Habitat alteration and the conservation of African primates: case study of Kibale National Park, Uganda

The primate-specific presence of interferon regulatory factor-5 pseudogene 1

Interferon regulatory factor 5 (IRF5) is a key transcription factor in inflammatory and immune responses, with its dysregulation linked to autoimmune diseases. Using bioinformatic approaches, including Basic Local Alignment Search Tool (BLAST) for sequence similarity searches, BLAST-Like Alignment Tool (BLAT) for genome-wide alignments, and several phylogenetics software, such as Multiple Alignment using Fast Fourier Transform (MAFFT), for phylogenetic analyses, we characterized the structure, origin, and evolutionary history of the human IRF5 pseudogene 1 (IRF5P1). Our analyses reveal that IRF5P1 is a chimeric processed pseudogene containing sequences derived from multiple sources, including IRF5-like sequences from disparate organisms. We find that IRF5P1 is specific to higher primates, likely originating through an ancient retroviral integration event approximately 60 million years ago. Interestingly, IRF5P1 resides within the triple QxxK/R motif-containing (TRIQK) gene, and its antisense strand is predominantly expressed as part of the TRIQK pre-messenger RNA (mRNA). Analysis of publicly available RNA-seq data suggests potential expression of antisense IRF5P1 RNA. We hypothesize that this antisense RNA may regulate IRF5 expression through complementary binding to IRF5 mRNA, with human genetic variants potentially modulating this interaction. The conservation of IRF5P1 in the primate lineage suggests its positive effects on primate evolution and innate immunity. This study highlights the importance of investigating pseudogenes and their potential regulatory roles in shaping lineage-specific immune adaptations.

Diurnal activity time budget of Grevy's zebra (Equus grevyi, Oustalet 1882) in a protected savannah area

Understanding natural history such as diurnal activity of wildlife species is important for their conservation intervention. The aim of the current study was to examine Grevy's zebra diurnal activity time budget in Hallaydeghe Asebot Proposed National Park (HAPNP) considering both wet and dry seasons. Scan sampling method was used. Activities of the species were recorded based on age and sex. Species were observed for 15 min (10 min activities recording followed 5 min rest). Analysis of Variance (ANOVA) was used to analysis data. Grazing (31.26%) was the highest followed by resting (30.24%) during the wet season and grazing (37.13%) was the highest followed by moving (27.25%) during dry season. The peak grazing time of species was morning 6:00-9:00 a.m. and late afternoon 16:00-18:00 p.m. while resting was observed during midday. The time the species spent over grazing (df = 1, F = 27.15, p = 0.000132), Grooming (df = 1, F = 24.082, p = 0.000231), mating (df = 1, F = 24.850, p = 0.0002) and moving (df = 1, F = 5.550, p = 0.0336) activity during both seasons were significantly different. There is statistical difference for grazing (df = 2, F = 9.336, p = 0.002653), mating (df = 2, F = 6.216, p = 0.0117), moving (df = 2, F = 5.604, p = 0.0163) and other (df = 2, F = 5.006, p = 0.0229) activities based on sex of species. The current study examined only diurnal activity time budget of the species. As a result, future research shall be conducted by taking into account the impact of different factors (temperature and livestock) that can influence the activity time budget of Grevy's zebra in HAPNP. Lastly, we recommend thorough species management plan in HAPNP for sustainable conservation of Grevy's zebra.

Fifty+ years of primate research illustrates complex drivers of abundance and increasing primate numbers

Many primate populations are threatened by human actions and a central tool used for their protection is establishing protected areas. However, even if populations in such areas are protected from hunting and deforestation, they still may be threatened by factors such as climate change and its cascading impacts on habitat quality and disease dynamics. Here we provide a long-term and geographically wide-spread population assessment of the five common diurnal primates of Kibale National Park, Uganda. Over 7 year-long or longer census efforts that spanned 52 years, our team walked 1466 km, and recorded 480 monkey groups. Populations were generally relatively stable with a few exceptions, for which no apparent causative factors could be identified. This stability is unexpected as many ecological changes documented over the last 34+ years (e.g., decreasing food abundance and quality) were predicted to have negative impacts. Populations of some species declined at some sites but increased at others. This highlights the need for large, protected areas so that declines in particular areas are countered by gains in others. Kibale has large areas of regenerating forest and this most recent survey revealed that after 20+ years, forest regeneration in many of these areas appears sufficient to sustain sizeable primate populations, except for blue monkeys that have not colonized these areas. Indeed, the average primate abundance in the regenerating forest was only 8.1% lower than in neighboring old-growth forest. Thus, park-wide primate abundance has likely increased, despite many pressures on the park having risen; however, some areas in the park remain to be assessed. Our study suggests that the restoration, patrolling, and community outreach efforts of the Uganda Wildlife Authority and their partners have contributed significantly to protecting the park and its animals.

High urinary oxidative DNA damage in wild chimpanzees ranging in proximity of agricultural fields in Sebitoli area, Uganda

Agriculture expansion is a major cause of habitat loss and exposure to phytochemical pollution for non-human primates. In addition to endocrine disruption, exposure to pesticides may have other sublethal physiological consequences for animals, such as generation of oxidative damage to macromolecules. In this study, we analyzed the pesticides contained in the river water across the home range of wild chimpanzees (Pan troglodytes) in Sebitoli area located on the Northern part of Kibale National Park (Uganda). We tested whether levels of three urinary markers of oxidative damage vary among individuals in relation to their ranging patterns, as a proxy for pesticide exposure intensity. To better characterize the foraging habitat use, the trophic level, and the energetic status of study individuals, we also quantified urinary levels of carbon and nitrogen stable isotope signatures and of C-peptide. Among the 511 pesticides screened, 18 compounds including herbicides, insecticides, and fungicides were found in the water sampled in the Western part of the home range of chimpanzees. In this area, chimpanzees used to feed on maize crops. By contrast, in the Eastern part where crop feeding was never observed, we found only seven pesticides. According to their ranging patterns and thus crop feeding frequency, the 139 urine samples collected from 43 Sebitoli chimpanzees were categorized as belonging to low, medium, and high exposure level. Chimpanzees from the high exposure zone had higher oxidative DNA damage (8-OHdG) than chimpanzees from both the low and medium exposure groups, who had similar levels of oxidative DNA damage. In addition, individuals with higher C-peptide tended to have significantly higher oxidative DNA damage and lipid peroxides. The three exposure groups had similar levels of urinary 8-isoprostanes and of urinary lipid peroxides. These results were robust for any potential confounding effect of other variables because neither age category nor sex or isotope levels were significantly associated with markers of oxidative damage. Our study points to genotoxic effects as one potential sublethal consequence of ranging in proximity of agricultural fields owing to exposure to pesticides or other unidentified sources of stress. Given our phylogenetic proximity, this information is relevant for the conservation of this species which is endangered and also sentinel for human health.

