Catastrophic ape decline in western equatorial Africa

Genetically encoded sensors for in vivo detection of neurochemicals relevant to depression

Depressive disorders are a common and debilitating form of mental illness with significant impacts on individuals and society. Despite the high prevalence, the underlying causes and mechanisms of depressive disorders are still poorly understood. Neurochemical systems, including serotonin, norepinephrine, and dopamine, have been implicated in the development and perpetuation of depressive symptoms. Current treatments for depression target these neuromodulator systems, but there is a need for a better understanding of their role in order to develop more effective treatments. Monitoring neurochemical dynamics during depressive symptoms is crucial for gaining a better a understanding of their involvement in depressive disorders. Genetically encoded sensors have emerged recently that offer high spatial-temporal resolution and the ability to monitor neurochemical dynamics in real time. This review explores the neurochemical systems involved in depression and discusses the applications and limitations of current monitoring tools for neurochemical dynamics. It also highlights the potential of genetically encoded sensors for better characterizing neurochemical dynamics in depression-related behaviors. Furthermore, potential improvements to current sensors are discussed in order to meet the requirements of depression research.

Absence of Coronavirus RNA in Faecal Samples from Wild Primates in Gabon, Central Africa

Coronaviruses (CoVs, Coronaviridae) are a diverse group of viruses that infect mammals, birds, and fish. Seven CoVs infect humans, among which Severe Acute Respiratory Syndrome CoVs-1 and -2 and Middle East respiratory syndrome CoVs have shown how they can impact global health and the economy. Their spillover from bats-the natural reservoir-to humans has required intermediary hosts. Prevention requires that active surveillance be conducted on animals. Today, there is no data concerning the genetic diversity of CoVs naturally circulating in wild primates. This study aimed to screen wild great apes and mandrills in Gabon for CoVs. A total of 229 faecal samples of great apes and mandrills collected from 2009 to 2012 in forests and national parks were used for the detection of CoVs by nested PCR using primers targeting a conserved region of the RNA-dependent RNA polymerase. While all samples were negative, this lack of detection could be related to sample size, the transient nature of the infection, or because faecal samples are not suitable for detecting CoVs in primates. A longitudinal study should be performed and other non-invasive methods used to collect respiratory samples to better evaluate the circulation of CoVs in these primates.

Projecting the impact of an ebola virus outbreak on endangered mountain gorillas

Ebola virus is highly lethal for great apes. Estimated mortality rates up to 98% have reduced the global gorilla population by approximately one-third. As mountain gorillas (Gorilla beringei beringei) are endangered, with just over 1000 individuals remaining in the world, an outbreak could decimate the population. Simulation modeling was used to evaluate the potential impact of an Ebola virus outbreak on the mountain gorilla population of the Virunga Massif. Findings indicate that estimated contact rates among gorilla groups are high enough to allow rapid spread of Ebola, with less than 20% of the population projected to survive at 100 days post-infection of just one gorilla. Despite increasing survival with vaccination, no modeled vaccination strategy prevented widespread infection. However, the model projected that survival rates greater than 50% could be achieved by vaccinating at least half the habituated gorillas within 3 weeks of the first infectious individual.

The challenges of open data for future epidemic preparedness: The experience of the 2022 Ebolavirus outbreak in Uganda

On 20 September 2022, the Ministry of Health in Uganda, together with the World Health Organization-Regional Office for Africa (WHO AFRO) confirmed an outbreak of EVD due to Sudan ebolavirus in Mubende District, after one fatal case was confirmed. Real-time information are needed to provide crucial information to understand transmissibility, risk of geographical spread, routes of transmission, risk factors of infection, and provide the basis for epidemiological modelling that can inform response and containment planning to reduce the burden of disease. We made an effort to build a centralized repository of the Ebola virus cases from verified sources, providing information on dates of symptom onset, locations (aggregated to the district level), and when available, the gender and status of hospitals, reporting bed capacity and isolation unit occupancy rate according to the severity status of the patient. The proposed data repository provides researchers and policymakers timely, complete, and easy-accessible data to monitor the most recent trends of the Ebola outbreak in Ugandan districts with informative graphical outputs. This favors a rapid global response to the disease, enabling governments to prioritize and adjust their decisions quickly and effectively in response to the rapidly evolving emergency, with a solid data basis.

Epidemiology of Ebolaviruses from an Etiological Perspective

Since the inception of the ebolavirus in 1976, 32 outbreaks have resulted in nearly 15,350 deaths in more than ten countries of the African continent. In the last decade, the largest (2013-2016) and second largest (2018-2020) ebolavirus outbreaks have occurred in West Africa (mainly Guinea, Liberia, and Sierra Leone) and the Democratic Republic of the Congo, respectively. The 2013-2016 outbreak indicated an alarming geographical spread of the virus and was the first to qualify as an epidemic. Hence, it is imperative to halt ebolavirus progression and develop effective countermeasures. Despite several research efforts, ebolaviruses' natural hosts and secondary reservoirs still elude the scientific world. The primary source responsible for infecting the index case is also unknown for most outbreaks. In this review, we summarize the history of ebolavirus outbreaks with a focus on etiology, natural hosts, zoonotic reservoirs, and transmission mechanisms. We also discuss the reasons why the African continent is the most affected region and identify steps to contain this virus.

