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The emergence of technology has been suggested to coincide with scarcity of staple resources that led to innovations in the form of tool-assisted strategies to diversify or augment typical diets. We examined seasonal patterns of several types of tool use exhibited by a chimpanzee (Pan troglodytes) population residing in central Africa, to determine whether their technical skills provided access to fallback resources when preferred food items were scarce. Chimpanzees in the Goualougo Triangle exhibit a diverse repertoire of tool behaviours, many of which are exhibited throughout the year. Further, they have developed specific tool sets to overcome the issues of accessibility to particular food items. Our conclusion is that these chimpanzees use a sophisticated tool technology to cope with seasonal changes in relative food abundance and gain access to high-quality foods. Subgroup sizes were smaller in tool using contexts than other foraging contexts, suggesting that the size of the social group may not be as important in promoting complex tool traditions as the frequency and type of social interactions. Further, reports from other populations and species showed that tool use may occur more often in response to ecological opportunities and relative profitability of foraging techniques than scarcity of resources.

The human parasite Plasmodium malariae has relatives infecting African apes ( Plasmodium rodhaini ) and New World monkeys ( Plasmodium brasilianum ), but its origins remain unknown. Using a novel approach to characterise P. malariae -related sequences in wild and captive African apes, we found that this group comprises three distinct lineages, one of which represents a previously unknown, highly divergent species infecting chimpanzees, bonobos and gorillas across central Africa. A second ape-derived lineage is much more closely related to the third, human-infective lineage P. malariae , but exhibits little evidence of genetic exchange with it, and so likely represents a separate species. Moreover, the levels and nature of genetic polymorphisms in P. malariae indicate that it resulted from the zoonotic transmission of an African ape parasite, reminiscent of the origin of P. falciparum . In contrast, P. brasilianum falls within the radiation of human P. malariae , and thus reflects a recent anthroponosis. Plasmodium malariae is a cause of malaria in humans and related species have been identified in non-human primates. Here, the authors use genomic analyses to establish that human P. malariae arose from a host switch of an ape parasite whilst a species infecting New World monkeys can be traced to a reverse zoonosis.

Plasmodium falciparum is the most prevalent and lethal of the malaria parasites infecting humans, yet the origin and evolutionary history of this important pathogen remain controversial. Here we develop a single-genome amplification strategy to identify and characterize Plasmodium spp. DNA sequences in faecal samples from wild-living apes. Among nearly 3,000 specimens collected from field sites throughout central Africa, we found Plasmodium infection in chimpanzees ( Pan troglodytes ) and western gorillas ( Gorilla gorilla ), but not in eastern gorillas ( Gorilla beringei ) or bonobos ( Pan paniscus ). Ape plasmodial infections were highly prevalent, widely distributed and almost always made up of mixed parasite species. Analysis of more than 1,100 mitochondrial, apicoplast and nuclear gene sequences from chimpanzees and gorillas revealed that 99% grouped within one of six host-specific lineages representing distinct Plasmodium species within the subgenus Laverania . One of these from western gorillas comprised parasites that were nearly identical to P. falciparum . In phylogenetic analyses of full-length mitochondrial sequences, human P. falciparum formed a monophyletic lineage within the gorilla parasite radiation. These findings indicate that P. falciparum is of gorilla origin and not of chimpanzee, bonobo or ancient human origin. Human malaria parasite traced to a fellow primate The evolutionary origin of Plasmodium falciparum , the most prevalent and lethal of the malaria parasites infecting humans, is much debated. Genetic analysis of thousands of fecal samples from wild-living African apes show that the parasites found in the western gorillas — rather than those of chimpanzees or bonobos — are most closely related to the human parasite. The data suggest that all extant human strains of the parasite evolved from a single host transfer event. The new findings are also relevant to the current antimalaria campaign, as they point to potential Plasmodium reservoirs in apes. The evolutionary origin of the human malaria parasite Plasmodium falciparum has been much debated. Genetic analysis of a large number of faecal samples from wild-living African apes now shows that Plasmodium parasites from Western gorillas are most closely related to the human parasite. The data suggest that human P. falciparum evolved from a gorilla parasite after a single host transfer event.