Primate population dynamics in Ngogo, Kibale National Park, Uganda, over nearly five decades

Many anthropogenic-driven changes, such as hunting, have clear and immediate negative impacts on wild primate populations, but others, like climate change, may take generations to become evident. Thus, informed conservation plans will require decades of population monitoring. Here, we expand the duration of monitoring of the diurnal primates at Ngogo in Kibale National Park, Uganda, from 32.9 to 47 years. Over the 3531 censuses that covered 15,340 km, we encountered 2767 primate groups. Correlation analyses using blocks of 25 census walks indicate that encounters with groups of black and white colobus, blue monkeys, and baboons neither increased nor decreased significantly over time, while encounters with groups of redtail monkeys and chimpanzees marginally increased. Encounters with mangabeys and L'Hoesti monkeys increased significantly, while red colobus encounters dramatically decreased. Detailed studies of specific groups at Ngogo document changes in abundances that were not always well represented in the censuses because these groups expanded into areas away from the transect, such as nearby regenerating forest. For example, the chimpanzee population increased steadily over the last 2 + decades but this increase is not revealed by our census data because the chimpanzees expanded, mainly to the west of the transect. This highlights that extrapolating population trends to large areas based on censuses at single locations should be done with extreme caution, as forests change over time and space, and primates adapt to these changes in several ways.

Djaffa Mountains guereza (Colobus guereza gallarum) abundance in forests of the Ahmar Mountains, Ethiopia

The size and density of a population are essential parameters in primate ecology and conservation. Such information, however, is still scarce for many forest primate species. The Djaffa Mountains guereza (Colobus guereza gallarum) is an endemic Ethiopian taxon for which data about its distribution and population size are missing. Therefore, we aimed to estimate the abundance and population size of the Djaffa Mountains guereza in four forests in the Ahmar Mountains southeast of the Ethiopian Rift Valley. We conducted line-transect surveys in the forests. Within an area of 183 km2 , we sampled 19 transects covering a distance of 75.9 km. We encountered 73 guereza clusters which most likely represent social groups. Since the detection distances and cluster sizes did not differ among the four forests, we applied a conventional distance sampling (CDS) model and estimated a population density of 20.6 clusters per square kilometer, i.e., 109.6 individuals per square kilometer or 20 061 individuals within the complete study area. This abundance is relatively high compared to other C. guereza taxa. However, given that the habitat and population of C . g . gallarum are already highly fragmented, further monitoring of the population and exploration of the possibilities of reconnecting its habitat should be priorities for the conservation of this taxon.

Chimpanzees select comfortable nesting tree species

Every evening, chimpanzees build sleeping "nests" in trees. In some studied communities, individuals appear to be selective about the tree species used, which has led researchers to hypothesize whether chimpanzees prefer trees that repel troublesome insects or/and that provide comfortable and stable structures. We investigate these hypotheses, or a trade-off between both, though study of tree species preference based on their biomechanical and/or biochemical properties in the Sebitoli chimpanzee community in Kibale National Park, Uganda. The ten tree species most frequently used for nesting were compared with ten abundant in their environment but not preferred for nesting. For these 20 tree species, we determined their biomechanical and morphological characteristics such as foliar density, foliar units form (shape and size) and branch rigidity. Their spatial repellent activity, previously tested against Anopheles gambiae was incorporated into the analysis. Chimpanzees chose tree species with medium-sized and elongated foliar units, high foliar density and branch with stiffer wood. In addition, most tree species with such mechanical and morphological properties also have mosquito repellent activity. These tree properties may provide a comfortable sleeping environment enhancing sleep quality. Finally, a comparison across chimpanzee communities would be relevant to understand whether these choices are not only ecological but also cultural.

Evolution and emergence of primate-specific interferon regulatory factor 9

The binding of interferon (IFN) to its receptors leads to formation of IFN-stimulated gene factor 3 (ISGF3) complex that activates the transcription of cellular IFN-regulated genes. IFN regulatory factor 9 (IRF9, also called ISGF3γ or p48) is a key component of ISGF3. However, there is limited knowledge regarding the molecular evolution of IRF9 among vertebrates. In this study, we have identified the existence of the IRF9 gene in cartilaginous fish (sharks). Among primates, several isoforms unique to old world moneys and great apes are identified. These IRF9 isoforms are named as primate-specific IRF9 (PS-IRF9) to distinguish from canonical IRF9. PS-IRF9 originates from a unique exon usage and differential splicing in the IRF9 gene. Although the N-terminus are identical for all IRF9s, the C-terminal regions of the PS-IRF9 are completely different from canonical IRF9. In humans, two PS-IRF9s are identified and their RNA transcripts were detected in human primary peripheral blood mononuclear cells. In addition, human PS-IRF9 proteins were detected in human cell lines. Sharing the N-terminal exons with the canonical IRF9 proteins, PS-IRF9 is predicted to bind to the same DNA sequences as the canonical IRF9 proteins. As the C-terminal regions of IRFs are the determinants of IRF functions, PS-IRF9 may offer unique biological functions and represent a novel signaling molecule involved in the regulation of the IFN pathway in a primate-specific manner.