Estimating animal abundance at multiple scales by spatially explicit capture-recapture

Information about how animal abundance varies across landscapes is needed to inform management action but is costly and time-consuming to obtain; surveys of a single population distributed over a large area can take years to complete. Surveys employing small, spatially replicated sampling units improve efficiency, but statistical estimators rely on assumptions that constrain survey design or become less reasonable as larger areas are sampled. Efficient methods that avoid assumptions about similarity of detectability or density among replicates are therefore appealing. Using simulations and data from >3500 black bears sampled on 73 independent study areas in Ontario, Canada, we (1) quantified bias induced by unmodeled spatial heterogeneity in detectability and density; (2) evaluated novel, design-based estimators of average density across replicate study areas; and (3) evaluated two estimators of the variance of average density across study areas: an analytic estimator that assumed an underlying homogeneous spatial Poisson point process for the distribution of animals' activity centers, and an empirical estimator of variance across study areas. In simulations where detectability varied in space, assuming spatially constant detectability yielded density estimates that were negatively biased by 20% to 30%; estimating local detectability and density from local data and treating study areas as independent, equal replicates when estimating average density across study areas using the design-based estimator yielded unbiased estimates at local and landscape scales. Similarly, detectability of black bears varied among study areas and estimates of bear density at landscape scales were higher when no information was shared across study areas when estimating detectability. This approach also maximized precision (relative SEs of estimates of average black bear density ranged from 7% to 18%) and computational efficiency. In simulations, the analytic variance estimator was robust to threefold variation in local densities but the empirical estimator performed poorly. Conducting multiple, similar SECR surveys and treating them as independent replicates during analyses allowed us to efficiently estimate density at multiple scales and extents while avoiding biases caused by pooling spatially heterogeneous data. This approach enables researchers to address a wide range of ecological or management-related questions and is applicable with most types of SECR data.

Phylogenetic Groups, Pathotypes and Antimicrobial Resistance of Escherichia coli Isolated from Western Lowland Gorilla Faeces (Gorilla gorilla gorilla) of Moukalaba-Doudou National Park (MDNP)

(1) Background: Terrestrial mammals in protected areas have been identified as a potential source of antimicrobial-resistant bacteria. Studies on antimicrobial resistance in gorillas have already been conducted. Thus, this study aimed to describe the phylogroups, pathotypes and prevalence of antimicrobial resistance of Escherichia coli isolated from western lowland gorilla's faeces living in MDNP. (2) Materials and Methods: Ninety-six faecal samples were collected from western lowland gorillas (Gorilla gorilla gorilla) during daily monitoring in the MDNP. Sixty-four E. coli isolates were obtained and screened for phylogenetic and pathotype group genes by polymerase chain reaction (PCR) after DNA extraction. In addition, antimicrobial susceptibility was determined by the disk diffusion method on Mueller Hinton agar. (3) Results: Sixty-four (64%) isolates of E. coli were obtained from samples. A high level of resistance to the beta-lactam family, a moderate rate for fluoroquinolone and a low rate for aminoglycoside was obtained. All E. coli isolates were positive in phylogroup PCR with a predominance of A (69% ± 11.36%), followed by B2 (20% ± 19.89%) and B1 (10% ± 8.90%) and low prevalence for D (1% ± 3.04%). In addition, twenty E. coli isolates (31%) were positive for pathotype PCR, such as EPEC (85% ± 10.82%) and EPEC/EHEC (15% ± 5.18%) that were obtained in this study. The majority of these MDR E. coli (DECs) belonged to phylogenetic group A, followed by MDR E. coli (DECs) belonging to group B2. (4) Conclusion: This study is the first description of MDR E. coli (DECs) assigned to phylogroup A in western lowland gorillas from the MDNP in Gabon. Thus, wild gorillas in MDNP could be considered as asymptomatic carriers of potential pathogenic MDR E. coli (DECs) that may present a potential risk to human health.

Global protected areas seem insufficient to safeguard half of the world's mammals from human-induced extinction

Protected areas are vital for conserving global biodiversity, but we lack information on the extent to which the current global protected area network is able to prevent local extinctions. Here we investigate this by assessing the potential size of individual populations of nearly 4,000 terrestrial mammals within protected areas. We find that many existing protected areas are too small or too poorly connected to provide robust and resilient protection for almost all mammal species that are threatened with extinction and for over 1,000 species that are not currently threatened. These results highlight that global biodiversity targets must reflect ecological realities by incorporating spatial structure and estimates of population viability, rather than relying simply on the total area of land protected.

Protected areas (PAs) are a cornerstone of global conservation and central to international plans to minimize global extinctions. During the coming century, global ecosystem destruction and fragmentation associated with increased human population and economic activity could make the long-term survival of most terrestrial vertebrates even more dependent on PAs. However, the capacity of the current global PA network to sustain species for the long term is unknown. Here, we explore this question for all nonvolant terrestrial mammals for which we found sufficient data, ∼4,000 species. We first estimate the potential population size of each such mammal species in each PA and then use three different criteria to estimate if solely the current global network of PAs might be sufficient for their long-term survival. Our analyses suggest that current PAs may fail to provide robust protection for about half the species analyzed, including most species currently listed as threatened with extinction and a third of species not currently listed as threatened. Hundreds of mammal species appear to have no viable protected populations. Underprotected species were found across all body sizes, taxonomic groups, and geographic regions. Large-bodied mammals, endemic species, and those in high-biodiversity tropical regions were particularly poorly protected by existing PAs. As new international biodiversity targets are formulated, our results suggest that the global network of PAs must be greatly expanded and most importantly that PAs must be located in diverse regions that encompass species not currently protected and must be large enough to ensure that protected species can persist for the long term.

Parasite dynamics in North American monarchs predicted by host density and seasonal migratory culling

Insect-pathogen dynamics can show seasonal and inter-annual variation that covaries with fluctuations in insect abundance and climate. Long-term analyses are especially needed to track parasite dynamics in migratory insects, in part because their vast habitat ranges and high mobility might dampen local effects of density and climate on infection prevalence. Monarch butterflies (Danaus plexippus) are commonly infected with the protozoan Ophryocystis elektroscirrha (OE). Because this parasite lowers monarch survival and flight performance, and because migratory monarchs have experienced declines in recent decades, it is important to understand patterns and drivers of infection. 3. Here we compiled data on OE infection spanning 50 years, from wild monarchs sampled in the USA, Canada, and Mexico during summer breeding, fall migrating, and overwintering periods. We examined eastern versus western North American monarchs separately, to ask how abundance estimates, resource availability, climate, and breeding season length impact infection trends. We further assessed the intensity of migratory culling, which occurs when infected individuals are removed from the population during migration. 4. Average infection prevalence was four times higher in western compared to eastern subpopulations. In eastern North America, the proportion of infected monarchs increased three-fold since the mid-2000s. In the western region, the proportion of infected monarchs declined sharply from 2000-2015, and increased thereafter. For both eastern and western subpopulations, years with greater summer adult abundance predicted greater infection prevalence, indicating that transmission increases with host breeding density. Environmental variables (temperature and NDVI) were not associated with changes in infected adults. We found evidence for migratory culling of infected butterflies, based on declines in parasitism during fall migration. We estimated that tens of millions fewer monarchs reach overwintering sites in Mexico as a result of OE, highlighting the need to consider the parasite as a potential threat to the monarch population. 5. Increases in infection among eastern North American monarchs post-2002 suggest that changes to the host's ecology or environment have intensified parasite transmission. Further work is needed to examine the degree to which human practices, such as mass caterpillar rearing and the widespread planting of exotic milkweed, have contributed to this trend.

