Risk perception and tolerance shape variation in agricultural use for a transboundary elephant population.

To conserve wide-ranging species in human-modified landscapes, it is essential to understand how animals selectively use or avoid cultivated areas. Use of agriculture leads to human-wildlife conflict, but evidence suggests that individuals may differ in their tendency to be involved in conflict. This is particularly relevant to wild elephant populations. We analysed GPS data of 66 free-ranging elephants in the Serengeti-Mara ecosystem to quantify their use of agriculture. We then examined factors influencing the level of agricultural use, individual change in use across years and differences in activity budgets associated with use. Using clustering methods, our data grouped into four agricultural use tactics: rare (<0.6% time in agriculture; 26% of population), sporadic (0.6%-3.8%; 34%), seasonal (3.9%-12.8%; 31%) and habitual (>12.8%; 9%). Sporadic and seasonal individuals represented two-thirds (67%) of recorded GPS fixes in agriculture, compared to 32% from habitual individuals. Increased agricultural use was associated with higher daily distance travelled and larger home range size, but not with age or sex. Individual tactic change was prevalent and the habitual tactic was maintained in consecutive years by only five elephants. Across tactics, individuals switched from diurnal to nocturnal activity during agricultural use, interpreted as representing similar risk perception of cultivated areas. Conversely, tactic choice appeared to be associated with differences in risk tolerance between individuals. Together, our results suggest that elephants are balancing the costs and benefits of crop usage at both fine (e.g. crop raid events) and long (e.g. yearly tactic change) temporal scales. The high proportion of sporadic and seasonal tactics also highlights the importance of mitigation strategies that address conflict arising from many animals, rather than targeted management of habitual crop raiders. Our approach can be applied to other species and systems to characterize individual variation in human resource use and inform mitigations for human-wildlife coexistence.

Identification of Bacillus anthracis, Brucella spp., and Coxiella burnetii DNA signatures from bushmeat.

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.

Potential impacts of climate change on geographical distribution of three primary vectors of African Trypanosomiasis in Tanzania's Maasai Steppe: G. m. morsitans, G. pallidipes and G. swynnertoni.

In the Maasai Steppe, public health and economy are threatened by African Trypanosomiasis, a debilitating and fatal disease to livestock (African Animal Trypanosomiasis -AAT) and humans (Human African Trypanosomiasis-HAT), if not treated. The tsetse fly is the primary vector for both HAT and AAT and climate is an important predictor of their occurrence and the parasites they carry. While understanding tsetse fly distribution is essential for informing vector and disease control strategies, existing distribution maps are old and were based on coarse spatial resolution data, consequently, inaccurately representing vector and disease dynamics necessary to design and implement fit-for-purpose mitigation strategies. Also, the assertion that climate change is altering tsetse fly distribution in Tanzania lacks empirical evidence. Despite tsetse flies posing public health risks and economic hardship, no study has modelled their distributions at a scale needed for local planning. This study used MaxEnt species distribution modelling (SDM) and ecological niche modeling tools to predict potential distribution of three tsetse fly species in Tanzania's Maasai Steppe from current climate information, and project their distributions to midcentury climatic conditions under representative concentration pathways (RCP) 4.5 scenarios. Current climate results predicted that G. m. morsitans, G. pallidipes and G swynnertoni cover 19,225 km2, 7,113 km2 and 32,335 km2 and future prediction indicated that by the year 2050, the habitable area may decrease by up to 23.13%, 12.9% and 22.8% of current habitable area, respectively. This information can serve as a useful predictor of potential HAT and AAT hotspots and inform surveillance strategies. Distribution maps generated by this study can be useful in guiding tsetse fly control managers, and health, livestock and wildlife officers when setting surveys and surveillance programs. The maps can also inform protected area managers of potential encroachment into the protected areas (PAs) due to shrinkage of tsetse fly habitats outside PAs.

Genetic connectivity and population structure of African savanna elephants (Loxodonta africana) in Tanzania.