Survey of ticks and tick-borne pathogens in wild chimpanzee habitat in Western Uganda

BACKGROUND

Ticks and tick-borne pathogens significantly impact both human and animal health and therefore are of major concern to the scientific community. Knowledge of tick-borne pathogens is crucial for prescription of mitigation measures. In Africa, much research on ticks has focused on domestic animals. Little is known about ticks and their pathogens in wild habitats and wild animals like the endangered chimpanzee, our closest relative.

METHODS

In this study, we collected ticks in the forested habitat of a community of 100 chimpanzees living in Kibale National Park, Western Uganda, and assessed how their presence and abundance are influenced by environmental factors. We used non-invasive methods of flagging the vegetation and visual search of ticks both on human team members and in chimpanzee nests. We identified adult and nymph ticks through morphological features. Molecular techniques were used to detect and identify tick-borne piroplasmids and bacterial pathogens.

RESULTS

A total of 470 ticks were collected, which led to the identification of seven tick species: Haemaphysalis parmata (68.77%), Amblyomma tholloni (20.70%), Ixodes rasus sensu lato (7.37%), Rhipicephalus dux (1.40%), Haemaphysalis punctaleachi (0.70%), Ixodes muniensis (0.70%) and Amblyomma paulopunctatum (0.35%). The presence of ticks, irrespective of species, was influenced by temperature and type of vegetation but not by relative humidity. Molecular detection revealed the presence of at least six genera of tick-borne pathogens (Babesia, Theileria, Borrelia, Cryptoplasma, Ehrlichia and Rickettsia). The Afrotopical tick Amblyomma tholloni found in one chimpanzee nest was infected by Rickettsia sp.

CONCLUSIONS

In conclusion, this study presented ticks and tick-borne pathogens in a Ugandan wildlife habitat whose potential effects on animal health remain to be elucidated.

Assessing the effects of survey-inherent disturbance on primate detectability: Recommendations for line transect distance sampling

Habitat destruction and over-hunting are increasingly threatening the arboreal primates of Central Africa. To establish effective conservation strategies, accurate assessments of primate density, abundance, and spatial distribution are required. To date, the method of choice for primate density estimation is line transect distance sampling. However, primates fleeing human observers violate methodological assumptions, biasing the accuracy of resulting estimates. In this study, we used line transect distance sampling to study five primate species along 378 km of transects in Salonga National Park, Democratic Republic of the Congo. We tested the effect of different levels of survey-inherent disturbance (i.e., cutting) on the number of observed (i) primate groups, and (ii) individuals within groups, by counting groups at three different time lags after disturbance of the transect, (i) a minimum of 3 h, (ii) 24 h, (iii) a minimum of 3 days. We found that survey-inherent disturbance led to underestimated densities, affecting both the number of encountered groups and of observed individuals. However, the response varied between species due to species-specific ecological and behavioral features. Piliocolobus tholloni and Colobus angolenis resumed an unaltered behavior only 24 h after disturbance, while Lophocebus aterrimus, Cercopithecus ascanius, and Cercopithecus wolfi required a minimum of 10 days. To minimize bias in density estimates, future surveys using line transect distance sampling should be designed considering survey-inherent disturbance. We recommend evaluating the factors driving primate response, including habitat type, niche occupation, and hunting pressure, peculiar to the survey-specific area and primate community under study.

Can electrical wires serve as canopy bridges? A case study of the dusky langur (Trachypithecus obscurus) in Thailand

In many parts of the world, primates and other arboreal and semi-arboreal species use electrical and telecommunication cables to cross open gaps. However, electrocutions can occur when the cables are uninsulated or damaged. Between 2001 and 2002, during a 12-month behavioural study of two dusky langur groups (Trachypithecus obscurus) at the Royal Thai Air Force Base in Prachuap Khiri Khan Province, peninsular Thailand, we recorded langur use of and mortality on electrical and telecommunications cables on an ad libitum basis. Before insulation of the cables in late 2001, five langurs died by electrocution; post insulation, that number decreased to only one case on March 5, 2002. In 2022, we returned to observe the langur groups and saw them continuing to use the cables for crossing and noted damage to the insulation, indicating the importance of maintenance. Electrical cables can provide canopy connectivity for langurs and prevent dangerous encounters with dogs on the ground, but cables must be insulated and inspected regularly. As additional mitigation measures, we suggest providing alternative substrates for travel such as planting more native trees and providing artificial canopy bridges.

Repellent activity against Anopheles gambiae of the leaves of nesting trees in the Sebitoli chimpanzee community of Kibale National Park, Uganda

BACKGROUND

Every evening, chimpanzees (Pan troglodytes) build a sleeping platform so called "nest" by intertwining branches of tree. Most of chimpanzees' communities studied have a preference for tree species in which they nest. As female mosquitoes are feeding on the blood of their host at nighttime, chimpanzees may prevent being disturbed and bitten by mosquitoes by selecting tree species having properties to repel them.

METHODS

To test the hypothesis that chimpanzees choose tree species for their aromatic properties, data related to 1,081 nesting trees built between 2017 and 2019 in the Sebitoli community of Kibale National Park (Uganda) were analysed. The 10 most used trees were compared to the 10 most common trees in the habitat that were not preferred for nesting. Leaves from the 20 trees species were collected and hydro-distillated to obtain essential oils and one of the by-products for behavioural bioassays against females of the African mosquito, Anopheles gambiae.

RESULTS

Sebitoli chimpanzees showed tree preferences: 10 species correspond to more than 80% of the nesting trees. Out of the essential oil obtained from the 10 nesting trees, 7 extracts for at least one concentration tested showed spatial repellency, 7 were irritant by contact and none were toxic. In the other hand, for the abundant trees in their habitat not used by chimpanzees, only 3 were repellent and 5 irritants.