The impacts of human activity on mammals in a community forest near the Dja Biosphere Reserve in Cameroon

Human activity in African tropical rainforests continues to threaten wild mammals. Many rural communities are dependent on hunting, yet there is a widespread lack of baseline data on ecology and the sustainability of hunting. We investigated the impacts of human activity on mammal species composition and distributions within a community forest surrounding a village in the buffer zone of the Dja Biosphere Reserve in south-east Cameroon. We conducted a camera-trap survey in August–November 2017 and detected 24 mammal species, including Critically Endangered western lowland gorilla Gorilla gorilla gorilla, Endangered central African chimpanzee Pan troglodytes troglodytes and Endangered tree pangolin Phataginus tricuspis. We used occupancy analysis to explore relationships between indicators of human activity (distance to a road and the Reserve), habitat quality (distance to the river and tree cover) and the distributions of species. We found that the local distribution of threatened mammals was not apparently limited by human activity, and proximity to the road did not negatively influence occupancy for any species. However, most of the Reserve's large species were not detected, including the African forest elephant Loxodonta cyclotis and the largest ungulates, and the occupancy of two species commonly hunted for wild meat was positively correlated with distance from the village, indicating hunting may be unsustainable. Our results show that the community forest provides habitat for threatened species outside the Reserve and in close proximity to people. However, effective conservation management will require continued monitoring and research to determine whether current rates of hunting are sustainable.

The complex Y-chromosomal history of gorillas

Studies of the evolutionary relationships among gorilla populations using autosomal and mitochondrial sequences suggest that male-mediated gene flow may have been important in the past, but data on the Y-chromosomal relationships among the gorilla subspecies are limited. Here, we genotyped blood and noninvasively collected fecal samples from 12 captives and 257 wild male gorillas of known origin representing all four subspecies (Gorilla gorilla gorilla, G. g. diehli, G. beringei beringei, and G. b. graueri) at 10 Y-linked microsatellite loci resulting in 102 unique Y-haplotypes for 224 individuals. We found that western lowland gorilla (G. g. gorilla) haplotypes were consistently more diverse than any other subspecies for all measures of diversity and comprised several genetically distinct groups. However, these did not correspond to geographical proximity and some closely related haplotypes were found several hundred kilometers apart. Similarly, our broad sampling of eastern gorillas revealed that mountain (G. b. beringei) and Grauer's (G. b. graueri) gorilla Y-chromosomal haplotypes did not form distinct clusters. These observations suggest structure in the ancestral population with subsequent mixing of differentiated haplotypes by male dispersal for western lowland gorillas, and postisolation migration or incomplete lineage sorting due to short divergence times for eastern gorillas.

Respiratory Disease Risk of Zoo-Housed Bonobos Is Associated with Sex and Betweenness Centrality in the Proximity Network

Infectious diseases can be considered a threat to animal welfare and are commonly spread through both direct and indirect social interactions with conspecifics. This is especially true for species with complex social lives, like primates. While several studies have investigated the impact of sociality on disease risk in primates, only a handful have focused on respiratory disease, despite it being a major cause of morbidity and mortality in both wild and captive populations and thus an important threat to primate welfare. Therefore, we examined the role of social-network position on the occurrence of respiratory disease symptoms during one winter season in a relatively large group of 20 zoo-housed bonobos with managed fission-fusion dynamics. We found that within the proximity network, symptoms were more likely to occur in individuals with higher betweenness centrality, which are individuals that form bridges between different parts of the network. Symptoms were also more likely to occur in males than in females, independent of their social-network position. Taken together, these results highlight a combined role of close proximity and sex in increased risk of attracting respiratory disease, two factors that can be taken into account for further welfare management of the species.

The genetic impact of an Ebola outbreak on a wild gorilla population

Background

Numerous Ebola virus outbreaks have occurred in Equatorial Africa over the past decades. Besides human fatalities, gorillas and chimpanzees have also succumbed to the fatal virus. The 2004 outbreak at the Odzala-Kokoua National Park (Republic of Congo) alone caused a severe decline in the resident western lowland gorilla (Gorilla gorilla gorilla) population, with a 95% mortality rate. Here, we explore the immediate genetic impact of the Ebola outbreak in the western lowland gorilla population.

Results

Associations with survivorship were evaluated by utilizing DNA obtained from fecal samples from 16 gorilla individuals declared missing after the outbreak (non-survivors) and 15 individuals observed before and after the epidemic (survivors). We used a target enrichment approach to capture the sequences of 123 genes previously associated with immunology and Ebola virus resistance and additionally analyzed the gut microbiome which could influence the survival after an infection. Our results indicate no changes in the population genetic diversity before and after the Ebola outbreak, and no significant differences in microbial community composition between survivors and non-survivors. However, and despite the low power for an association analysis, we do detect six nominally significant missense mutations in four genes that might be candidate variants associated with an increased chance of survival.

Conclusion

This study offers the first insight to the genetics of a wild great ape population before and after an Ebola outbreak using target capture experiments from fecal samples, and presents a list of candidate loci that may have facilitated their survival.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08025-y.

