The future of the biodiversity of the Gran Caldera Scientific Reserve: Translating science into policy to develop an effective management plan

White paper prepared for the Workshop on ‘The future of the biodiversity of the Gran Caldera Scientific Reserve', celebrated in Malabo, Equatorial Guinea, in June 201

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 infuenced the nest decay rate over the early stage of the lifetime of the nests. The study confrms 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

Do primate action plans work?

John Oates authored the first primate conservation Action Plan in 1986, which assessed the status of and proposed conservation actions for all mainland African primate species. A revised version of the continent-wide plan was published in 1996, but since then, action plans have generally evolved into prioritizing actions for specific species, often within defined landscapes. We will review and evaluate the content and success of conservation action plans for the nine currently recognized taxa of chimpanzees and gorillas in Africa. Since 2003, six detailed action plans and one population viability analysis have been published, covering priority actions and landscapes for seven of the nine great ape taxa in Africa. Two further action plans (for gorillas and chimpanzees in Eastern DRC and for bonobos) are in the final stages of review and may also be included in the analysis. Assessments for western chimpanzees, Cross River gorillas, western lowland gorillas and central chimpanzees have been peer reviewed, and we will consider their recommendations and the challenges of quantitatively evaluating the success of primate conservation action plans

The relationship between the abundance of the Nigeria-Cameroon chimpanzee (Pan troglodytes ellioti) and its habitat: a conservation concern in Mbam-Djerem National Park, Cameroon

Background Understanding the relationship between great apes and their habitat is essential for the development of successful conservation strategies. The chimpanzee Pan troglodytes ellioti is endemic to Nigeria and Cameroon, and occupies an ecologically diverse range of habitats from forests to forest-savannah mosaic in Mbam-Djerem National Park (MDNP) in Cameroon. The habitat variation in chimpanzees is poorly understood in MDNP which provides an excellent opportunity to assess ecological factors that shape the abundance and distribution patterns of P. t. ellioti over a small geographic scale. Results We counted 249 nests along 132 km of transects in total. Of these, 119 nests along 68 km occurred in dense forest and 130 nests along 64 km in forest-savannah mosaic. Chimpanzee density was 0.88 [95% CI (0.55–1.41)] individuals/km2 in the dense forest and 0.59 [95% CI (0.19–1.76)] in the forest-savannah mosaic. Nest abundance varied with vegetation type and was higher in areas with dense canopy cover, steeper slopes and relatively higher altitudes. Conclusions Our estimates of chimpanzee densities were lower than reported in other studied populations in the range of the Nigeria-Cameroon chimpanzee. However, we found that habitat features, slope and altitude likely play a role in shaping patterns of chimpanzee nesting ecology. Further studies need to be focused on nest decay rates and phenology of useful plants in order to model chimpanzee abundance and distribution in Mbam-Djerem National Park

Chimpanzee population structure in Cameroon and Nigeria is associated with habitat variation that may be lost under climate change

Background: The Nigeria-Cameroon chimpanzee (Pan troglodytes ellioti) is found in the Gulf of Guinea biodiversity hotspot located in western equatorial Africa. This subspecies is threatened by habitat fragmentation due to logging and agricultural development, hunting for the bushmeat trade, and possibly climate change. Although P. t. ellioti appears to be geographically separated from the neighboring central chimpanzee (P. t. troglodytes) by the Sanaga River, recent population genetics studies of chimpanzees from across this region suggest that additional factors may also be important in their separation. The main aims of this study were: 1) to model the distribution of suitable habitat for P. t. ellioti across Cameroon and Nigeria, and P. t. troglodytes in southern Cameroon, 2) to determine which environmental factors best predict their optimal habitats, and 3) to compare modeled niches and test for their levels of divergence from one another. A final aim of this study was to examine the ways that climate change might impact suitable chimpanzee habitat across the region under various scenarios. Results: Ecological niche models (ENMs) were created using the software package Maxent for the three populations of chimpanzees that have been inferred to exist in Cameroon and eastern Nigeria: (i) P. t. troglodytes in southern Cameroon, (ii) P. t. ellioti in northwestern Cameroon, and (iii) P. t. ellioti in central Cameroon. ENMs for each population were compared using the niche comparison test in ENMtools, which revealed complete niche divergence with very little geographic overlap of suitable habitat between populations. Conclusions: These findings suggest that a positive relationship may exist between environmental variation and the partitioning of genetic variation found in chimpanzees across this region. ENMs for each population were also projected under three different climate change scenarios for years 2020, 2050, and 2080. Suitable habitat of P. t. ellioti in northwest Cameroon / eastern Nigeria is expected to remain largely unchanged through 2080 in all considered scenarios. In contrast, P. t. ellioti in central Cameroon, which represents half of the population of this subspecies, is expected to experience drastic reductions in its ecotone habitat over the coming century