Increasing human population growth, exurban development, and associated habitat fragmentation is accelerating the isolation of many natural areas and wildlife populations across the planet. In Tanzania, rapid and ongoing habitat conversion to agriculture has severed many of the country's former wildlife corridors between protected areas. To identify historically linked protected areas, we investigated the genetic structure and gene flow of African savanna elephants in Tanzania using microsatellite and mitochondrial DNA markers in 688 individuals sampled in 2015 and 2017. Our results indicate distinct population genetic structure within and between ecosystems across Tanzania, and reveal important priority areas for connectivity conservation. In northern Tanzania, elephants sampled from the Tarangire-Manyara ecosystem appear marginally, yet significantly isolated from elephants sampled from the greater Serengeti ecosystem (mean F ST = 0.03), where two distinct subpopulations were identified.Unexpectedly, elephants in the Lake Manyara region appear to be more closely related to those across the East African Rift wall in the Ngorongoro Conservation Area than they are to the neighboring Tarangire subpopulations. We concluded that the Rift wall has had a negligible influence on genetic differentiation up to this point, but differentiation may accelerate in the future because of ongoing loss of corridors in the area. Interestingly, relatively high genetic similarity was found between elephants in Tarangire and Ruaha although they are separated by >400 km. In southern Tanzania, there was little evidence of female-mediated gene flow between Ruaha and Selous, probably due to the presence of the Udzungwa Mountains between them. Despite observing evidence of significant isolation, the populations of elephants we examined generally exhibited robust levels of allelic richness (mean A R = 9.96), heterozygosity (mean µH E = 0.73), and effective population sizes (mean N e = 148). Our results may inform efforts to restore wildlife corridors between protected areas in Tanzania in order to facilitate gene flow for long-term survival of elephants and other species.

Molecular species identification of bushmeat recovered from the Serengeti ecosystem in Tanzania.

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.

Microbial Diversity in Bushmeat Samples Recovered from the Serengeti Ecosystem in Tanzania.

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.

Cross-boundary human impacts compromise the Serengeti-Mara ecosystem.

Protected areas provide major benefits for humans in the form of ecosystem services, but landscape degradation by human activity at their edges may compromise their ecological functioning. Using multiple lines of evidence from 40 years of research in the Serengeti-Mara ecosystem, we find that such edge degradation has effectively "squeezed" wildlife into the core protected area and has altered the ecosystem's dynamics even within this 40,000-square-kilometer ecosystem. This spatial cascade reduced resilience in the core and was mediated by the movement of grazers, which reduced grass fuel and fires, weakened the capacity of soils to sequester nutrients and carbon, and decreased the responsiveness of primary production to rainfall. Similar effects in other protected ecosystems worldwide may require rethinking of natural resource management outside protected areas.

Pastoralists' Vulnerability to Trypanosomiasis in Maasai Steppe.

Trypanosomiasis is a neglected tropical disease of both livestock and humans. Although pastoral communities of the Maasai Steppe have been able to adapt to trypanosomiasis in the past, their traditional strategies are now constrained by changes in climate and land regimes that affect their ability to move with their herds and continually shape the communities' vulnerability to trypanosomiasis. Despite these constraints, information on communities' vulnerability and adaptive capacity to trypanosomiasis is limited. A cross-sectional study was therefore conducted in Simanjiro and Monduli districts of the Maasai Steppe to establish pastoralists' vulnerability to animal trypanosomiasis and factors that determined their adaptation strategies. A weighted overlay approach in ArcGIS 10.4 was used to analyze vulnerability levels while binomial and multinomial logistic regressions in R 3.3.2 were used to analyze the determinants of adaptation. Simanjiro district was the most vulnerable to trypanosomiasis. The majority (87.5%, n = 136) of the respondents were aware of trypanosomiasis in animals, but only 7.4% (n = 136) knew about the human form of the disease. Reported impacts of animal trypanosomiasis were low milk production (95.6%, n = 136), death of livestock (96.8%, n = 136) and emaciation of animals (99.9%, n = 136). Crop farming was the most frequently reported animal trypanosomiasis adaptation strategy (66%, n = 136). At a 95% confidence interval, accessibility to livestock extension services (ß = 7.61, SE = 3.28, df = 135, P = 0.02), years of livestock keeping experience (ß = 6.17, SE = 1.95, df = 135, P = 0.001), number of cattle owned (ß = 5.85, SE = 2.70, df = 135, P = 0.03) and membership in associations (ß = - 4.11, SE = 1.79, df = 135, P = 0.02) had a significant impact on the probability of adapting to animal trypanosomiasis.

Patterns of tsetse abundance and trypanosome infection rates among habitats of surveyed villages in Maasai steppe of northern Tanzania.