Rapid transmission of respiratory infections within but not between mountain gorilla groups

Minimizing disease transmission between humans and wild apes and controlling outbreaks in ape populations is vital to both ape conservation and human health, but information on the transmission of real infections in wild populations is rare. We analyzed respiratory outbreaks in a subpopulation of wild mountain gorillas (Gorilla beringei beringei) between 2004 and 2020. We investigated transmission within groups during 7 outbreaks using social networks based on contact and proximity, and transmission between groups during 15 outbreaks using inter-group encounters, transfers and home range overlap. Patterns of contact and proximity within groups were highly predictable based on gorillas' age and sex. Disease transmission within groups was rapid with a median estimated basic reproductive number (R0) of 4.18 (min = 1.74, max = 9.42), and transmission was not predicted by the social network. Between groups, encounters and transfers did not appear to have enabled disease transmission and the overlap of groups' ranges did not predict concurrent outbreaks. Our findings suggest that gorilla social structure, with many strong connections within groups and weak ties between groups, may enable rapid transmission within a group once an infection is present, but limit the transmission of infections between groups.

Mitigating Impacts of the COVID-19 Pandemic on Gorilla Conservation: Lessons From Bwindi Impenetrable Forest, Uganda

The COVID-19 pandemic, affecting all countries, with millions of cases and deaths, and economic disruptions due to lockdowns, also threatens the health and conservation of endangered mountain gorillas. For example, increased poaching due to absence of tourism income, led to the killing on 1st June 2020 of a gorilla by a hungry community member hunting duiker and bush pigs. Conservation Through Public Health (CTPH), a grassroots NGO and non-profit founded in 2003 promotes biodiversity conservation by enabling people to co-exist with wildlife through integrated programs that improve animal health, community health, and livelihoods in and around Africa's protected areas and wildlife rich habitats. Through these programs, we have helped to mitigate these impacts. CTPH worked with Uganda Wildlife Authority and other NGOs to improve great ape viewing guidelines and prevent transmission of COVID-19 between people and gorillas. Park staff, Gorilla Guardians herding gorillas from community land to the park and Village Health and Conservation Teams were trained to put on protective face masks, enforce hand hygiene and a 10-meter great ape viewing distance. To reduce the communities' need to poach, CTPH found a UK-based distributor, for its Gorilla Conservation Coffee social enterprise enabling coffee farmers to earn revenue in the absence of tourism and provided fast growing seedlings to reduce hunger in vulnerable community members. Lessons learned show the need to support non-tourism dependent community livelihoods, and more responsible tourism to the great apes, which CTPH is advocating to governments, donors and tour companies through an Africa CSO Biodiversity Alliance policy brief.

What does it mean to be wild? Assessing human influence on the environments of nonhuman primate specimens in museum collections

OBJECTIVES

Natural history collections are often thought to represent environments in a pristine natural state-free from human intervention-the so-called "wild." In this study, we aim to assess the level of human influence represented by natural history collections of wild-collected primates over 120 years at the Smithsonian Institution's National Museum of Natural History (NMNH).

MATERIALS AND METHODS

Our sample consisted of 875 catarrhine primate specimens in NMNH collections, representing 13 genera collected in 39 countries from 1882 to 2004. Using archival and accession information we determined the approximate locations from which specimens were collected. We then plotted location coordinates onto publicly available anthrome maps created by Ellis et al. (Global Ecology and Biogeography, 2010, 19, 589), which delineate terrestrial biomes of human population density and land use worldwide since the 1700s.

RESULTS

We found that among primates collected from their native ranges, 92% were from an environment that had some level of human impact, suggesting that the majority of presumed wild-collected primate specimens lived in an environment influenced by humans during their lifetimes.

DISCUSSION

The degree to which human-modified environments may have impacted the lives of primates currently held in museum collections has been historically ignored, implicating unforeseen consequences for collection-based research. While unique effects related to commensalism with humans remain understudied, effects currently attributed to natural phenomena may, in fact, be related to anthropogenic pressures on unmanaged populations of primates.

Primate conservation: Lessons learned in the last 20 years can guide future efforts

Twenty years ago, we published an assessment of the threats facing primates and with the passing of two decades, we re-evaluate identified threats, consider emerging pressures, identify exciting new avenues of research, and tackle how to change the system to rapidly advance primate and primate habitat conservation. Habitat destruction and hunting have increased, the danger of looming climate change is clearer, and there are emerging threats such as the sublethal effects of microplastics and pesticides. Despite these negative developments, protected areas are increasing, exciting new tools are now available, and the number of studies has grown exponentially. Many of the changes that need to occur to make rapid progress in primate conservation are in our purview to modify. We identify several dimensions indicating the time is right to make large advances; however, the question that remains is do we have the will to prevent widespread primate annihilation and extinction?

Consumption of cultivated subterranean plant organs by chimpanzees in a human-dominated landscape

Although chimpanzees (Pan troglodytes) are ripe fruit specialists, they sometimes consume other plant parts including subterranean organs like roots and tubers. Such plant parts, which include underground storage organs (USOs), have been found to play a key role in the diets of some chimpanzee populations as well as, potentially, our hominin ancestors. We report the confirmed consumption of subterranean plant organs of three species — sweet potatoes (Ipomoea batatas), yams (Dioscorea alata) and peanuts (Arachis hypogaea), as well as unconfirmed consumption of cassava (Manihot esculenta) — by chimpanzees in a human-dominated landscape in western Uganda. These observations point toward the dietary flexibility of chimpanzees inhabiting anthropogenic landscapes, though mechanisms of novel food acquisition, particularly for subterranean fruits and tubers, are not well understood. Dietary flexibility may help chimpanzees survive as natural forest resources disappear, but simultaneously may bring them into greater conflict with their human neighbours, thereby further imperilling them.

A great ape perspective on the origins and evolution of human viruses

Over the last two decades, the viromes of our closest relatives, the African great apes (AGA), have been intensively studied. Comparative approaches have unveiled diverse evolutionary patterns, highlighting both stable host-virus associations over extended evolutionary timescales and much more recent viral emergence events. In this chapter, we summarize these findings and outline how they have shed a new light on the origins and evolution of many human-infecting viruses. We also show how this knowledge can be used to better understand the evolution of human health in relation to viral infections.

