Kibale Chimpanzee Project

Abstract Tropical forests are rich in biodiversity but face the rapid loss of their wildlife due to increasing anthropogenic pressure, underscoring the urgent need for effective monitoring. Remote‐sensing tools such as camera traps offer faster, less invasive alternatives to human observations. These technologies can provide complementary insights into elusive species, especially in habitats that are difficult to access through direct observation. However, analysing the large volumes of data they produce is labour‐intensive, often leaving datasets underutilised due to limited human resources. Deep learning algorithms can automate aspects of data analysis, but their value to research and conservation efforts depends on their ability to reliably identify target species and be easily deployed in field conditions. To improve wildlife monitoring in African forests using camera trap data, we develop DeepForestVision, the first deep learning algorithm tailored to these challenging habitats that can be used in the field to process both photographs and videos. DeepForestVision was trained on an unprecedented dataset of 2,775,671 photographs and 221,982 videos gathered from camera traps from more than 63 research sites across 11 African countries. It identifies 33 non‐human vertebrate taxa, including 31 mammal taxa, from the most common to the most threatened ones observed on ground‐level camera traps, as well as humans, vehicles and blank photographs or videos. Classification tests demonstrate that DeepForestVision achieves an accuracy of 87.7% on the video test set with 23 taxa. It outperforms the three existing species identification algorithms applicable to these environments: Zamba by 13.1%, Mbaza by 45.0% and SpeciesNet by 37.7%. We provide the model weights for researchers and developers and offer DeepForestVision through a free offline interface. The interface is designed to function in the field in a low‐resource setting and requires no programming expertise. Solution : DeepForestVision is a reliable field tool for monitoring species observed on camera trap photos and videos in African tropical forests. Used by research, conservation, private or political actors, it can guide conservation strategies inside and outside of protected areas, and thus contribute to reducing the loss of biodiversity in African tropical forests.

Reverse zoonotic respiratory diseases threaten great apes across Sub-Saharan Africa. Studies of wild chimpanzees have identified the causative agents of most respiratory disease outbreaks as “common cold” paediatric human pathogens, but reverse zoonotic transmission pathways have remained unclear. Between May 2019 and August 2021, we conducted a prospective cohort study of 234 children aged 3–11 years in communities bordering Kibale National Park, Uganda, and 30 adults who were forest workers and regularly entered the park. We collected 2047 respiratory symptoms surveys to quantify clinical severity and simultaneously collected 1989 nasopharyngeal swabs approximately monthly for multiplex viral diagnostics. Throughout the course of the study, we also collected 445 faecal samples from 55 wild chimpanzees living nearby in Kibale in social groups that have experienced repeated, and sometimes lethal, epidemics of human-origin respiratory viral disease. We characterized respiratory pathogens in each cohort and examined statistical associations between PCR positivity for detected pathogens and potential risk factors. Children exhibited high incidence rates of respiratory infections, whereas incidence rates in adults were far lower. COVID-19 lockdown in 2020–2021 significantly decreased respiratory disease incidence in both people and chimpanzees. Human respiratory infections peaked in June and September, corresponding to when children returned to school. Rhinovirus, which caused a 2013 outbreak that killed 10% of chimpanzees in a Kibale community, was the most prevalent human pathogen throughout the study and the only pathogen present at each monthly sampling, even during COVID-19 lockdown. Rhinovirus was also most likely to be carried asymptomatically by adults. Although we did not detect human respiratory pathogens in the chimpanzees during the cohort study, we detected human metapneumovirus in two chimpanzees from a February 2023 outbreak that were genetically similar to viruses detected in study participants in 2019. Our data suggest that respiratory pathogens circulate in children and that adults become asymptomatically infected during high-transmission times of year. These asymptomatic adults may then unknowingly carry the pathogens into forest and infect chimpanzees. This conclusion, in turn, implies that intervention strategies based on respiratory symptoms in adults are unlikely to be effective for reducing reverse zoonotic transmission of respiratory viruses to chimpanzees.