DISCUSSION AND CONCLUSION

This study contributes to evidence that chimpanzees, to avoid annoying mosquitoes, may select their nesting trees according to their repellent properties (linked to chemical parameters), a potential inspiration for human health.

Phenotypical characterization of African savannah and forest elephants, with special emphasis on hybrids: the case of Kibale National Park, Uganda

The IUCN now recognizes the savannah Loxodonta africana and forest Loxodonta cyclotis elephants to be separate species. Despite ecological, behavioural and morphological differences, and different habitat ranges, genetic studies confirm that the two species and hybrids coexist in forest–savannah ecotones. However, the hybrid phenotypes have not yet been described. In this survey we examined whether the phenotypes of the two species and of hybrids can be distinguished. In the first step, we used a machine learning algorithm (K-nearest neighbours) to compare 296 reference images of African elephants from five forest areas and six savannah areas where hybrids have not been recorded, confirming that six morphological criteria can be used to distinguish the species with more than 90% confidence. In the second step, we analysed 1,408 videos of elephants from 14 camera traps in Sebitoli, in Kibale National Park, Uganda, part of the main hybridization area. We used a multiple correspondence analysis and a species assignment key, highlighting the presence of three categories of phenotypes. Compared to the savannah and forest phenotypes (36.8 and 12.1%, respectively), the intermediate phenotypes, which could include hybrids, were more frequent (51.1%). Further studies combining morphology and genetics of the same individuals will be necessary to refine this species assignment key to characterize phenotypes confidently. This non-invasive, fast and inexpensive phenotypical-based method could be a valuable tool for conservation programmes.

Between forest and croplands: Nocturnal behavior in wild chimpanzees of Sebitoli, Kibale National Park, Uganda

Some animal species have been presumed to be purely diurnal. Yet, they show flexibility in their activity rhythm, and can occasionally be active at night. Recently, it has been suggested that chimpanzees may rarely engage in nocturnal activities in savannah forests, in contrast to the frequent nocturnal feeding of crops observed at Sebitoli, Kibale National Park, Uganda. Here we thus aimed to explore the factors that might trigger such intense nocturnal activity (e.g. harsher weather conditions during daytime, low wild food availability or higher diurnal foraging risk) in this area. We used camera-traps set over 18 km2 operating for 15 months. We report activities and group composition from records obtained either within the forest or at the forest interface with maize fields, the unique crop consumed. Maize is an attractive and accessible food source, although actively guarded by farmers, particularly during daytime. Out of the 19 156 clips collected, 1808 recorded chimpanzees. Of these, night recordings accounted for 3.3% of forest location clips, compared to 41.8% in the maize fields. Most nocturnal clips were obtained after hot days, and most often during maize season for field clips. At night within the forest, chimpanzees were travelling around twilight hours, while when at the border of the fields they were foraging on crops mostly after twilight and in smaller parties. These results suggest that chimpanzees change their activity rhythm to access cultivated resources when human presence and surveillance is lower. This survey provides evidence of behavioral plasticity in chimpanzees in response to neighboring human farming activities, and emphasizes the urgent need to work with local communities to mitigate human-wildlife conflict related to crop-feeding.

Constraints on population growth of blue monkeys (Cercopithecus mitis) in Kibale National Park, Uganda

Changes in population size are driven by environmental and social factors. In spite of repeated efforts to identify the constraints on an unusually low-density population of blue monkeys (Cercopithecus mitis), it remains unclear why this generalist species fails to thrive in Kibale National Park in Uganda. While an unidentified disease may occasionally obstruct conception, it does not seem to limit overall reproductive rates. Infanticide at this site is infrequent due to the long tenures of resident males. Our analyses indicate that the single biggest constraint on blue monkey densities may be feeding competition with grey-cheeked mangabeys (Lophocebus albigena): across Kibale, the densities of these two species are strongly and negatively correlated. Though further analysis is needed to understand the timing and strength of feeding competition between them, we conclude that blue monkeys at Ngogo experience competitive exclusion from grey-cheeked mangabeys, possibly resolving the 50-year mystery surrounding this population.

Chimpanzee exposure to pollution revealed by human biomonitoring approaches

Wildlife is increasingly exposed to environmental pollution, but data illustrating to what extent this exposure can impact health and survival of endangered species is missing. In humans, hair matrix analysis is a reliable tool for assessing cumulative exposure to organic pollutants such as pesticides but has rarely been used in other primates for this purpose. LC/MS-MS and GC/MS-MS multi-residue methods were used to screen the presence of 152 organic pollutants and their metabolites belonging to 21 different chemical families in hair samples from our closest relative, the chimpanzee. Samples were collected from 20 wild chimpanzees in Sebitoli, Kibale National Park, Uganda and 9 captive chimpanzees in the Réserve Africaine de Sigean, France. In total, 90 chemicals were detected, 60 in wild chimpanzees and 79 in captive chimpanzees. The median concentrations of detected chemicals in captive individuals were significantly higher than those in wild chimpanzees. Hair from the captive individuals at RAS was sampled a second time after 6 months in an environment of reduced exposure to these pollutants (diet of organic food, decreased use of plastic food and water containers). The number of chemicals detected in captive chimpanzees reduced from 79 to 63, and their concentrations were also significantly reduced. In the present study we report for the first time the use of hair analysis to detect organic pollutants in primate hair. We conclude that both wild and captive chimpanzees are exposed to a large range of different chemicals through their diet. Our study provides surprising and alarming evidence that besides the direct threats of poaching, deforestation and diseases, wild chimpanzees might be endangered by indirect consequences of anthropic activities. As chimpanzees are our closest relatives, our results should be considered as an alert for human health as well.