No time to rest: How the effects of climate change on nest decay threaten the conservation of apes in the wild

Since 1994, IUCN Red List assessments apply globally acknowledged standards to assess species distribution, abundance and trends. The extinction risk of a species has a major impact on conservation science and international funding mechanisms. Great ape species are listed as Endangered or Critically Endangered. Their populations are often assessed using their unique habit of constructing sleeping platforms, called nests. As nests rather than apes are counted, it is necessary to know the time it takes for nests to disappear to convert nest counts into ape numbers. However, nest decomposition is highly variable across sites and time and the factors involved are poorly understood. Here, we used 1,511 bonobo (Pan paniscus) nests and 15 years of climatic data (2003-2018) from the research site LuiKotale, Democratic Republic of the Congo, to investigate the effects of climate change and behavioural factors on nest decay time, using a Bayesian gamma survival model. We also tested the logistic regression method, a recommended time-efficient option for estimating nest decay time. Our climatic data showed a decreasing trend in precipitation across the 15 years of study. We found bonobo nests to have longer decay times in recent years. While the number of storms was the main factor driving nest decay time, nest construction type and tree species used were also important. We also found evidence for bonobo nesting behaviour being adapted to climatic conditions, namely strengthening the nest structure in response to unpredictable, harsh precipitation. By highlighting methodological caveats, we show that logistic regression is effective in estimating nest decay time under certain conditions. Our study reveals the impact of climate change on nest decay time in a tropical remote area. Failure to account for these changes would invalidate biomonitoring estimates of global significance, and subsequently jeopardize the conservation of great apes in the wild.

Long-term trends in a forest ungulate community: park establishment increases numbers, but poaching is a constant threat

Deforestation represents one of the greatest threats to tropical forest mammals, and the situation is greatly exacerbated by bushmeat hunting. To construct informed conservation plans, information must be gathered about responses to habitat degradation, regeneration, and hunting over a sufficiently long period to allow demographic responses. We quantified changes in the abundance of three commonly occurring ungulate species (i.e., bushbuck, Tragelaphus scriptus; red duiker, Cephalophus sp.; blue duiker, Cephalophus monticola) at eight sites in Kibale National Park, Uganda (old growth=3; logged=3; regenerating=2) for 23 years. Changes in abundance (363 surveys totaling 1 450 km) were considered in regard to the park's management strategy, regional economic indicators, and estimates of illegal hunting. Bushbuck abundance increased in old-growth and logged forests from 1996 to 2009, and then oscillated around this level or declined. Duiker abundance demonstrated a similar pattern, but abundance in the old-growth forests showed a general increase from 1996 to present day. Duiker abundance in the logged forests exhibited an early increase, but subsequent oscillation. Poaching signs per patrol have remained stable over the last decade, despite increases in the size of the surrounding population, cost of living, and cost of schooling, thus reflecting successful efforts in conservation education and enforcement. Our study highlights the positive impact of park establishment, patrol, and conservation efforts on ungulate populations and shows the adaptability of forest mammal populations to different management schemes.

Serological Evidence for Henipa-like and Filo-like Viruses in Trinidad Bats

Bat-borne zoonotic pathogens belonging to the family Paramxyoviridae, including Nipah and Hendra viruses, and the family Filoviridae, including Ebola and Marburg viruses, can cause severe disease and high mortality rates on spillover into human populations. Surveillance efforts for henipaviruses and filoviruses have been largely restricted to the Old World; however, recent studies suggest a potentially broader distribution for henipaviruses and filoviruses than previously recognized. In the current study, we screened for henipaviruses and filoviruses in New World bats collected across 4 locations in Trinidad near the coast of Venezuela. Bat tissue samples were screened using previously established reverse-transcription polymerase chain reaction assays. Serum were screened using a multiplex immunoassay to detect antibodies reactive with the envelope glycoprotein of viruses in the genus Henipavirus and the family Filoviridae. Serum samples were also screened by means of enzyme-linked immunosorbent assay for antibodies reactive with Nipah G and F glycoproteins. Of 84 serum samples, 28 were reactive with ≥1 henipavirus glycoprotein by ≥1 serological method, and 6 serum samples were reactive against ≥1 filovirus glycoproteins. These data provide evidence of potential circulation of viruses related to the henipaviruses and filoviruses in New World bats.

Human Activity and Forest Degradation Threaten Populations of the Nigeria–Cameroon Chimpanzee (Pan troglodytes ellioti) in Western Cameroon

Increased human activities such as commodity-led deforestation, extension of agriculture, urbanization, and wildfires are major drivers of forest loss worldwide. In Cameroon, these activities cause a loss of suitable primate habitat and could ultimately threaten the survival of chimpanzees (Pan troglodytes). We derived independent estimates of the population size of the Endangered Nigeria–Cameroon chimpanzee (Pan troglodytes ellioti) in Kom-Wum Forest Reserve, Cameroon, and surrounding unprotected forest areas through 1) direct observations, 2) camera trapping, 3) distance sampling, 4) marked nest counts, and 5) standing crop nest counts. In addition, we georeferenced signs of chimpanzee and human activity along line transects. We used a generalized linear mixed model to predict the occurrence of chimpanzees in response to edge length (measured as the perimeter of core forest patches), core area of forest patches (measured as area of forest patches beyond an edge width of 100 m), habitat perforation (measured as the perimeter of nonforested landscape within core forest patches), patch size(measured as area of forest patches), and forest cover. Chimpanzee density estimates ranged from 0.1 (direct observation) to 0.9 (distance sampling) individuals km−2 depending on estimation method with a mean nest group size of 7 ± 5.4 (SD). The mean encounter rate for signs of chimpanzee activity was significantly higher in mature forests (2.3 signs km−1) than in secondary forests (0.3 signs km−1) and above 1000 m elevation (4.0 signs km−1) than below 1000 m (1.0 signs km−1). The mean encounter rate for signs of human activity was significantly higher in secondary (8.0 signs km−1) than in mature forests (0.9 signs km−1). Secondary forests, habitat perforation, and edge length had a significant negative effect on the occurrence of chimpanzee signs. Overall, human activity and forest degradation affected the number of observed chimpanzee signs negatively. Regular antipoaching patrols and reforestation programs in degraded areas could potentially reduce threats to populations of endangered species and may increase suitable habitat area.