Respiratory infections are a leading cause of death in developing countries. Infants and young children are especially susceptible to disease because they lack immunity, whereas adults who have acquired immunity can be infected asymptomatically. Great ape species, all of which are endangered, are similarly susceptible to respiratory illnesses caused by human respiratory pathogens. We obtained 432 nasopharyngeal swab samples (127 from adults and 305 from children) in a cross-sectional study that took place between February and October 2022 at four sites in Western Uganda (Budongo Central Forest Reserve, Bulindi Town Council, Bwindi Impenetrable National Park, and Kibale National Park) where the participants live in communities where interaction with apes is frequent. Prior research at Kibale has shown that locally circulating human respiratory pathogens have led to multiple lethal outbreaks in wild eastern chimpanzees (Pan troglodytes schweinfurthii). We used a multiplex PCR panel to characterize respiratory pathogens, with the goal of assessing whether respiratory illnesses in the chimpanzees of Budongo and Bulindi and the mountain gorillas (Gorilla beringei beringei) of Bwindi might have originated in local children and been introduced to the apes via asymptomatic adult carriers. The prevalence of respiratory pathogens was twice as high in Bwindi (44.0%) as it was in Budongo (24.0%) and Bulindi (20.8%), while the prevalence was intermediate at Kibale (34.4%). Rates of respiratory pathogen detection were higher but statistically indistinguishable in children compared to adults at Budongo and Bulindi, and children were 15.0 times more likely than adults to have positive detections at Kibale. At Bwindi, however, the pattern was reversed, with adults 2.6 times more likely than children to have positive detections. Rhinovirus, metapneumovirus, human parainfluenza virus 3, respiratory syncytial virus, and coronavirus OC43, all of which have been identified as causative agents of respiratory disease outbreaks in great ape populations across sub-Saharan Africa, accounted for three quarters (73.6%) of detected pathogens. Our data support the idea that human respiratory pathogens that can infect great apes occur at high frequencies in human populations in Western Uganda that live close to and interact with wild apes that have suffered from lethal outbreaks caused by these same pathogens. Reducing respiratory infections in local children, thereby reducing both carriage of those infections into the forest by people and ape exposure to these pathogens when they enter human spaces, should decrease the risk of respiratory disease outbreaks in apes.

Abstract Chimpanzees (Pan troglodytes) are avid tool users, although tool uses and functions vary among communities. Some chimpanzees use stones or wood in extractive foraging to crack open nuts, whereas others use long stems to consume termites or ants. Leaf sponges are versatile and widespread tools used by chimpanzees, created by crumpling leaves in the mouth and then using the hands to immerse the tool to procure liquids from difficult‐to‐access locations. Here we describe leaf sponge use by two female chimpanzees in Kibale National Park, Uganda, documenting for the first time tool use in the Buraiga chimpanzee community.

The majority of nonhuman primates are found in habitats impacted by humans. Therefore, conservation interventions in anthropogenic landscapes are critical for the long-term survival of primate populations. Due to their intelligence and socioecological flexibility, many primates exhibit behaviours deemed problematic such as crop feeding, property damage, and livestock depredation. Large-bodied primates may also pose a physical risk to people. In this chapter, we first revise the common criteria for selecting primate conservation priorities and consider them in the context of shared landscapes. We discuss the importance of inclusive conservation approaches and provide recommendations for addressing negative human-primate interactions based on existing information. Three case studies that illustrate conservation efforts in shared environments are presented: (1) the Bulindi Chimpanzee and Community Project in Uganda, (2) community conservation of orangutans and Javan slow lorises in Indonesia, and (3) inclusive conservation of golden lion tamarins in Brazil’s Atlantic Forest. The active participation of a diverse group of stakeholders, including local community groups, in all conservation stages is essential to fully understand the complexities of human-primate interactions in shared landscapes, address negative interactions, mitigate conservation conflicts, advocate for equity, and promote long-term human-primate coexistence.