BACKGROUND: Changes of land cover modify the characteristics of habitat, host-vector interaction and consequently infection rates of disease causing agents. In this paper, we report variations in tsetse distribution patterns, abundance and infection rates in relation to habitat types and age in the Maasai Steppe of northern Tanzania. In Africa, Tsetse-transmitted trypanosomiasis negatively impacted human life where about 40 million people are at risk of contracting the disease with dramatic socio-economical consequences, for instance, loss of livestock, animal productivity, and manpower. METHODS: We trapped tsetse flies in dry and wet seasons between October 2014 and May 2015 in selected habitats across four villages: Emboreet, Loiborsireet, Kimotorok and Oltukai adjacent to protected areas. Data collected include number and species of tsetse flies caught in baited traps, PCR identification of trypanosome species and extraction of monitored Normalized Difference Vegetation Index (NDVI) data from Moderate Resolution Imaging Spectrometer (MODIS). RESULTS: Our findings demonstrate the variation of tsetse fly species abundance and infection rates among habitats in surveyed villages in relation to NDVI and host abundance. Results have shown higher tsetse fly abundance in Acacia-swampy ecotone and riverine habitats for Emboreet and other villages, respectively. Tsetse abundance was inconsistent among habitats in different villages. Emboreet was highly infested with Glossina swynnertoni (68%) in ecotone and swampy habitats followed by G. morsitans (28%) and G. pallidipes (4%) in riverine habitat. In the remaining villages, the dominant tsetse fly species by 95% was G. pallidipes in all habitats. Trypanosoma vivax was the most prevalent species in all infected flies (95%) with few observations of co-infections (with T. congolense or T. brucei). CONCLUSIONS: The findings of this study provide a framework to mapping hotspots of tsetse infestation and trypanosomiasis infection and enhance the communities to plan for effective control of trypanosomiasis.

Variation of tsetse fly abundance in relation to habitat and host presence in the Maasai Steppe, Tanzania.

Human activities modify ecosystem structure and function and can also alter the vital rates of vectors and thus the risk of infection with vector-borne diseases. In the Maasai Steppe ecosystem of northern Tanzania, local communities depend on livestock and suitable pasture that is shared with wildlife, which can increase tsetse abundance and the risk of trypanosomiasis. We monitored the monthly tsetse fly abundance adjacent to Tarangire National Park in 2014-2015 using geo-referenced, baited epsilon traps. We examined the effect of habitat types and vegetation greenness (NDVI) on the relative abundance of tsetse fly species. Host availability (livestock and wildlife) was also recorded within 100×100 m of each trap site. The highest tsetse abundance was found in the ecotone between Acacia-Commiphora woodland and grassland, and the lowest in riverine woodland. Glossina swynnertoni was the most abundant species (68%) trapped throughout the entire study, while G. pallidipes was the least common (4%). Relative species abundance was negatively associated with NDVI, with greatest abundance observed in the dry season. The relationship with the abundance of wildlife and livestock was more complex, as we found positive and negative associations depending on the host and fly species. While habitat is important for tsetse distribution, hosts also play a critical role in affecting fly abundance and, potentially, trypanosomiasis risk.

Seasonal variation of tsetse fly species abundance and prevalence of trypanosomes in the Maasai Steppe, Tanzania.

Tsetse flies, the vectors of trypanosomiasis, represent a threat to public health and economy in sub-Saharan Africa. Despite these concerns, information on temporal and spatial dynamics of tsetse and trypanosomes remain limited and may be a reason that control strategies are less effective. The current study assessed the temporal variation of the relative abundance of tsetse fly species and trypanosome prevalence in relation to climate in the Maasai Steppe of Tanzania in 2014-2015. Tsetse flies were captured using odor-baited Epsilon traps deployed in ten sites selected through random subsampling of the major vegetation types in the area. Fly species were identified morphologically and trypanosome species classified using PCR. The climate dataset was acquired from the African Flood and Drought Monitor repository. Three species of tsetse flies were identified: G. swynnertoni (70.8%), G. m. morsitans (23.4%), and G.pallidipes (5.8%). All species showed monthly changes in abundance with most of the flies collected in July. The relative abundance of G. m. morsitans and G. swynnertoni was negatively correlated with maximum and minimum temperature, respectively. Three trypanosome species were recorded: T. vivax (82.1%), T. brucei (8.93%), and T. congolense (3.57%). The peak of trypanosome infections in the flies was found in October and was three months after the tsetse abundance peak; prevalence was negatively correlated with tsetse abundance. A strong positive relationship was found between trypanosome prevalence and temperature. In conclusion, we find that trypanosome prevalence is dependent on fly availability, and temperature drives both tsetse fly relative abundance and trypanosome prevalence.

Opportunities for the application of advanced remotely-sensed data in ecological studies of terrestrial animal movement.