Potential Contribution of Groundnut Residues to Soil N and the Influence of Farmer Management in Western Uganda

Through symbiotic biological nitrogen fixation (BNF), grain legumes, such as groundnuts, can enhance soil nitrogen (N) and be an important source of N fertility, as well as a critical component of human nutrition and food security. Because legumes obtain N from soil N stocks as well as BNF, legume residues are key to capturing potential N benefits for soils, which may contribute to increased yields and food production. Here, we conducted a detailed survey at household and field level within a six-village corridor along the western boundary of Kibale National Park (KNP) in western Uganda. We focused on groundnut production and residue management practices and soil organic carbon (SOC) and total N (TN) in fields managed by 100 different households. We also determined SOC and TN in adjacent uncultivated KNP soils. We tested for relationships between socioeconomic factors and farmer groundnut management practices. We calculated a partial N balance and estimated potential N benefits under three scenarios for groundnut BNF. Within the study area, groundnut residue management varied greatly with 51% of surveyed farmers retaining residues on fields through spreading or incorporation, and 49% removing residues, either by transfer to banana groves or burning. Groundnut population density was relatively high with 43% of fields having >30 plants m−2. Despite providing net N inputs of up to 27 kg N ha−1, there was no observed effect of groundnut residue management practices on SOC, TN, or soil C:N ratios. Compared to uncultivated KNP soils, groundnut fields had lower mean levels of SOC and TN and wider C:N ratios. These values are consistent with cultivated soils; however, losses of SOC and TN were lower compared to losses previously reported for conversion from tropical forest to agricultural use. We found that farmer valuation and perception of groundnut residues were influential factors in residue management practices. Overall, we estimated that groundnut residues have the potential to contribute to SOC and TN stocks if retained in the field, but, conversely, removal will result in sizable losses. We find that both environmental and social contexts must be considered when recommending legumes for N provisioning services.

Long-term trends in fruit production in a tropical forest at Ngogo, Kibale National Park, Uganda

Fruit production in tropical forests varies considerably in space and time, with important implications for frugivorous consumers. Characterizing temporal variation in forest productivity is thus critical for understanding adaptations of tropical forest frugivores, yet long-term phenology data from the tropics, in particular from African forests, are still scarce. Similarly, as the abiotic factors driving phenology in the tropics are predicted to change with a warming climate, studies documenting the relationship between climatic variables and fruit production are increasingly important. Here we present data from 19 years of monitoring the phenology of 20 tree species at Ngogo in Kibale National Park, Uganda. Our aims were to characterize short- and long-term trends in productivity and to understand the abiotic factors driving temporal variability in fruit production. Short-term (month-to-month) variability in fruiting was relatively low at Ngogo, and overall fruit production increased significantly through the first half of the study. Among the abiotic variables we expected to influence phenology patterns (including rainfall, solar irradiance, and average temperature), only average temperature was a significant predictor of monthly fruit production. We discuss these findings as they relate to the resource base of the frugivorous vertebrate community inhabiting Ngogo.

Cercopithecine and Colobine Abundance Across Protected and Unprotected Land in the Greater Mahale Ecosystem, Western Tanzania

Most primates live in unprotected land where abundances and threats may differ from those in protected areas. We therefore need to establish population densities in both unprotected and protected areas to effectively inform conservation planning. The Greater Mahale Ecosystem in western Tanzania is a region of mixed protected status with seven cercopithecine and colobine species: blue (Cercopithecus mitis doggetti), red-tailed (C. ascanius schmidi), and vervet (Chlorocebus pygerythrus) monkeys; ashy red colobus (Piliocolobus tephrosceles); black-and-white colobus (Colobus angolensis); and olive (Papio anubis) and yellow (P. cynocephalus) baboons. These species may be threatened by increasing human activity; however, except for ashy red colobus, no data on local abundances are available. We walked over 350 km of line transects in legally protected (Village Forest Reserves) and unprotected general land between August 2011 and October 2012 to estimate densities of primates and human activity. Primate densities were consistently low across the Greater Mahale Ecosystem. Blue and red-tailed monkey and ashy red colobus densities were especially low compared to populations in predominantly forested landscapes. Primate and human activity densities did not differ significantly inside and outside of reserves. Low primate densities could be natural responses to the lower proportions and quality of riparian forest habitat in the region. High levels of human activity and the absence of significantly higher primate densities in reserves suggest unprotected land could provide important refuges for primates in the Greater Mahale Ecosystem. This result further reinforces a broad need to include unprotected areas in primate conservation strategies.

Competition and specialization in an African forest carnivore community

Globally, human activities have led to the impoverishment of species assemblages and the disruption of ecosystem function. Determining whether this poses a threat to future ecosystem stability necessitates a thorough understanding of mechanisms underpinning community assembly and niche selection. Here, we tested for niche segregation within an African small carnivore community in Kibale National Park, Uganda. We used occupancy modeling based on systematic camera trap surveys and fine-scale habitat measures, to identify opposing preferences between closely related species (cats, genets, and mongooses). We modeled diel activity patterns using kernel density functions and calculated the overlap of activity periods between related species. We also used co-occupancy modeling and activity overlap analyses to test whether African golden cats Caracal aurata influenced the smaller carnivores along the spatial and/or temporal axes. There was some evidence that related species segregated habitat and activity patterns. Specialization was particularly strong among forest species. The cats and genets partitioned habitat, while the mongooses partitioned both habitat and activity period. We found little evidence for interference competition between African golden cats and other small carnivores, although weak interference competition was suggested by lower detection probabilities of some species at stations where African golden cats were present. This suggests that community assembly and coexistence in this ecosystem are primarily driven by more complex processes. The studied carnivore community contains several forest specialists, which are typically more prone to localized extinction. Preserving the observed community assemblage will therefore require the maintenance of a large variety of habitats, with a particular focus on those required by the more specialized carnivores.

Food abundance and weather influence habitat-specific ranging patterns in forest- and savanna mosaic-dwelling red-tailed monkeys (Cercopithecus ascanius)

OBJECTIVES

Primates that live in predominantly forested habitats and open, savanna mosaics should exhibit behavioral responses to differing food distributions and weather. We compared ecological constraints on red-tailed monkey ranging behavior in forest and savanna mosaic environments. Intraspecific variation in adaptations to these conditions may reflect similar pressures faced by hominins during the Plio-Pleistocene.

