CD4 receptor diversity in chimpanzees protects against SIV infection.

Human and simian immunodeficiency viruses (HIV/SIVs) use CD4 as the primary receptor to enter target cells. Here, we show that the chimpanzee CD4 is highly polymorphic, with nine coding variants present in wild populations, and that this diversity interferes with SIV envelope (Env)-CD4 interactions. Testing the replication fitness of SIVcpz strains in CD4+ T cells from captive chimpanzees, we found that certain viruses were unable to infect cells from certain hosts. These differences were recapitulated in CD4 transfection assays, which revealed a strong association between CD4 genotypes and SIVcpz infection phenotypes. The most striking differences were observed for three substitutions (Q25R, Q40R, and P68T), with P68T generating a second N-linked glycosylation site (N66) in addition to an invariant N32 encoded by all chimpanzee CD4 alleles. In silico modeling and site-directed mutagenesis identified charged residues at the CD4-Env interface and clashes between CD4- and Env-encoded glycans as mechanisms of inhibition. CD4 polymorphisms also reduced Env-mediated cell entry of monkey SIVs, which was dependent on at least one D1 domain glycan. CD4 allele frequencies varied among wild chimpanzees, with high diversity in all but the western subspecies, which appeared to have undergone a selective sweep. One allele was associated with lower SIVcpz prevalence rates in the wild. These results indicate that substitutions in the D1 domain of the chimpanzee CD4 can prevent SIV cell entry. Although some SIVcpz strains have adapted to utilize these variants, CD4 diversity is maintained, protecting chimpanzees against infection with SIVcpz and other SIVs to which they are exposed.

Human engagement and great ape conservation in Africa.

Despite large investments of funding into great ape conservation in Africa, wild populations of gorillas (Gorilla ssp), chimpanzees (Pan troglodytes ssp) and bonobos (Pan paniscus) continue to decline. Causes for this decline fall into three broad categories: habitat loss, illegal hunting, and disease. Contributing factors to all of these causes are linked to pressure from the expanding human population competing for forest resources. We have moved beyond the time of debating the pros and cons of including human engagement activities in conservation. If humans are part of the problem, they must also be part of the solution. To move our understanding of which human engagement activities are effective, what methodologies are being used and best practices for setting up a successful framework, we interviewed practitioners representing 53 projects working in great ape habitat in Africa. The interviewees represented almost 900 years of experience with African great ape conservation. We found that all practitioners agreed that for conservation to succeed, projects must engage with humans utilizing resources from great ape habitats. However, evaluation of such work was elusive. Projects that employed at least one person designated as an educator were more likely to have structured programs, regular engagement activities, and to evaluate their work. To date, little information on the success or failure of the activities has been published, thus perpetuating the problem of relying on personal experience rather than evidence when developing new engagement programs. Additionally, linking human engagement activities to biological impact remains a challenge. The results presented in this paper demonstrate the importance placed on human engagement activities to effectively conserve great apes in Africa while at the same time identifies gaps in our understanding on the link between such activities and project success.

Commentary: Challenges of evaluating the effectiveness of public awareness campaigns in Congo Republic.

Conservation groups are always challenged with assigning limited resources to interventions they assume will have the most effective impact in addressing threats to their conservation targets. These decisions are often made based on experience and perceived outcomes, rather than evidence. In the past decade, multiple public awareness and proactive law enforcement activities have been initiated in the Congo Republic to address the illegal wildlife trade. This paper presents the challenges faced and lessons learned in shifting from experience to evidence-based program evaluation related to the effectiveness of billboards in informing and inspiring local populations to support positive conservation behavior with regard to great apes.

Successful acclimatization of mandrills (Mandrillus sphinx) translocated to Conkouati-Douli National Park, Republic of Congo, as measured by fecal glucocorticoid metabolites.

Translocation and reintroduction are common tools in conservation management and can be very successful. However, translocation can be stressful for the animals involved, and stress is implicated as a major cause of failure in release programs. Conservation managers should therefore seek to understand how the stages of translocation impact stress physiology in the animals involved. We quantified fecal glucocorticoid metabolites (fGCMs) as a noninvasive measure of response to potential stressors during a translocation of 15 mandrills (Mandrillus sphinx) into Conkouati-Douli National Park, Republic of Congo. The mandrills were initially housed in a sanctuary, transferred to a pre-release enclosure in the National Park and then released into the forest. We collected repeated fecal samples (n = 1101) from known individuals and quantified fGCMs using a previously validated enzyme immunoassay. Transfer from the sanctuary to the pre-release enclosure correlated with a significant 1.93-fold increase in fGCMs, suggesting that transfer was a stressor for the mandrills. fGCM values decreased over time in the pre-release enclosure, suggesting that the mandrills recovered from the transfer and acclimatized to the enclosure. Release to the forest was not linked to a significant increase in fGCMs over the final values in the enclosure. Following release, fGCMs continued to decrease, fell below sanctuary values after just over a month and were about half the sanctuary values after 1 year. Overall, our results suggest that the translocation, although initially presenting a physiological challenge to the animals, was not detrimental to the well-being of the animals over the timescale of the study and, in fact, may have been beneficial. Our findings show the value of non-invasive physiology in monitoring, evaluating and designing wildlife translocations and, ultimately, contributing to their success.

