Genetic Sampling of Unhabituated Chimpanzees (Pan troglodytes schweinfurthii) in Gishwati Forest Reserve, an Isolated Forest Fragment in Western Rwanda

Camera traps unveil demography, social structure, and home range of six unhabituated Western chimpanzee groups in the Moyen Bafing National Park, Guinea

Precise estimates of population dynamics and social grouping patterns are required for effective conservation of wild animal populations. It is difficult to obtain such information on non-human great apes as they have slow reproductive rates. To gain a better understanding of demography in these populations, previous research has typically involved habituation\, a process that requires years. Here, we collected data continuously over year-long periods to monitor an unhabituated population of critically endangered Western chimpanzees (Pan troglodytes verus) in the Moyen Bafing National Park, Guinea. We used two arrays of 100 camera traps that were placed opportunistically in two distinct 100 km2 sites, named Bakoun and Koukoutamba. We identified 227 individuals in Bakoun and 207 in Koukoutamba through their unique facial features. Our camera trap data make clear that these individuals belong to six and seven closed groups, respectively. Six of those groups were near-completely sampled with an average minimum size of 46.8 individuals (range: 37-58), and a mean adult sex ratio of 1.32 (range: 0.93-2.10). We described the demographic composition of these groups and use Bayesian social network analysis to understand population structure. The network analyses suggested that the social bonds within the two populations were structured by sex homophily, with male chimpanzees being more or equally likely to be observed together than other adult associations. Through estimation of minimum convex polygons, we described the minimum home range for those groups. Compared to other chimpanzee groups living in a similar environment (mosaic savanna-forest), the Moyen Bafing region seems to host a high-density of chimpanzees with small home ranges for their group size. Our research highlights the potential of camera traps for studying the demographic composition of chimpanzee populations with high resolution and obtaining crucial information on several groups in a time-efficient and cost-effective way.

Species richness, relative abundance and occupancy of ground-dwelling mammals denote the ineffectiveness of chimpanzee as flagship species

In conservation biology, flagship species are defined as species that can raise support for biodiversity conservation in a given place or social context. In the newly established Gishwati–Mukura National Park in Rwanda, the Eastern chimpanzee was considered such an ambassador. To test whether the flagship species concept was effective in the park, we studied species richness, relative abundance, and species distribution (occupancy) of medium- to large-sized, ground-dwelling mammals using camera trapping technology. The impact of three environmental and three anthropogenic variables on species distribution was investigated and the ecological diversity of the fauna in the national park assessed. Over a period of 9 months, two 4 × 4 camera trapping grids were deployed in Gishwati and Mukura Forest. Sampling effort in each forest equated to 32 and 29 camera trapping locations, yielding 258 and 242 independent photographic events of eight and six species, respectively. In both forests, the Emin's giant poached rat was the most frequently encountered species, while all other species showed high relative abundance only in Gishwati Forest. The relative abundance of the endangered Eastern chimpanzee in Gishwati Forest was 0.54, the estimated occupancy was 0.31. Single-species, single-season occupancy models revealed that forest cover, altitude and distance to forest edge influenced the detectability of L'Hoest's monkey and squirrel species, while no effect was found on their occupancy. Notably, no larger herbivore or carnivore species were observed in the park, while the flagship species, i.e., the Eastern chimpanzee, was relatively abundant. Moreover, in both forests, all detected carnivores were small- to medium-sized, suggesting a meso-predator release phenomenon, i.e., populations of medium-sized predators increased after the removal of larger, top carnivores, due to relaxed competition. It appears that the prioritization of the flagship species resulted in the neglect of other mammalian species, leading eventually into the demise of entire functional guilds. Based on these results, the Gishwati–Mukura NP was categorized as a ‘depleted forest’. We, therefore, strongly object chimpanzees as a suitable flagship species—at least in the Gishwati–Mukura NP—and recommend collating more knowledge on the release of meso-predators and the loss of forest ungulates to improve their future conservation in Afro-montane forest habitats.