Accessibility to protected areas increases primate hunting intensity in Bioko Island, Equatorial Guinea

Bioko is one of the most important sites for African primate conservation; yet it has seen a severe decline in its primate populations due to illegal hunting to supply a thriving wildmeat trade. The completion in 2015 of a new road bisecting the Gran Caldera Scientific Reserve (GCSR), where rugged terrain and lack of infrastructure once served as a natural barrier, further threatened this last stronghold for Bioko’s primates. Here we used passive acoustic monitoring to study factors affecting hunting patterns within GCSR through the automatic detection of shotgun sounds. Ten acoustic sensors were placed in locations that varied in terrain heterogeneity, distance to the new road, human settlements, research camps (i.e., Moraka and Moaba) and elevation. Sensors recorded continuously between January 2018 and January 2020, collecting 2671 site-days of audio. In total 596 gunshots were detected, including in the most remote areas. There were significant differences in hunting rate between areas (Kruskal-Wallis, χ2 = 102.71, df = 9, p < 0.001). We also found there were significantly fewer gunshots during 2019 than during 2018 (V = 55, p < 0.001). Occupancy modelling showed that hunting increased with decreasing terrain heterogeneity and decreasing distance to roads and villages; and decreased with increasing proximity to Research Camps. These results demonstrated that increasing accessibility increased primate hunting in GCSR, which was exacerbated by the opening of the new road. We also demonstrated that research presence was effective at reducing primate hunting. Unless strict conservation interventions are implemented, including road checkpoints, increasing biomonitoring and hunting patrols, and an island-wide, enforced ban on firearms, GCSR will see a significant decrease in primate density over the next decade, including the potential extinction of Critically Endangered Pennant’s red colobus, whose entire population is restricted to GCSR and is a primary target of hunters

Regional Action Plan for the Conservation of the Nigeria–Cameroon Chimpanzee (Pan troglodytes ellioti)

First paragraph: This document represents the consensus of views from forestry and wildlife conservation agencies in Nigeria and Cameroon, local and international nongovernmental conservation organizations, and university-based researchers who met at a series of workshops in Cameroon and Nigeria to formulate a set of actions that, if implemented, will increase the longterm survival prospects of the Nigeria-Cameroon chimpanzee, Pan troglodytes ellioti. The Nigeria-Cameroon chimpanzee is the most endangered of all currently recognized chimpanzee subspecies, with a total remaining population of between 3,500 and 9,000 living in forested habitat to the north of the Sanaga River in Cameroon, the eastern edge of Nigeria, and in forest fragments in the Niger Delta and southwestern Nigeri

The time scale of recombination rate evolution in great apes

We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequence data from 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez J, et al. 2013. Great ape genetic diversity and population history. Nature 499:471-475). We also identified species-specific recombination hotspots in each group using a modified LDhot framework, which greatly improves statistical power to detect hotspots at varying strengths. We show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time scale of complete hotspot turnover. Further, using species-specific PRDM9 sequences to predict potential binding sites (PBS), we show higher predicted PRDM9 binding in recombination hotspots as compared to matched cold spot regions in multiple great ape species, including at least one chimpanzee subspecies. We found that correlations between broad-scale recombination rates decline more rapidly than nucleotide divergence between species. We also compared the skew of recombination rates at centromeres and telomeres between species and show a skew from chromosome means extending as far as 10-15Mb from chromosome ends. Further, we examined broad-scale recombination rate changes near a translocation in gorillas and found minimal differences as compared to other great ape species perhaps because the coordinates relative to the chromosome ends were unaffected. Finally, on the basis of multiple linear regression analysis, we found that various correlates of recombination rate persist throughout the African great apes including repeats, diversity, and divergence. Our study is the first to analyze within- And between-species genome-wide recombination rate variation in several close relatives

The evolution of resistance to Simian Immunodeficiency Virus (SIV): A review

Abstract Examining how pathogens cross species boundaries, spread within species, and persist within their hosts is an essential part of understanding the factors that underpin the evolution of virulence and host resistance. Here, we review current knowledge about the genetic diversity, molecular epidemiology, prevalence, and pathogenicity of simian immunodeficiency viruses (SIVs). SIVs have crossed species boundaries from simian hosts to humans on at least 12 separate occasions, one of which led to the global HIV-AIDS crisis. Though SIVs infect a wide range of primates, scientists have only recently begun to describe the natural history of SIV infection in their natural hosts. Several new studies reveal how both viral and host factors are responsible for the transmission to, and adaptation in, new hosts. These studies also suggest that the spread of the virus may be affected by host-specific traits, including social structure, mating system and demographic history. These studies challenge the traditional view that SIV is relatively benign in its natural host, and instead suggest that a highly dynamic relationship exists between SIV and its simian hosts