METHODS

We followed six groups in moist evergreen forest at Ngogo (Uganda) and one group in a savanna-woodland mosaic at the Issa Valley (Tanzania). We used spatial analyses to compare home range sizes and daily travel distances (DTD) between sites. We used measures of vegetation density and phenology to interpolate spatially explicit indices of food (fruit, flower, and leaves) abundance. We modeled DTD and range use against food abundance. We modeled DTD and at Issa hourly travel distances (HTD), against temperature and rainfall.

RESULTS

Compared to Issa, monkeys at Ngogo exhibited significantly smaller home ranges and less variation in DTD. DTD related negatively to fruit abundance, which had a stronger effect at Issa. DTD and HTD related negatively to temperature but not rainfall. This effect did not differ significantly between sites. Home range use did not relate to food abundance at either site.

CONCLUSIONS

Our results indicate food availability and thermoregulatory constraints influence red-tailed monkey ranging patterns. Intraspecific variation in home range sizes and DTD likely reflects different food distributions in closed and open habitats. We compare our results with hypotheses of evolved hominin behavior associated with the Plio-Pleistocene shift from similar closed to open environments.

Extensive sampling reveals the phenology and habitat use of Afrotropical parasitoid wasps (Hymenoptera: Ichneumonidae: Rhyssinae)

Tropical invertebrates, such as the ichneumonids of tropical forests, are poorly known. Here, we report the first results of extensive sampling at Kibale National Park, Uganda, by providing some of the first tropical ecological data for the ichneumonid subfamily Rhyssinae. We sampled ichneumonids with 34 Malaise traps for a year in 10 sites, in habitats ranging from primary forest to farmland. We also gathered weather and vegetation data. The total sampling effort was 373 trap months and we caught 444 rhyssines in six species. We caught the most rhyssines in dry weather, and towards the end of the sampling year. The rhyssines showed a clear preference for decaying logs and for primary forest. We fitted a model which can be used to predict future catches at the site, and draw conclusions on when rhyssines emerge and on their adult lifespan. Sampling extensively gave us a wealth of ecological data on a poorly known parasitoid wasp subfamily. We recommend that future tropical sampling collect ecological data, and that existing data from previous large-scale surveys be used for ecological analyses.

Metagenomic analyses reveal previously unrecognized variation in the diets of sympatric Old World monkey species

Insectivory, or the consumption of insects and other arthropods, is a significant yet cryptic component of omnivorous primate diets. Here, we used high-throughput DNA sequencing to identify arthropods from fecal DNA and assess variation in insectivory by closely-related sympatric primates. We identified arthropod prey taxa and tested the hypothesis that variation in insectivory facilitates niche differentiation and coexistence among closely-related species with high dietary overlap. We collected 233 fecal samples from redtail (Cercopithecus ascanius; n = 118) and blue monkeys (C. mitis; n = 115) and used a CO1 metabarcoding approach to identify arthropod DNA in each fecal sample. Arthropod DNA was detected in 99% of samples (N = 223 samples), and a total of 68 families (15 orders) were identified. Redtails consumed arthropods from 54 families, of which 12 (21.8%) were absent from blue monkey samples. Blue monkeys consumed arthropods from 56 families, of which 14 (24.6%) were absent from redtail samples. For both species, >97% of taxa present belonged to four orders (Araneae, Diptera, Hymenoptera, Lepidoptera). Redtail samples contained more Lepidoptera taxa (p<0.05), while blue monkey samples contained more Araneae (p<0.05). Blue monkeys consumed a greater diversity of arthropod taxa than redtail monkeys (p<0.05); however, the average number of arthropod families present per fecal sample was greater in the redtail monkey samples (p<0.05). These results indicate that while overlap exists in the arthropod portion of their diets, 20-25% of taxa consumed are unique to each group. Our findings suggest that variation in arthropod intake may help decrease dietary niche overlap and hence facilitate coexistence of closely-related primate species.

Atmospheric Occurrence of Legacy Pesticides, Current Use Pesticides, and Flame Retardants in and around Protected Areas in Costa Rica and Uganda

Protected areas have developed alongside intensive changes in land use and human settlements in the neighboring landscape. Here, we investigated the occurrence of 21 organochlorine pesticides (OCPs), 14 current use pesticides (CUPs), 47 halogenated flame retardants (HFRs), and 19 organophosphate esters (OPEs) in air around Las Cruces (LC) and La Selva (LS) Biological Stations, Costa Rica, and Kibale National Park (KNP), Uganda using passive air samplers (PAS) with polyurethane foam (PUF) discs (PAS-PUF). Significantly higher concentrations of CUPs were observed around LS, while LC had a higher concentration of OCPs. Land use analysis indicated that LS had a higher fraction of agriculture than LC (33% vs 14%), suggesting the higher CUPs concentration at LS was related to pesticide intensive crops, while higher OCPs concentration at LC may be attributed to the area's long agricultural history characterized by small-scale subsistence farming or long-range transport. In Uganda, CUPs and OCPs were generally lower than in Costa Rica, but high concentrations of HFRs were observed inside KNP, possibly due to human activity at research camps near the protected forest. This is the first study that documented the occurrence of anthropogenic chemicals in the air at protected areas with tropical forests.