Animal movement patterns in space and time are a central aspect of animal ecology. Remotely-sensed environmental indices can play a key role in understanding movement patterns by providing contiguous, relatively fine-scale data that link animal movements to their environment. Still, implementation of newly available remotely-sensed data is often delayed in studies of animal movement, calling for a better flow of information to researchers less familiar with remotely-sensed data applications. Here, we reviewed the application of remotely-sensed environmental indices to infer movement patterns of animals in terrestrial systems in studies published between 2002 and 2013. Next, we introduced newly available remotely-sensed products, and discussed their opportunities for animal movement studies. Studies of coarse-scale movement mostly relied on satellite data representing plant phenology or climate and weather. Studies of small-scale movement frequently used land cover data based on Landsat imagery or aerial photographs. Greater documentation of the type and resolution of remotely-sensed products in ecological movement studies would enhance their usefulness. Recent advancements in remote sensing technology improve assessments of temporal dynamics of landscapes and the three-dimensional structures of habitats, enabling near real-time environmental assessment. Online movement databases that now integrate remotely-sensed data facilitate access to remotely-sensed products for movement ecologists. We recommend that animal movement studies incorporate remotely-sensed products that provide time series of environmental response variables. This would facilitate wildlife management and conservation efforts, as well as the predictive ability of movement analyses. Closer collaboration between ecologists and remote sensing experts could considerably alleviate the implementation gap. Ecologists should not expect that indices derived from remotely-sensed data will be directly analogous to field-collected data and need to critically consider which remotely-sensed product is best suited for a given analysis.

Quantity and configuration of available elephant habitat and related conservation concerns in the Lower Kinabatangan floodplain of Sabah, Malaysia.

The approximately 300 (298, 95% CI: 152-581) elephants in the Lower Kinabatangan Managed Elephant Range in Sabah, Malaysian Borneo are a priority sub-population for Borneo's total elephant population (2,040, 95% CI: 1,184-3,652). Habitat loss and human-elephant conflict are recognized as the major threats to Bornean elephant survival. In the Kinabatangan region, human settlements and agricultural development for oil palm drive an intense fragmentation process. Electric fences guard against elephant crop raiding but also remove access to suitable habitat patches. We conducted expert opinion-based least-cost analyses, to model the quantity and configuration of available suitable elephant habitat in the Lower Kinabatangan, and called this the Elephant Habitat Linkage. At 184 km(2), our estimate of available habitat is 54% smaller than the estimate used in the State's Elephant Action Plan for the Lower Kinabatangan Managed Elephant Range (400 km(2)). During high flood levels, available habitat is reduced to only 61 km(2). As a consequence, short-term elephant densities are likely to surge during floods to 4.83 km(-2) (95% CI: 2.46-9.41), among the highest estimated for forest-dwelling elephants in Asia or Africa. During severe floods, the configuration of remaining elephant habitat and the surge in elephant density may put two villages at elevated risk of human-elephant conflict. Lower Kinabatangan elephants are vulnerable to the natural disturbance regime of the river due to their limited dispersal options. Twenty bottlenecks less than one km wide throughout the Elephant Habitat Linkage, have the potential to further reduce access to suitable habitat. Rebuilding landscape connectivity to isolated habitat patches and to the North Kinabatangan Managed Elephant Range (less than 35 km inland) are conservation priorities that would increase the quantity of available habitat, and may work as a mechanism to allow population release, lower elephant density, reduce human-elephant conflict, and enable genetic mixing.

Identifying source populations and genetic structure for savannah elephants in human-dominated landscapes and protected areas in the Kenya-Tanzania borderlands.

We investigated the genetic metapopulation structure of elephants across the trans Rift Valley region of Kenya and Tanzania, one of the remaining strongholds for savannah elephants (Loxodonata africana) in East Africa, using microsatellite and mitochondrial DNA (mtDNA) markers. We then examined this population structure to determine the source population for a recent colonization event of savannah elephants on community-owned land within the trans rift valley region. Four of the five sampled populations showed significant genetic differentiation (p<0.05) as measured with both mtDNA haplotypes and microsatellites. Only the samples from the adjacent Maasai Mara and Serengeti ecosystems showed no significant differentiation. A phylogenetic neighbour-joining tree constructed from mtDNA haplotypes detected four clades. Clade four corresponds to the F clade of previous mtDNA studies that reported to have originated in forest elephants (Loxodonta cyclotis) but to also be present in some savannah elephant populations. The split between clade four and the other three clades corresponded strongly to the geographic distribution of mtDNA haplotypes across the rift valley in the study area. Clade four was the dominant clade detected on the west side of the rift valley with rare occurrences on the east side. Finally, the strong patterns of population differentiation clearly indicated that the recent colonists to the community-owned land in Kenya came from the west side of the rift valley. Our results indicate strong female philopatry within the isolated populations of the trans rift valley region, with gene flow primarily mediated via male movements. The recent colonization event from Maasai Mara or Serengeti suggests there is hope for maintaining connectivity and population viability outside formal protected areas in the region.