Mapping suitable great ape habitat in and around the Lobéké National Park, South-East Cameroon

As a result of extensive data collection efforts over the last 20-30 years, there is quite a good understanding of the large-scale geographic distribution and range limits of African great apes. However, as human activities increasingly fragment great ape spatial distribution, a better understanding of what constitutes suitable great ape habitat is needed to inform conservation and resource extraction management. Chimpanzees (Pan troglodytes troglodytes) and gorillas (Gorilla gorilla gorilla) inhabit the Lobéké National Park and its surrounding forest management units (FMUs) in South-East Cameroon. Both park and neighboring forestry concessions require reliable evidence on key factors driving great ape distribution for their management plans, yet this information is largely missing and incomplete. This study aimed at mapping great ape habitat suitability in the area and at identifying the most influential predictors among three predictor categories, including landscape predictors (dense forest, swampy forest, distance to water bodies, and topography), human disturbance predictors (hunting, deforestation, distance to roads, and population density), and bioclimatic predictor (annual precipitation). We found that about 63% of highly to moderately suitable chimpanzee habitat occurred within the Lobéké National Park, while only 8.4% of similar habitat conditions occurred within FMUs. For gorillas, highly and moderately suitable habitats occurred within the Lobéké National Park and its surrounding FMUs (82.6% and 65.5%, respectively). Key determinants of suitable chimpanzee habitat were hunting pressure and dense forest, with species occurrence probability optimal at relatively lower hunting rates and at relatively high-dense forest areas. Key determinants of suitable gorilla habitat were hunting pressure, dense forests, swampy forests, and slope, with species occurrence probability optimal at relatively high-dense and swampy forest areas and at areas with mild slopes. Our findings show differential response of the two ape species to forestry activities in the study area, thus aligning with previous studies.

Detection of Ebola Virus Antibodies in Fecal Samples of Great Apes in Gabon

Based on a large study conducted on wild great ape fecal samples collected in regions of Gabon where previous human outbreaks of Ebola virus disease have occurred between 1994 and 2002, we provide evidence for prevalence of Zaire ebolavirus (EBOV)-specific antibodies of 3.9% (immunoglobulin G (IgG)) and 3.5% (immunoglobulin M (IgM)) in chimpanzees and 8.8% (IgG) and 2.4% (IgM) in gorillas. Importantly, we observed a high local prevalence (31.2%) of anti-EBOV IgG antibodies in gorilla samples. This high local rate of positivity among wild great apes raises the question of a spatially and temporally localized increase in EBOV exposure risk and the role that can be played by these animals as sentinels of the virus’s spread or reemergence in a given area.

Long-term collapse in fruit availability threatens Central African forest megafauna

Afrotropical forests host much of the world's remaining megafauna, although these animals are confined to areas where direct human influences are low. We used a rare long-term dataset of tree reproduction and a photographic database of forest elephants to assess food availability and body condition of an emblematic megafauna species at Lopé National Park, Gabon. Our analysis reveals an 81% decline in fruiting over a 32-year period (1986-2018) and an 11% decline in body condition of fruit-dependent forest elephants from 2008 to 2018. Fruit famine in one of the last strongholds for African forest elephants should raise concern about the ability of this species and other fruit-dependent megafauna to persist in the long term, with potential consequences for broader ecosystem and biosphere functioning.

Rethinking assessment of success of mitigation strategies for elephant-induced crop damage

Crop damage is the most common impact of negative interactions between people and elephants and poses a significant threat to rural livelihoods and conservation efforts. Numerous approaches to mitigate and prevent crop damage have been implemented throughout Africa and Asia. Despite the documented high efficacy of many approaches, losses remain common, and in many areas, damage is intensifying. We examined the literature on effectiveness of crop-damage-mitigation strategies and identified key gaps in evaluations. We determined there is a need to better understand existing solutions within affected communities and to extend evaluations of effectiveness beyond measurement of efficacy to include rates of and barriers to adoption. We devised a conceptual framework for evaluating effectiveness that incorporates the need for increased emphasis on adoption and can be used to inform the design of future crop-damage mitigation assessments for elephants and conflict species more widely. The ability to prevent crop loss in practice is affected by both the efficacy of a given approach and rates of uptake among target users. We identified the primary factors that influence uptake as local attitudes, sustainability, and scalability and examined each of these factors in detail. We argue that even moderately efficacious interventions may make significant progress in preventing damage if widely employed and recommend that wherever possible scientists and practitioners engage with communities to build on and strengthen existing solutions and expertise. When new approaches are required, they should align with local attitudes and fit within limitations on labor, financial requirements, and technical capacity.

Variation in Gut Microbiota of Captive Bengal Slow Lorises

Gastrointestinal microbiome plays an important role in animal metabolism, immune system and pathology associated with health and disease. Many wild slow lorises were confiscated from illegal trade into captivities and experienced a range of changes in living environment and diet. Microbiome analysis contributes to improving captive management by identifying the alteration in their gastrointestinal microbial communities and aiding in determining the factors affecting the health of captive slow lorises. The fecal samples of eighteen Bengal slow lorises (Nycticebus bengalensis) were used to compare gut microbiota from four rescue centers located in Dehong, Gejiu, Nanning and Puer cities of China. The results showed a significant site-dependent difference in microbial community diversity. Similar to other Lorisinae species, the Phyla including Bacteroidetes, Firmicutes and Proteobacteria dominated their gut microbiome composition. The Gejiu group exhibited a higher overall diversity and the unique OTUs, which is resulted from long-term isolated husbandry and heavy human disturbances. The scarcity of gums in the captive diet was likely to cause a lower abundance of Prevotella associated with soluble fiber degradation. The variation of intestinal microbiota in different environments highlights the necessity to improve feed preparation and husbandry management for the captive Bengal slow lorises.

Extensive Serological Survey of Multiple African Nonhuman Primate Species Reveals Low Prevalence of Immunoglobulin G Antibodies to 4 Ebola Virus Species

Bats are considered a reservoir species for Ebola viruses, but nonhuman primates (NHPs) have represented a source of infection in several outbreaks in humans. Here we report serological screening of blood or fecal samples from monkeys (n = 2322) and apes (n = 2327). Thirty-six NHP species from Cameroon, Democratic Republic of the Congo, and Ivory Coast were tested with a sensitive and specific Luminex-based assay for immunoglobulin G antibodies to 4 Ebola virus species. Using the simultaneous presence of antibodies to nucleoproteins and glycoproteins to define positivity, we showed that specific Ebola virus antibodies are not widespread among NHPs. Only 1 mustached monkey (Cercopithecus cephus) from Cameroon was positive for Sudan ebolavirus. These observations support that NHPs are most likely intermediate hosts for Ebola viruses. With the increasing frequency of Ebola outbreaks, it is crucial to identify the animal reservoir and understand the ecology of Ebola viruses to inform disease control.