Distribution and conservation status of the golden monkey Cercopithecus mitis kandti in Rwanda

Habitat loss and fragmentation are major threats to primate populations globally. The Endangered golden monkey Cercopithecus mitis kandti is only found in two small forest fragments: the Virunga massif in Rwanda, Uganda and the Democratic Republic of the Congo, and the Gishwati Forest in Rwanda. Little is known about the abundance and distribution of this subspecies, or threats to its survival. During 2007–2018, we collected data along 893.7 km of line transects and 354.2 km of recce trails in Volcanoes National Park and in Gishwati–Mukura National Park to estimate golden monkey density and examine any threats. In Volcanoes National Park, golden monkeys were found almost exclusively in the bamboo zone, and in Gishwati–Mukura National Park they occurred only in the remnant tropical montane Gishwati Forest. In Volcanoes National Park, density was estimated to be 7.89 (95% CI: 3.85–16.19), 5.41 (2.64–11.08), and 5.47 (3.68–8.14) groups per km2 in 2007, 2011 and 2017–2018, respectively. This corresponds to a total of 4,331 individuals (95% CI: 2,723–5,938) in 2007, 4,487 (2,903–6,071) in 2011 and 4,626 (4,165–5,088) in 2017–2018. In Gishwati Forest, group density averaged 1.98 (95% CI: 1.27–3.16) per km2, corresponding to 172 (95% CI: 154–190) individuals in 2017–2018. Survey results from Volcanoes National Park suggest that the golden monkey population has been stable during 2007–2018. Limited habitat, illegal activities such as harvesting of bamboo and firewood, and the presence of feral dogs, threaten the golden monkey in Rwanda and require continued monitoring. The development of a conservation action plan is a priority to protect this species.

Soil-litter ant (Hymenoptera: Formicidae) community response to reforested lands of Gishwati tropical montane forest, northern-western part of Rwanda

Recently, human activities have impacted biodiversity-rich forest in western Rwanda, creating a need to enhance restoration activities of degraded lands in the region. To evaluate the effects of reforestation activities on the community composition of soil-litter ants, research was conducted in Gishwati tropical montane forest, located in northern-western part of Rwanda. The ant fauna was studied in reforested lands dominated by regenerated native species and exotic tree species. Further, a primary forest made of native trees served as a reference. In each forest type, nine sampling points were used to sample ants. Ant specimens were collected using pitfalls, hand sampling and Winkler extractor. They were identified to subfamilies, genus and species levels using dichotomous keys, and also statistically analysed for species richness, diversity, evenness and community composition. We collected a total of 2,481 individuals from 5 subfamilies, 18 genera and 35 species. Higher abundance, diversity and species richness were found in soil-litter under natural primary and secondary forests dominated by regenerated native plant species compared to exotic tree forest. The ant community composition analysis indicated higher similarities in ant species sampled under primary native forest and secondary forest dominated by regenerated native species. Reforestation by regenerating native species may be given priority in restoration of degraded lands due to their importance in species richness and species diversity.

Recent genetic connectivity and clinal variation in chimpanzees

Much like humans, chimpanzees occupy diverse habitats and exhibit extensive behavioural variability. However, chimpanzees are recognized as a discontinuous species, with four subspecies separated by historical geographic barriers. Nevertheless, their range-wide degree of genetic connectivity remains poorly resolved, mainly due to sampling limitations. By analyzing a geographically comprehensive sample set amplified at microsatellite markers that inform recent population history, we found that isolation by distance explains most of the range-wide genetic structure of chimpanzees. Furthermore, we did not identify spatial discontinuities corresponding with the recognized subspecies, suggesting that some of the subspecies-delineating geographic barriers were recently permeable to gene flow. Substantial range-wide genetic connectivity is consistent with the hypothesis that behavioural flexibility is a salient driver of chimpanzee responses to changing environmental conditions. Finally, our observation of strong local differentiation associated with recent anthropogenic pressures portends future loss of critical genetic diversity if habitat fragmentation and population isolation continue unabated.

Community-based conservation and chimpanzee research in Gishwati forest, Rwanda

As great ape populations around the world continue to decline, largely due to anthropogenic activities, conservation programs aimed at supporting these efforts have had mixed success. Here, we evaluate our community-based conservation program in Gishwati forest, Rwanda, aimed at helping to restore biodiversity and ecosystem services using chimpanzees as a flagship species. We examine the effectiveness of this program on reducing one of the ongoing threats to Gishwati's population of chimpanzees, illegal cattle grazing as well as the program's influence on the size of the chimpanzee population. We monitored illegal cattle grazing during several study periods between 2009 and 2019 in Gishwati forest following the implementation of our conservation program in 2008 that included law enforcement, community engagement, and research components. We found that when our conservation program was active, illegal cattle grazing was reduced to low levels. We also observed an increase in the chimpanzee population size during the 11 years since we started our conservation program. We examine how this reduction in cattle grazing and increase in chimpanzee population size may have been influenced by our community-centered approach and discuss the future of our conservation work in Gishwati.

