous from those in dogs, suggesting that other wildlife species may play a role in a potentially complex maintenance community. Widespread mass vaccination of domestic dogs reduced the probability of infection in dogs and the size of outbreaks but did not prevent transmission to or peaks of infection in lions. This study demonstrates the complexity of CDV dynamics in natural ecosystems and the value of long-term, large-scale datasets for investigating transmission patterns and evaluating disease control strategies.

We tested wildlife inhabiting areas near domestic livestock, pastures, and water sources in the Ngorongoro district in the Serengeti ecosystem of northern Tanzania and found 63% seropositivity for peste des petits ruminants virus. Sequencing of the viral genome from sick sheep in the area confirmed lineage II virus circulation.