A Second Genome Sequence of an Enterovirus C99 Detected in a Healthy Chimpanzee.

We report the nearly complete genome sequence of an enterovirus 99 strain (Cpz-IJC08) detected in a healthy chimpanzee from the Tchimpounga Sanctuary in the Republic of Congo. According to the phylogeny, Cpz-IJC08 clustered with Cpz-IJC04, a previously identified chimpanzee enterovirus from the same sanctuary, isolated from an animal with signs of acute flaccid paralysis.

Bonobos have a more human-like second-to-fourth finger length ratio (2D:4D) than chimpanzees: a hypothesized indication of lower prenatal androgens.

The ratio of the second-to-fourth finger lengths (2D:4D) has been proposed as an indicator of prenatal sex differentiation. However, 2D:4D has not been studied in the closest living human relatives, chimpanzees (Pan troglodytes) and bonobos (Pan paniscus). We report the results from 79 chimpanzees and 39 bonobos of both sexes, including infants, juveniles, and adults. We observed the expected sex difference in 2D:4D, and substantially higher, more human-like, 2D:4D in bonobos than chimpanzees. Previous research indicates that sex differences in 2D:4D result from differences in prenatal sex hormone levels. We hypothesize that the species difference in 2D:4D between bonobos and chimpanzees suggests a possible role for early exposure to sex hormones in the development of behavioral differences between the two species.

Biochemical and biological validations of a faecal glucocorticoid metabolite assay in mandrills (Mandrillus sphinx).

Stress is a major factor in determining success when releasing endangered species into the wild but is often overlooked. Mandrills (Mandrills sphinx) are vulnerable to extinction due to habitat loss and demand for bush meat and the pet trade. To help bolster in situ populations, rehabilitated rescued mandrills recently were released into a protected area in the Republic of Congo. The goal of this study was to validate the use of faecal glucocorticoid metabolite enzyme immunoassays (EIAs) in mandrills and test field-friendly faecal hormone extraction techniques that can subsequently be used to monitor the stress physiology and welfare of mandrills throughout the release process. Using faecal samples collected from ex situ mandrills, we tested cortisol, corticosterone, 11ß-hydroxyetiocholanolone (69a), and 11-oxoetiocholanolone EIAs. Absolute concentrations, hormone profiles following medical procedures or translocation, and high-performance liquid chromatography fraction immunoreactivity showed that the 69a assay was the best choice to monitor the stress response in this species. Samples with delayed extraction or drying times had 40-80% lower 69a concentrations than samples extracted immediately post-collection and frozen. The 69a EIA is an appropriate assay for monitoring welfare in this species in situ or ex situ, and results indicated that consistent extraction methods are important for accurate comparisons.

Allometry and Ecology of the Bilaterian Gut Microbiome.

Classical ecology provides principles for construction and function of biological communities, but to what extent these apply to the animal-associated microbiota is just beginning to be assessed. Here, we investigated the influence of several well-known ecological principles on animal-associated microbiota by characterizing gut microbial specimens from bilaterally symmetrical animals (Bilateria) ranging from flies to whales. A rigorously vetted sample set containing 265 specimens from 64 species was assembled. Bacterial lineages were characterized by 16S rRNA gene sequencing. Previously published samples were also compared, allowing analysis of over 1,098 samples in total. A restricted number of bacterial phyla was found to account for the great majority of gut colonists. Gut microbial composition was associated with host phylogeny and diet. We identified numerous gut bacterial 16S rRNA gene sequences that diverged deeply from previously studied taxa, identifying opportunities to discover new bacterial types. The number of bacterial lineages per gut sample was positively associated with animal mass, paralleling known species-area relationships from island biogeography and implicating body size as a determinant of community stability and niche complexity. Samples from larger animals harbored greater numbers of anaerobic communities, specifying a mechanism for generating more-complex microbial environments. Predictions for species/abundance relationships from models of neutral colonization did not match the data set, pointing to alternative mechanisms such as selection of specific colonists by environmental niche. Taken together, the data suggest that niche complexity increases with gut size and that niche selection forces dominate gut community construction.IMPORTANCE The intestinal microbiome of animals is essential for health, contributing to digestion of foods, proper immune development, inhibition of pathogen colonization, and catabolism of xenobiotic compounds. How these communities assemble and persist is just beginning to be investigated. Here we interrogated a set of gut samples from a wide range of animals to investigate the roles of selection and random processes in microbial community construction. We show that the numbers of bacterial species increased with the weight of host organisms, paralleling findings from studies of island biogeography. Communities in larger organisms tended to be more anaerobic, suggesting one mechanism for niche diversification. Nonselective processes enable specific predictions for community structure, but our samples did not match the predictions of the neutral model. Thus, these findings highlight the importance of niche selection in community construction and suggest mechanisms of niche diversification.