Classifying Chimpanzee (Pan troglodytes) Landscapes Across Large-Scale Environmental Gradients in Africa

Primates are sometimes categorized in terms of their habitat. Although such categorization can be oversimplistic, there are scientific benefits from the clarity and consistency that habitat categorization can bring. Chimpanzees (Pan troglodytes) inhabit various environments, but researchers often refer to “forest” or “savanna” chimpanzees. Despite the wide use of this forest–savanna distinction, clear definitions of these landscapes for chimpanzees, based on environmental variables at study sites or determined in relation to existing bioclimatic classifications, are lacking. The robustness of the forest–savanna distinction thus remains to be assessed. We review 43 chimpanzee study sites to assess how the landscape classifications of researchers fit with the environmental characteristics of study sites and with three bioclimatic classifications. We use scatterplots and principal components analysis to assess the distribution of chimpanzee field sites along gradients of environmental variables (temperature, rainfall, precipitation seasonality, forest cover, and satellite-derived Hansen tree cover). This revealed an environmental continuum of chimpanzee study sites from savanna to dense forest, with a rarely acknowledged forest mosaic category in between, but with no natural separation into these three classes and inconsistencies with the bioclimatic classifications assessed. The current forest–savanna dichotomy therefore masks a progression of environmental adaptation for chimpanzees, and we propose that recognizing an additional, intermediate “forest mosaic” category is more meaningful than focusing on the ends of this environmental gradient only. Future studies should acknowledge this habitat continuum, place their study sites on the forest–savanna gradient, and include detailed environmental data to support further attempts at quantification.

Fecal DNA isolation and degradation in clam Cyclina sinensis: noninvasive DNA isolation for conservation and genetic assessment

Background

To avoid destructive sampling for conservation and genetic assessment, we isolated the DNA of clam Cyclina sinensis from their feces. DNA electrophoresis and PCR amplification were used to determine the quality of fecal DNA. And we analyzed the effects of different conditions on the degradation of feces and fecal DNA.

Results

The clear fecal DNA bands were detected by electrophoresis, and PCR amplification using clam fecal DNA as template was effective and reliable, suggesting that clam feces can be used as an ideal material for noninvasive DNA isolation. In addition, by analyzing the effects of different environmental temperatures and soaking times on the degradation of feces and fecal DNA, we found that the optimum temperature was 4 °C. In 15 days, the feces maintained good texture, and the quality of fecal DNA was good. At 28 °C, the feces degraded in 5 days, and the quality of fecal DNA was poor.

Conclusions

The clam feces can be used as an ideal material for noninvasive DNA isolation. Moreover, the quality of fecal DNA is negatively correlated with environmental temperature and soaking time.

Fixing the ecosystem: Conservation, crisis and capital in Rwanda's Gishwati Forest

Conservation-development projects are increasingly enacted across large expanses of land where human livelihoods hang in the balance. Recent initiatives-often called 'landscape approaches' or 'ecosystem-based' conservation-aim to achieve economic development and conservation goals through managing hybrid spaces. I argue that the landscape/ecosystem approach is a socioecological fix: an effort to resolve social-environmental crises through sinking capital (financial, natural, and social) into an imagined ecosystem. Rwanda's Gishwati Forest has been the locus of diverse crises and fixes over the past 40 years, including an industrial forestry and dairy project, a refugee settlement, a privately managed chimpanzee sanctuary, a carbon sequestration platform, and, most recently, an "integrated silvo-pastoral conservation landscape." This paper considers how these governance schemes have intersected with broader processes of agrarian change to generate crises that subsequent conservation/development projects then attempt to resolve. I demonstrate how visions for ecosystems privilege certain forms of governance around which imagined socioecological histories are mobilized to frame problems and legitimize certain solutions, technologies, and actors. The Gishwati ecosystem and its fixes are repeatedly defined through an imaginary of crisis and degradation that engenders large-scale landscape modification while foreclosing reflection about root causes of crises or how these might be addressed. Thus, even while conservation/development paradigms have shifted over the past 40 years (from separating people and nature to integrating them in conservation landscapes), this crisis-fix metabolism has consistently generated livelihood insecurity for the tens of thousands of people living in and around Gishwati. Imagining and enacting more just and inclusive social-environmental landscapes will require making space for diverse voices to define ecosystem form and function as well as addressing deeply rooted power imbalances that are at the heart of recurrent crises.