Maximising camera trap data: Using attractants to improve detection of elusive species in multi-species surveys

Camera traps are a key tool in ecological studies, and are increasingly being used to understand entire communities. However, robust inferences continue to be hampered by low detection of rare and elusive species. Attractants can be used to increase detection rates, but may also alter behaviour, and little research has evaluated short-term, localized response to the presence of attractants. We conducted three camera trap surveys in Kibale National Park, Uganda, using food baits and scent lures (“attractants”) at each camera station to entice small carnivores to pass in front of camera stations. To examine the interrelationship between scavenging and response to attractants, we also placed camera traps at five food refuse pits. We modelled the effect of attractant and duration of trap placement on the detection probability of small carnivores and selected African golden cat Caracal aurata prey items. We examine transient site response of each species, by comparing our observed likelihood of detection in each 24 h period from 1–7 d following refreshing of attractants to randomly generated capture histories. African civet Civettictis civetta, rusty-spotted genet Genetta maculata, African palm civet Nandinia binotata, and marsh mongoose Atilax paludinosus detection probabilities were highest and Weyns’s red duiker Cephalophus wenysi detection probability was lowest immediately after attractants were placed. Within 24 h after attractant was placed, rusty-spotted genet and African palm civet were more likely to be detected and African golden cat, red duiker, and blue duiker Philantomba monticola were less likely to be detected. Our results suggest that attractants can increase detection of small-bodied species and include some arboreal species in terrestrial camera trap sampling. However, attractants may also alter short-term visitation rates of some species, with potentially cascading effects on others. Community level and intraguild interaction studies should control for the potentially confounding effects of attractants on spatial activity patterns.

Facial dysplasia in wild forest olive baboons (Papio anubis) in Sebitoli, Kibale National Park, Uganda: Use of camera traps to detect health defects

BACKGROUND

Primate populations are in decline, mainly affected by agriculture leading to habitat loss, fragmentation but also chemical pollution. Kibale National Park (Uganda), Sebitoli forest, surrounded by tea and crop fields, is the home range of chimpanzees presenting congenital facial dysplasia. This study aimed to identify to what extent the same phenotypical features are observed in baboons (Papio anubis) of this area.

METHODS

A total of 25 390 clips recorded by 14 camera traps between January 2017 and April 2018 were analyzed.

RESULTS

We identified 30 immature and adult baboons of both sexes with nose and lip deformities. They were more frequently observed in the northwestern part of the area.

CONCLUSIONS

A possible effect of pesticides used in crops at the border of their habitat is suspected to alter the embryonic development. This study emphasizes the importance of non-invasive methods to detect health problems in wild primates that can act as sentinels for human health.

Effects of Environmental Stress on Primate Populations

Environmental stress on primate populations can take many forms. Abiotic factors, such as temperature and precipitation, may directly influence the behavior of primates owing to physiological demands of thermoregulation or through indirect influences on vegetation that primates rely on for food. These effects can also scale up to the macro scale, impacting primate distributions and evolution. Primates also encounter stress during interactions within and between species (i.e., biotic interactions). For example, selective pressure from male-perpetrated infanticide can drive the development of female counterstrategies and can impact life-history traits. Predation on primates can modify group size, ranging behavior, and habitat use. Finally, humans have influenced primate populations for millennia. More recently, hunting, habitat disturbance, disease, and climate change have increased in frequency and severity with detrimental impacts on primate populations worldwide. These effects and recent evidence from camera traps emphasize the importance of maintaining protected areas for conserving primate populations.

The evolution of fruit colour: phylogeny, abiotic factors and the role of mutualists

The adaptive significance of fruit colour has been investigated for over a century. While colour can fulfil various functions, the most commonly tested hypothesis is that it has evolved to increase fruit visual conspicuousness and thus promote detection and consumption by seed dispersing animals. However, fruit colour is a complex trait which is subjected to various constraints and selection pressures. As a result, the effect of animal selection on fruit colour are often difficult to identify, and several studies have failed to detect it. Here, we employ an integrative approach to examine what drives variation in fruit colour. We quantified the colour of ripe fruit and mature leaves of 97 tropical plant species from three study sites in Madagascar and Uganda. We used phylogenetically controlled models to estimate the roles of phylogeny, abiotic factors, and dispersal mode on fruit colour variation. Our results show that, independent of phylogeny and leaf coloration, mammal dispersed fruits are greener than bird dispersed fruits, while the latter are redder than the former. In addition, fruit colour does not correlate with leaf colour in the visible spectrum, but fruit reflection in the ultraviolet area of the spectrum is strongly correlated with leaf reflectance, emphasizing the role of abiotic factors in determining fruit colour. These results demonstrate that fruit colour is affected by both animal sensory ecology and abiotic factors and highlight the importance of an integrative approach which controls for the relevant confounding factors.

Two Cases of Cleft Lip and Other Congenital Anomalies in Wild Chimpanzees Living in Kibale National Park, Uganda

Design

Observations of wild chimpanzees ( Pan troglodytes schweinfurthii) were conducted in Kibale National Park, Uganda, at the sites of Sebitoli and Ngogo.

Results

We report the first two cases of cleft lip in wild chimpanzees. Additionally, some other chimpanzees in the Sebitoli community show facial dysplasia and congenital anomalies, such as patches of depigmented hairs and limb defects.

Conclusions

Cleft lip has been documented in several species of nonhuman primates, but much remains unknown about the occurrence of cleft lip and cleft palate in great apes, probably because such malformations are rare, wild apes are difficult to monitor and observe, and severe cases associated with cleft palates render suckling impossible and lead to early death of infants. The genetic basis of such defects in great apes warrants investigation, as does the possibility that environmental toxins contribute to their etiology in Kibale in ways that could affect humans as well.

Agricultural expansion as risk to endangered wildlife: Pesticide exposure in wild chimpanzees and baboons displaying facial dysplasia