The gut microbiome of primates is known to be influenced by both host genetic background and subsistence strategy. However, these inferences have been made mainly based on adaptations in bacterial composition - the bacteriome and have commonly overlooked the fungal fraction - the mycobiome. To further understand the factors that shape the gut mycobiome of primates and mycobiome-bacteriome interactions, we sequenced 16 S rRNA and ITS2 markers in fecal samples of four different nonhuman primate species and three human groups under different subsistence patterns (n = 149). The results show that gut mycobiome composition in primates is still largely unknown but highly plastic and weakly structured by primate phylogeny, compared with the bacteriome. We find significant gut mycobiome overlap between captive apes and human populations living under industrialized subsistence contexts; this is in contrast with contemporary hunter-gatherers and agriculturalists, who share more mycobiome traits with diverse wild-ranging nonhuman primates. In addition, mycobiome-bacteriome interactions were specific to each population, revealing that individual, lifestyle and intrinsic ecological factors affect structural correspondence, number, and kind of interactions between gut bacteria and fungi in primates. Our findings indicate a dominant effect of ecological niche, environmental factors, and diet over the phylogenetic background of the host, in shaping gut mycobiome composition and mycobiome-bacteriome interactions in primates.

Abstract 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.

Chimpanzees (Pan troglodytes) are notable for exhibiting high levels of male-to-female aggression. Much of this aggression from adult males serves sexually coercive functions. Despite being smaller and lower-ranking than adult males, adolescent males also engage in regular aggression against adult females. Here, we test whether the primary function of this aggression is sexual coercion, as in adult males, or, alternatively, whether adolescent males use aggression to establish social dominance over females. We analyzed 1771 copulations and 1812 instances of male-initiated aggression between adolescent males (aged nine through 14 years) and adult females across 21 years of observation of the Kanyawara chimpanzee community in Kibale National Park, Uganda. Our test of the sexual coercion hypothesis revealed that adolescent males did not selectively target cycling females for aggression, nor did aggression against cycling females predict rates of copulation with those females. Our test of the social dominance hypothesis showed that males succeeded in dominating all adult females before, or soon after, dominating their first adult male. Additionally, we found that adolescent males dominated females approximately in the order of the females' own ranks, from the bottom to the top of the female hierarchy. Our data illustrate that the establishment of social dominance was more important than sexual coercion in explaining patterns of adolescent male aggression toward females. In comparison, evidence for sexual coercion was clear and compelling in adult males. These findings highlight that the primary function of male-to-female aggression differs between adolescent and adult males.

Uganda’s Kibale National Park contains a particularly diverse primate population, including about 1400 chimpanzees (Pan troglodytes). It is threatened by poaching and illegal deforestation, both of which are promoted by the extreme poverty, exponential population growth, and low educational achievements of local people. This poster describes a multifaceted approach to conservation taken by the Kibale Chimpanzee Project. We highlight its within-forest organization (Kibale Snare Removal Project, KSRP) and its partner NGO working with 10,000 children in the surrounding communities (The Kasiisi Project). Within the Park, KSRP rangers interact closely with the Ugandan Wildlife Authority to monitor illegal activity. In 2013 KSRP rangers reported over 1400 incidents of illegal activity in the forest and removed over 700 snares. Outside the Park, the Kasiisi Project focuses on changing attitudes and behavior through combining conservation education, community development, and higher standards in 14 primary schools. The Kasiisi Project’s philosophy is to meet people’s needs (better education, less reliance on forest resources) while providing the information, skills and motivation to reduce environmental degradation. KSRP rangers link within-forest and community activities by participating in school conservation education. Since we began, students in Kasiisi-partnered schools have achieved exceptionally high National Exam scores and show increased positive feelings towards chimpanzees and the Park. Our results suggest that because the rising human population threatens all Ugandan forests, within-forest and community activity should be combined wherever possible in order to maximize the effectiveness of conservation efforts.