Non-invasive genetic censusing and monitoring of primate populations

Knowing the density or abundance of primate populations is essential for their conservation management and contextualizing socio-demographic and behavioral observations. When direct counts of animals are not possible, genetic analysis of non-invasive samples collected from wildlife populations allows estimates of population size with higher accuracy and precision than is possible using indirect signs. Furthermore, in contrast to traditional indirect survey methods, prolonged or periodic genetic sampling across months or years enables inference of group membership, movement, dynamics, and some kin relationships. Data may also be used to estimate sex ratios, sex differences in dispersal distances, and detect gene flow among locations. Recent advances in capture-recapture models have further improved the precision of population estimates derived from non-invasive samples. Simulations using these methods have shown that the confidence interval of point estimates includes the true population size when assumptions of the models are met, and therefore this range of population size minima and maxima should be emphasized in population monitoring studies. Innovations such as the use of sniffer dogs or anti-poaching patrols for sample collection are important to ensure adequate sampling, and the expected development of efficient and cost-effective genotyping by sequencing methods for DNAs derived from non-invasive samples will automate and speed analyses.

Genetic Mark–Recapture Improves Estimates of Maternity Colony Size for Indiana Bats

Genetic mark–recapture methods are increasingly being used to estimate demographic parameters in species where traditional techniques are problematic or imprecise. The federally endangered Indiana bat Myotis sodalis has declined dramatically and threats such as white-nose syndrome continue to afflict this species. To date, important demographic information for Indiana bats has been difficult to estimate precisely using traditional techniques such as emergence counts. Successful management and protection of Indiana bats requires better methods to estimate population sizes and survival rates throughout the year, particularly during summer when these bats reproduce and are widely dispersed away from their winter hibernacula. In addition, the familial makeup of maternity colonies is unknown, yet important for understanding local and regional population dynamics. We had four objectives in this study. For the first two objectives we investigated the potential use of DNA from fecal samples (fecal DNA) collected at roosts to obtain genetically based mark–recapture estimates of 1) colony size and 2) survival rates, for an Indiana bat maternity colony in Indianapolis, Indiana. The third objective was to compare our genetically based colony-size estimates with emergence counts conducted at the same roost tree to evaluate the genetic mark–recapture method. Our fourth objective was to use fecal DNA to estimate levels of relatedness among individuals sampled at the roost. In the summer of 2008, we collected fecal pellets and conducted emergence counts at a prominent roost tree during three time periods each lasting 7 or 8 d. We genotyped fecal DNA using five highly polymorphic microsatellite loci to identify individuals and used a robust-design mark–recapture approach to estimate survival rates as well as colony size at the roost tree. Emergence count estimates at the roost tree ranged from 100 to 215, whereas genetic mark–recapture estimates were higher, ranging from 122 to 266 and more precise. Apparent survival was 0.994 (SE = 0.04) between sampling periods suggesting that few bats died or permanently emigrated during the course of the study. Relatedness estimates, r, between all pairs of individuals averaged 0.055 ranging from 0 to 0.779, indicating that most individuals were not closely related. We demonstrate here the promise of using fecal DNA to estimate demographic information for Indiana bats and potentially other bat species.

Non-dietary analytical features of chimpanzee scats

Non-dietary aspects of ape scats such as scat weight and diameter are correlated with age and sex of defaecator for gorillas and orangutans. Defaecation rates of primates, including apes, illuminate their role as primary seed dispersers. We assess if non-dietary features of scats for East African chimpanzees (Pan troglodytes schweinfurthii) reveal such insights for members of the Kanyawara community in Kibale National Park, Uganda. Our objective is to see if such data yield useful perspectives for future census work on unhabituated chimpanzees, that is, what can scats tell us about a wild study population, beyond diet? We followed ten adults from this community, as well as travelling parties, comparing observed vs. unobserved defaecations, and collected data on scat weight and dimensions, defaecation rate, scat encounter rate, and interval between defaecations. Few non-dietary features of chimpanzee scats significantly differentiated sex or age of the defaecator, but total scat length and height distinguished adults from juveniles/infants. Defaecation rates and distance travelled were similar for adult males and females, indicating the importance of both sexes as potential primary seed dispersers. Observed travelling parties vs. non-observed travelling parties yielded similar data, indicating the potential to assess party size from scat encounter rates over a set distance. We provide detailed measurements of scat dimensions for this ape taxon which previously have been lacking. This research builds upon prior work by recording more in-depth data for focal subjects and travelling parties on defaecation and scat encounter rates. The findings presented should assist in the interpretation of scat data when censusing unhabituated chimpanzees.