Prenatal exposure to environmental endocrine disruptors can affect development and induce irreversible abnormalities in both humans and wildlife. The northern part of Kibale National Park, a mid-altitude rainforest in western Uganda, is largely surrounded by industrial tea plantations and wildlife using this area (Sebitoli) must cope with proximity to human populations and their activities. The chimpanzees and baboons in this area raid crops (primarily maize) in neighboring gardens. Sixteen young individuals of the 66 chimpanzees monitored (25%) exhibit abnormalities including reduced nostrils, cleft lip, limb deformities, reproductive problems and hypopigmentation. Each pathology could have a congenital component, potentially exacerbated by environmental factors. In addition, at least six of 35 photographed baboons from a Sebitoli troop (17%) have similar severe nasal deformities. Our inquiries in villages and tea factories near Sebitoli revealed use of eight pesticides (glyphosate, cypermethrin, profenofos, mancozeb, metalaxyl, dimethoate, chlorpyrifos and 2,4-D amine). Chemical analysis of samples collected from 2014 to 2016 showed that mean levels of pesticides in fresh maize stems and seeds, soils, and river sediments in the vicinity of the chimpanzee territory exceed recommended limits. Notably, excess levels were found for total DDT and its metabolite pp'-DDE and for chlorpyrifos in fresh maize seeds and in fish from Sebitoli. Imidacloprid was detected in coated maize seeds planted at the edge the forest and in fish samples from the Sebitoli area, while no pesticides were detected in fish from central park areas. Since some of these pesticides are thyroid hormone disruptors, we postulate that excessive pesticide use in the Sebitoli area may contribute to facial dysplasia in chimpanzees and baboons through this endocrine pathway. Chimpanzees are considered as endangered by IUCN and besides their intrinsic value and status as closely related to humans, they have major economic value in Uganda via ecotourism. Identifying and limiting potential threats to their survival such be a conservation priority.

Changing perceptions of protected area benefits and problems around Kibale National Park, Uganda

Local residents' changing perceptions of benefits and problems from living next to a protected area in western Uganda are assessed by comparing household survey data from 2006, 2009, and 2012. Findings are contextualized and supported by long-term data sources for tourism, protected area-based employment, tourism revenue sharing, resource access agreements, and problem animal abundance. We found decreasing perceived benefit and increasing perceived problems associated with the protected area over time, with both trends dominated by increased human-wildlife conflict due to recovering elephant numbers. Proportions of households claiming benefit from specific conservation strategies were increasing, but not enough to offset crop raiding. Ecosystem services mitigated perceptions of problems. As human and animal populations rise, wildlife authorities in Sub-Saharan Africa will be challenged to balance perceptions and adapt policies to ensure the continued existence of protected areas. Understanding the dynamic nature of local people's perceptions provides a tool to adapt protected area management plans, prioritize conservation resources, and engage local communities to support protected areas.

Spatial Overlap Between People and Non-human Primates in a Fragmented Landscape

In western Uganda, the landscape surrounding Kibale National Park (KNP) contains households, trading centers, roads, fields, and forest fragments. The mosaic arrangement of these landscape features is thought to enhance human-primate interaction, leading to primate population declines and increased bi-directional disease transmission. Using a social-ecological systems research framework that captures the complexity of interaction among people, wildlife, and environment, we studied five forest fragments near KNP and conducted intensive on-the-ground mapping to identify locations of human-primate spatial overlap. Primate locations and human activities were distributed within, on the edges, and far beyond fragment borders. Analysis of shared spaces indicated that 5.5% of human space overlapped with primate spaces, while 69.5% of primate spaces overlapped with human spaces. Nearest neighbor analysis indicated that human activities were significantly spatially clustered within and around individual fragments, as were primate locations. Getis-Ord statistics revealed statistically significant "hotspots" of human activity and primate activity, but only one location where spatial overlap between humans and primates was statistically significant. Human activities associated with collecting fuelwood and other forest products were the primary drivers of human-primate overlap; however, primates also spent time outside of forest fragments in agricultural spaces. These results demonstrate that fragmented landscapes are not uniform with respect to human-primate overlap, and that the implications of human-primate interaction, such as primate population declines and possible cross-species disease transmission, are spatially aggregated.

The Paucity of Frugivores in Madagascar May Not Be Due to Unpredictable Temperatures or Fruit Resources

The evolution of ecological idiosyncrasies in Madagascar has often been attributed to selective pressures stemming from extreme unpredictability in climate and resource availability compared to other tropical areas. With the exception of rainfall, few studies have investigated these assumptions. To assess the hypothesis that Madagascar's paucity of frugivores is due to unreliability in fruiting resources, we use statistical modeling to analyze phenology datasets and their environmental correlates from two tropical wet forests, the Réserve Naturelle Intégrale Betampona in Madagascar, and Kibale National Park in Uganda. At each site we found that temperature is a good environmental predictor of fruit availability. We found no evidence of a significant difference in the predictability of fruit availability between the two sites, although the shorter duration of phenological monitoring at Betampona (two years, versus 15 years at Kibale) limits our ability to infer long-term patterns. Comparisons of long-term temperature data from each site (15 years from Kibale and 14 from Betampona) indicate that temperature is more predictable at Betampona than at Kibale. However, there does appear to be a difference between the two sites in the total fruit availability at any given time, with fruit being generally less abundant at Betampona. Our results appear contrary to the prevailing hypothesis of a selective force imposed by unpredictable resource availability or temperature, and we suggest other possible explanations for Madagascar's unique biota.

The successional pathway of the tree community and how it shapes the fruit-feeding butterfly community in an Afrotropical forest

The relative importance of different bottom-up-mediated effects in shaping insect communities in tropical secondary forests are poorly understood. Here, we explore the roles of vegetation structure, forest age, local topography (valley vs. hill top) and soil variables in predicting fruit-feeding butterfly and tree community composition, and tree community composition in predicting fruit-feeding butterfly community composition, in different-aged naturally regenerating and primary forests of Kibale National Park, Uganda. We also examine which variables are best predictors of fruit-feeding butterfly species richness or diversity. Butterflies (88 species) were sampled with a banana-baited trap and trees (98 taxa) with a 40 × 20-m sampling plot at 80 sampling sites. The environmental variables explained 31% of the variation in the tree community composition, the best predictors being local topography, forest age and cover of Acanthus pubescens (a shrub possibly arresting succession). The fruit-feeding butterfly community composition was better predicted by tree community composition (explaining 10% of the variation) rather than vegetation structure, local topography or soil factors. Environmental variables and tree species richness (or diversity) were poor predictors of butterfly species richness (or diversity). Our results emphasize the importance of tree community to recovery of herbivorous insect communities in tropical secondary forests.