Recalibrating Veterinary Medicine through Animal Welfare Science and Ethics for the 2020s

What should leading discourses and innovation regarding animal welfare look like for the veterinary profession in the 2020s? This essay considers four main challenges into which veterinarians are increasingly being drawn, as they respond to increasing public expectation for them to be scientific and moral authorities in animal welfare in addition to their traditional role as trusted health experts. They include: (1) to go beyond traditional conceptions of health by adopting a holistic view that also considers animal welfare, not only disease treatment; (2) to reimagine their professional duties when it comes to disease prevention at the intersection of animal-human-ecosystem health; (3) to develop core competencies/proficiency in animal welfare science and ethics in order to navigate discourses concerning competing priorities and socio-political ideologies and to provide professional leadership in animal welfare; (4) to provide feedback on novel networked devices, monitoring technologies and automated animal welfare solutions and their impact on animals' welfare. To competently navigate the intricacies of the socio-political and connected world as trusted authorities and conduits for innovation in and through animal welfare, veterinarians and veterinary students are encouraged to: (a) develop core competencies in veterinary ethics, animal welfare science and deliberative capacities that are well-informed by current multidisciplinary frameworks, such as One Health; (b) engage interested parties in more effective collaboration and ethical decision-making in order to address animal welfare related concerns within their immediate sphere of influence (e.g., in a given community); and (c) participate in the process of engineering and technological design that incorporates animals' welfare data (such as their preferences) for real-time animal monitoring through adding animal scientific and values-aware evidence in information technology systems. In order to tackle these challenges, four pillars are suggested to help guide veterinarians and the veterinary profession. They are: Collaboration, Critical Engagement, Centeredness on Research, and Continuous Self-Critique.

The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography

The gut microbiome can vary across differences in host lifestyle, geography, and host species. By comparing closely related host species across varying lifestyles and geography, we can evaluate the relative contributions of these factors in structuring the composition and functions of the microbiome. Here we show that the gut microbial taxa, microbial gene family composition, and resistomes of great apes and humans are more related by host lifestyle than geography. We show that captive chimpanzees and gorillas are enriched for microbial genera commonly found in non-Westernized humans. Captive ape microbiomes also had up to ~34-fold higher abundance and up to ~5-fold higher richness of all antibiotic resistance genes compared with wild apes. Through functional metagenomics, we identified a number of novel antibiotic resistance genes, including a gene conferring resistance to colistin, an antibiotic of last resort. Finally, by comparing our study cohorts to human and ape gut microbiomes from a diverse range of environments and lifestyles, we find that the influence of host lifestyle is robust to various geographic locations.

The Ebola virus glycoprotein and its immune responses across multiple vaccine platforms

Introduction: For over 40 years, ebolaviruses have been responsible for sporadic outbreaks of severe and often fatal hemorrhagic fever in humans and nonhuman primates across western and central Africa. In December 2013, an unprecedented Ebola virus (EBOV) epidemic began in West Africa and resulted in the largest outbreak to date. The past and current epidemics in West Africa and the Democratic Republic of the Congo has focused attention on the potential vaccine platforms developed over the past 20 years.Areas covered: This review summarizes the extraordinary progress using a variety of vaccination platforms including DNA, subunit, and several viral vector approaches, replicating and non-replicating, incorporating the primary antigen of EBOV, the glycoprotein. These vaccine constructs have shown varying degrees of protective efficacy in the 'gold-standard' nonhuman primate model for EBOV infections and were immunogenic in human clinical trials.Expert commentary: A number of these vaccine platforms have moved into phase III clinical trials over the past years and with the recent approval of the first EBOV vaccine in the European Union and the USA there is a strong potential to prevent future outbreaks/epidemics of EBOV infections on the scale of the West African epidemic.

Potential distributions of Bacillus anthracis and Bacillus cereus biovar anthracis causing anthrax in Africa

BACKGROUND

Bacillus cereus biovar anthracis (Bcbva) is an emergent bacterium closely related to Bacillus anthracis, the etiological agent of anthrax. The latter has a worldwide distribution and usually causes infectious disease in mammals associated with savanna ecosystems. Bcbva was identified in humid tropical forests of Côte d'Ivoire in 2001. Here, we characterize the potential geographic distributions of Bcbva in West Africa and B. anthracis in sub-Saharan Africa using an ecological niche modeling approach.

METHODOLOGY/PRINCIPAL FINDINGS

Georeferenced occurrence data for B. anthracis and Bcbva were obtained from public data repositories and the scientific literature. Combinations of temperature, humidity, vegetation greenness, and soils values served as environmental variables in model calibrations. To predict the potential distribution of suitable environments for each pathogen across the study region, parameter values derived from the median of 10 replicates of the best-performing model for each pathogen were used. We found suitable environments predicted for B. anthracis across areas of confirmed and suspected anthrax activity in sub-Saharan Africa, including an east-west corridor from Ethiopia to Sierra Leone in the Sahel region and multiple areas in eastern, central, and southern Africa. The study area for Bcbva was restricted to West and Central Africa to reflect areas that have likely been accessible to Bcbva by dispersal. Model predicted values indicated potential suitable environments within humid forested environments. Background similarity tests in geographic space indicated statistical support to reject the null hypothesis of similarity when comparing environments associated with B. anthracis to those of Bcbva and when comparing humidity values and soils values individually. We failed to reject the null hypothesis of similarity when comparing environments associated with Bcbva to those of B. anthracis, suggesting that additional investigation is needed to provide a more robust characterization of the Bcbva niche.