Chimpanzee seed dispersal in a montane forest fragment in Rwanda

Primate seed dispersal plays an important role in forest regeneration. It may be particularly important to anthropogenically disturbed habitats such as forest fragments. However, few studies have examined primate seed dispersal in these types of environments. Chimpanzees (Pan troglodytes) are frugivorous and large-bodied, and are therefore able to disperse both large and small seeds, making them an important seed dispersal species. We examined chimpanzee seed dispersal in Gishwati forest, a 14 km² montane rainforest fragment in Rwanda. We systematically collected ≤24-hr-old fecal samples and counted the number of seeds of each fruit species. We also recorded observations of seeds found in wadges. We found that chimpanzees dispersed at least 18 fruit species in 14 families in their feces. Ninety-five percent of feces had seeds, the most common of which were Ficus spp., Myrianthus holstii, and Maesa lanceolata. We estimated that the Gishwati chimpanzee community with a density of 1.7 individuals per km² dispersed an average of 592 (>2 mm) seeds km^-2  day^-1 . We also found that chimpanzees dispersed the seeds of at least two fruit species, Ficus spp. and Chrysophyllum gorungosanum, in their wadges. In addition, 17% of the tree species recorded in our vegetation plots were chimpanzee-dispersed. This study emphasizes the importance of chimpanzees as large seed dispersers in regenerating forest fragments.

RESEARCH HIGHLIGHTS

Chimpanzees in Gishwati disperse a significant number of large seeds. Large-bodied seed dispersers, like chimpanzees, are particularly important in regenerating forest fragments.

Genetic censusing identifies an unexpectedly sizeable population of an endangered large mammal in a fragmented forest landscape

Background

As habitat degradation and fragmentation continue to impact wildlife populations around the world, it is critical to understand the behavioral flexibility of species in these environments. In Uganda, the mostly unprotected forest fragment landscape between the Budongo and Bugoma Forests is a potential corridor for chimpanzees, yet little is known about the status of chimpanzee populations in these fragments.

Results

From 2011 through 2013, we noninvasively collected 865 chimpanzee fecal samples across 633 km² and successfully genotyped 662 (77%) at up to 14 microsatellite loci. These genotypes corresponded to 182 chimpanzees, with a mean of 3.5 captures per individual. We obtained population size estimates of 256 (95% confidence interval 246–321) and 319 (288–357) chimpanzees using capture-with-replacement and spatially explicit capture–recapture models, respectively. The spatial clustering of associated genotypes suggests the presence of at least nine communities containing a minimum of 8–33 individuals each. Putative community distributions defined by the locations of associated genotypes correspond well with the distribution of 14 Y-chromosome haplotypes.

Conclusions

These census figures are more than three times greater than a previous estimate based on an extrapolation from small-scale nest count surveys that tend to underestimate population size. The distribution of genotype clusters and Y-chromosome haplotypes together indicate the presence of numerous male philopatric chimpanzee communities throughout the corridor habitat. Our findings demonstrate that, despite extensive habitat loss and fragmentation, chimpanzees remain widely distributed and exhibit distinct community home ranges. Our results further imply that elusive and rare species may adapt to degraded habitats more successfully than previously believed. Their long-term persistence is unlikely, however, if protection is not afforded to them and habitat loss continues unabated.

Electronic supplementary material

The online version of this article (doi:10.1186/s12898-015-0052-x) contains supplementary material, which is available to authorized users.