Counting primates for conservation: primate surveys in Uganda.

Primate census techniques have been developed over the past 35-40 years yet there is still some confusion and great variation in the methods used. This precludes comparisons between sites where different techniques have been used. This paper discusses the variations between the methods that seem to be practiced currently and then describes a census of primates in the forests of western Uganda. Primate density and biomass varied greatly between forests as well as within forests and this is probably related to food availability. Chimpanzee (Pan troglodytes) density was strongly correlated with nest encounter rates from reconnaissance walks in the forest. This result can be used to estimate chimpanzee density in forests where it is difficult to survey this species (e.g., due to security reasons). A total of 4,980 chimpanzee was estimated for Uganda which is higher than previously guessed, but still of conservation concern. Only four forests had more than 500 individuals which gives concern for long-term population viability.

Multigenomic Delineation of Plasmodium Species of the Laverania Subgenus Infecting Wild-Living Chimpanzees and Gorillas.

Plasmodium falciparum, the major cause of malaria morbidity and mortality worldwide, is only distantly related to other human malaria parasites and has thus been placed in a separate subgenus, termed Laverania Parasites morphologically similar to P. falciparum have been identified in African apes, but only one other Laverania species, Plasmodium reichenowi from chimpanzees, has been formally described. Although recent studies have pointed to the existence of additional Laverania species, their precise number and host associations remain uncertain, primarily because of limited sampling and a paucity of parasite sequences other than from mitochondrial DNA. To address this, we used limiting dilution polymerase chain reaction to amplify additional parasite sequences from a large number of chimpanzee and gorilla blood and fecal samples collected at two sanctuaries and 30 field sites across equatorial Africa. Phylogenetic analyses of more than 2,000 new sequences derived from the mitochondrial, nuclear, and apicoplast genomes revealed six divergent and well-supported clades within the Laverania parasite group. Although two of these clades exhibited deep subdivisions in phylogenies estimated from organelle gene sequences, these sublineages were geographically defined and not present in trees from four unlinked nuclear loci. This greatly expanded sequence data set thus confirms six, and not seven or more, ape Laverania species, of which P. reichenowi, Plasmodium gaboni, and Plasmodium billcollinsi only infect chimpanzees, whereas Plasmodium praefalciparum, Plasmodium adleri, and Pladmodium blacklocki only infect gorillas. The new sequence data also confirm the P. praefalciparum origin of human P. falciparum.

Burial, excavation, and preparation of primate skeletal material for morphological study.

Inclusion of osteological material in primatological research has a long history, and use of skeletal remains continues to be important in anatomical and anthropological research. Here we report a set of proven methods, including equipment, protocol, and procedure, which enable relatively simple acquisition of skeletal material from naturally deceased animals in field sites and sanctuaries. Such skeletal material, often with extensive accompanying life-history data, is a unique and valuable source of data for both academic and conservation-based research.

First Detection of an Enterovirus C99 in a Captive Chimpanzee with Acute Flaccid Paralysis, from the Tchimpounga Chimpanzee Rehabilitation Center, Republic of Congo.

Enteroviruses, members of the Picornaviridae family, are ubiquitous viruses responsible for mild to severe infections in human populations around the world. In 2010 Pointe-Noire, Republic of Congo recorded an outbreak of acute flaccid paralysis (AFP) in the humans, caused by wild poliovirus type 1 (WPV1). One month later, in the Tchimpounga sanctuary near Pointe-Noire, a chimpanzee developed signs similar to AFP, with paralysis of the lower limbs. In the present work, we sought to identify the pathogen, including viral and bacterial agents, responsible for this illness. In order to identify the causative agent, we evaluated a fecal specimen by PCR and sequencing. A Human enterovirus C, specifically of the EV-C99 type was potentially responsible for the illness in this chimpanzee. To rule out other possible causative agents, we also investigated the bacteriome and the virome using next generation sequencing. The majority of bacterial reads obtained belonged to commensal bacteria (95%), and the mammalian virus reads matched mainly with viruses of the Picornaviridae family (99%), in which enteroviruses were the most abundant (99.6%). This study thus reports the first identification of a chimpanzee presenting AFP most likely caused by an enterovirus and demonstrates once again the cross-species transmission of a human pathogen to an ape.