CONCLUSIONS/SIGNIFICANCE

This study represents the first time that the environmental and geographic distribution of Bcbva has been mapped. We document likely differences in ecological niche-and consequently in geographic distribution-between Bcbva and typical B. anthracis, and areas of possible co-occurrence between the two. We provide information crucial to guiding and improving monitoring efforts focused on these pathogens.

Assessment of in situ nest decay rate for chimpanzees (Pan troglodytes ellioti Matschie, 1914) in Mbam-Djerem National Park, Cameroon: implications for long-term monitoring

Accurate assessment of great ape populations is a prerequisite for conservation planning. Indirect survey methods using nest and dung, and a set of conversion parameters related to nest decay rates, are increasingly used. Most surveys use the standing crop nest count (SCNC) method, whereby nests are counted along transects and the estimated nest density is converted into chimpanzee density using an often non-local nest decay rate. The use of non-local decay rate is thought to introduce substantial bias to ape population estimates given that nest decay rates vary with location, season, rainfall, nest shape, and tree species used. SCNC method has previously been applied in Mbam-Djerem National Park (MDNP) in Cameroon, for chimpanzee surveys using a non-local nest decay rate. This current study aimed to measure a local nest decay rate for MDNP and implications for chimpanzee population estimates in the MDNP. The mean nest decay rate estimated using a logistic regression analysis was 127 [95% CI (100–160)] days. Moreover, the results suggested that rainfall strongly influenced the nest decay rate over the early stage of the lifetime of the nests. The study confirms that estimates of chimpanzee density and abundance using non-local decay rates should be treated with caution. Our research emphasized the importance of using local nest decay rates and other survey methods which do not depend on decay rates to obtain more accurate estimates of chimpanzee densities in order to inform conservation strategies of these great apes in MDNP.

Filovirus Disease Outbreaks: A Chronological Overview

Filoviruses cause outbreaks which lead to high fatality in humans and non-human primates, thus tagging them as major threats to public health and species conservation. In this review, we give account of index cases responsible for filovirus disease outbreaks that have occurred over the past 52 years in a chronological fashion, by describing the circumstances that led to the outbreaks, and how each of the outbreaks broke out. Since the discovery of Marburg virus and Ebola virus in 1967 and 1976, respectively, more than 40 filovirus disease outbreaks have been reported; majority of which have occurred in Africa. The chronological presentation of this review is to provide a concise overview of filovirus disease outbreaks since the discovery of the viruses, and highlight the patterns in the occurrence of the outbreaks. This review will help researchers to better appreciate the need for surveillance, especially in areas where there have been no filovirus disease outbreaks. We conclude by summarizing some recommendations that have been proposed by health and policy decision makers over the years.

Sharing conservation burdens fairly

We examined how, from the point of view of justice, the burdens of paying for conservation should be shared. I resisted simple answers to the question of who should pay for conservation that lean on a single moral principle. I identified 3 relevant principles that relate to who causes conservation challenges, who has greater capacity to carry burdens, and who stands to benefit from conservation. I argue for a distinctive pluralist framework for allocating conservation burdens that grants a proper role to all 3 principles. A multistep process can be used to put the framework into practice. First, identify cases in which conservation is necessary. Second, consider whether people knew or could have been expected to anticipate the consequences of their activities and whether they had reasonable alternatives to acting the way they did. Third, turn to facts about benefits; when no culprit for conservation challenges can be found, ask who benefits from acts of conservation. In the second and third stages, consideration must also be given to ability to pay.

From groups to communities in western lowland gorillas

Social networks are the result of interactions between individuals at different temporal scales. Thus, sporadic intergroup encounters and individual forays play a central role in defining the dynamics of populations in social species. We assessed the rate of intergroup encounters for three western lowland gorilla ( Gorilla gorilla gorilla) groups with daily observations over 5 years, and non-invasively genotyped a larger population over four months. Both approaches revealed a social system much more dynamic than anticipated, with non-aggressive intergroup encounters that involved social play by immature individuals, exchanges of members between groups likely modulated by kinship, and absence of infanticide evidenced by infants not fathered by the silverback of the group where they were found. This resulted in a community composed of groups that interacted frequently and not-aggressively, contrasting with the more fragmented and aggressive mountain gorilla ( G. beringei beringei) societies. Such extended sociality can promote the sharing of behavioural and cultural traits, but might also increase the susceptibility of western lowland gorillas to infectious diseases that have decimated their populations in recent times.

Habitat differentiation among three Nigeria-Cameroon chimpanzee (Pan troglodytes ellioti) populations

Ecological niche models (ENMs) are often used to predict species distribution patterns from datasets that describe abiotic and biotic factors at coarse spatial scales. Ground-truthing ENMs provide important information about how these factors relate to species-specific requirements at a scale that is biologically relevant for the species. Chimpanzees are territorial and have a predominantly frugivorous diet. The spatial and temporal variation in fruit availability for different chimpanzee populations is thus crucial, but rarely depicted in ENMs. The genetic and geographic distinction within Nigeria-Cameroon chimpanzee (Pan troglodytes ellioti) populations represents a unique opportunity to understand fine scale species-relevant ecological variation in relation to ENMs. In Cameroon, P. t. ellioti is composed of two genetically distinct populations that occupy different niches: rainforests in western Cameroon and forest-woodland-savanna mosaic (ecotone) in central Cameroon. We investigated habitat variation at three representative sites using chimpanzee-relevant environmental variables, including fruit availability, to assess how these variables distinguish these niches from one another. Contrary to the assumption of most ENM studies that intact forest is essential for the survival of chimpanzees, we hypothesized that the ecotone and human-modified habitats in Cameroon have sufficient resources to sustain large chimpanzee populations. Rainfall, and the diversity, density, and size of trees were higher at the rainforest. The ecotone had a higher density of terrestrial herbs and lianas. Fruit availability was higher at Ganga (ecotone) than at Bekob and Njuma. Seasonal variation in fruit availability was highest at Ganga, and periods of fruit scarcity were longer than at the rainforest sites. Introduced and secondary forest species linked with anthropogenic modification were common at Bekob, which reduced seasonality in fruit availability. Our findings highlight the value of incorporating fine scale species-relevant ecological data to create more realistic models, which have implications for local conservation planning efforts.