Estimation of chimpanzee community size and genetic diversity in Kahuzi-Biega National Park, Democratic Republic of Congo

A small chimpanzee habitat in the montane forest of Kahuzi-Biega National Park, Democratic Republic of Congo, is connected with the lowland forest of this park through a corridor, which is affected by human encroachment. To assess the conservation status of the chimpanzee population in this small habitat, we estimated the size of the community and evaluated its genetic diversity by using 279 fecal samples collected in the montane forest of Kahuzi. Using autosomal microsatellite (or short tandem repeat, STR) loci, we identified 32 individuals, comprising 19 females and 13 males. Samples from 24 individuals were collected at least twice and a genetic mark-recapture analysis estimated that the community size was 36 (range: 32-42). Data on nest site sharing confirmed that all the samples belonged to the same community. Nest site sharing information may be useful in population studies of unhabituated chimpanzees. The genetic structure and diversity of the 32 genotyped individuals was assessed using Y-chromosomal short tandem repeat (Y-STR) loci and mitochondrial D-loops. One dominant Y-STR haplotype was found, whereas there was no dominant haplotype in the mitochondrial region, reflecting a female-biased dispersal pattern, which is typical of chimpanzees. The genetic diversity for three markers in Kahuzi chimpanzees was comparable to that in other eastern chimpanzee populations. A relatively high heterozygosity and negative inbreeding coefficient (F_IS ) for STR loci suggests that the study community belongs to an outbreeding chimpanzee population. These findings suggest that individuals of the study community may have reproductive contact with other chimpanzee individuals from neighboring communities in Kahuzi-Biega National Park, at least in the recent past. Am. J. Primatol. 77:1015-1025, 2015. © 2015 Wiley Periodicals, Inc.

A population estimate of chimpanzees (Pan troglodytes schweinfurthii) in the Ugalla region using standard and spatially explicit genetic capture-recapture methods

Population parameters such as size, density, and distribution of a species across a landscape are important metrics that inform conservation science and are key to management strategies. In this study, we used genetic capture-recapture methods to estimate the population size and density of the little-studied chimpanzees in the Ugalla region of western Tanzania. From 237 fecal samples collected non-invasively over a 10-month period, we identified a minimum of 113 individuals. Based on the two-innate rate method (TIRM) modeled in the software capwire, we obtained a maximum-likelihood estimate of 322 (CI 227-373) individuals over the 624 km(2) area surveyed. Using a spatially explicit capture-recapture (SECR) method, we estimated a population density of 0.25 (CI 0.16-0.38) individuals/km(2) . Observations of nests and search effort data revealed areas of more intense usage. The findings of this study are an important step in the characterization of the Ugalla chimpanzees, and substantially improve our understanding of the number of chimpanzees that occupy this savanna-woodland region at the easternmost extent of the geographic range of this endangered subspecies.

Eastern chimpanzees, but not bonobos, represent a simian immunodeficiency virus reservoir

Chimpanzees in west central Africa (Pan troglodytes troglodytes) are endemically infected with simian immunodeficiency viruses (SIVcpzPtt) that have crossed the species barrier to humans and gorillas on at least five occasions, generating pandemic and nonpandemic forms of human immunodeficiency virus type 1 (HIV-1) as well as gorilla SIV (SIVgor). Chimpanzees in east Africa (Pan troglodytes schweinfurthii) are also infected with SIVcpz; however, their viruses (SIVcpzPts) have never been found in humans. To examine whether this is due to a paucity of natural infections, we used noninvasive methods to screen wild-living eastern chimpanzees in the Democratic Republic of the Congo (DRC), Uganda, and Rwanda. We also screened bonobos (Pan paniscus) in the DRC, a species not previously tested for SIV in the wild. Fecal samples (n = 3,108) were collected at 50 field sites, tested for species and subspecies origin, and screened for SIVcpz antibodies and nucleic acids. Of 2,565 samples from eastern chimpanzees, 323 were antibody positive and 92 contained viral RNA. The antibody-positive samples represented 76 individuals from 19 field sites, all sampled north of the Congo River in an area spanning 250,000 km(2). In this region, SIVcpzPts was common and widespread, with seven field sites exhibiting infection rates of 30% or greater. The overall prevalence of SIVcpzPts infection was 13.4% (95% confidence interval, 10.7% to 16.5%). In contrast, none of the 543 bonobo samples from six sites was antibody positive. All newly identified SIVcpzPts strains clustered in strict accordance to their subspecies origin; however, they exhibited considerable genetic diversity, especially in protein domains known to be under strong host selection pressure. Thus, the absence of SIVcpzPts zoonoses cannot be explained by an insufficient primate reservoir. Instead, greater adaptive hurdles may have prevented the successful colonization of humans by P. t. schweinfurthii viruses.