Earth’s environments harbor complex consortia of microbes that affect processes ranging from host health to biogeochemical cycles. Understanding their evolution and function is limited by an inability to isolate genomes in a high-throughput manner. Here, we present a workflow for bacterial whole-genome sequencing using open-source labware and the OpenTrons robotics platform, reducing costs to approximately $10 per genome. We assess genomic diversity within 45 gut bacterial species from wild-living chimpanzees and bonobos. We quantify intraspecific genomic diversity and reveal divergence of homologous plasmids between hosts. This enables population genetic analyses of bacterial strains not currently possible with metagenomic data alone.

The malaria parasite Plasmodium falciparum causes substantial human mortality, primarily in equatorial Africa. Enriched in affected African populations, the B*53 variant of HLA-B, a cell surface protein that presents peptide antigens to cytotoxic lymphocytes, confers protection against severe malaria. Gorilla, chimpanzee, and bonobo are humans’ closest living relatives. These African apes have HLA-B orthologs and are infected by parasites in the same subgenus ( Laverania ) as P. falciparum , but the consequences of these infections are unclear. Laverania parasites infect bonobos ( Pan paniscus ) at only one (TL2) of many sites sampled across their range. TL2 spans the Lomami River and has genetically divergent subpopulations of bonobos on each side. Papa-B, the bonobo ortholog of HLA-B, includes variants having a B*53-like (B07) peptide-binding supertype profile. Here we show that B07 Papa-B occur at high frequency in TL2 bonobos and that malaria appears to have independently selected for different B07 alleles in the two subpopulations. A variant of MHC class I is protective against severe malaria disease and enriched in affected African populations. Here, Wroblewski et al., characterise the consequences of malaria infection in wild bonobo populations showing that the presence of malaria drives a similar evolution in immune genes.

We present the first cross-continental comparison of the flowering and fruiting phenology of tropical forests across Africa. Flowering events of 5446 trees from 196 species across 12 sites and fruiting events of 4595 trees from 191 species across 11 sites were monitored over periods of 6 to 29 years and analyzed to describe phenology at the continental level. To study phenology, we used Fourier analysis to identify the dominant cycles of flowering and fruiting for each individual tree and we identified the time of year African trees bloom and bear fruit and their relationship to local seasonality. Reproductive strategies were diverse, and no single regular cycle was found in >50% of individuals across all 12 sites. Additionally, we found annual flowering and fruiting cycles to be the most common. Sub-annual cycles were the next most common for flowering, whereas supra-annual patterns were the next most common for fruiting. We also identify variation in different subsets of species, with species exhibiting mainly annual cycles most common in West and West Central African tropical forests, while more species at sites in East Central and East African forests showed cycles ranging from sub-annual to supra-annual. Despite many trees showing strong seasonality, at most sites some flowering and fruiting occurred all year round. Environmental factors with annual cycles are likely to be important drivers of seasonal periodicity in trees across Africa, but proximate triggers are unlikely to be constant across the continent.

Several populations of wild chimpanzees use tools to raid bee nests, but preliminary observations of chimpanzees in the Congo Basin indicate that they may have developed sophisticated technical solutions to gather honey that differ from those of apes in other regions. Despite the lack of habituated groups within the range of the central subspecies, there have been several reports of different types of tools used by chimpanzees to open beehives and gather honey. Researchers have observed some of these behaviors (honey dipping) in populations of western and eastern chimpanzees, whereas others (hive pounding) may be limited to this region. Toward evaluating hypotheses of regional tool using patterns, we provide the first repeated direct observations and systematic documentation of tool use in honey-gathering by a population of Pan troglodytes troglodytes. Between 2002 and 2006, we observed 40 episodes of tool use in honey-gathering by chimpanzees in the Goualougo Triangle, Republic of Congo. Pounding was the most common and successful strategy to open beehives. Chimpanzees at this site used several tools in a single tool-using episode and could also attribute multiple functions to a single tool. They exhibited flexibility in responses toward progress in opening a hive and hierarchical structuring of tool sequences. Our results support suggestions of regional tool using traditions in honey-gathering, which could be shaped by variation in bee ecology across the chimpanzee range. Further, we suggest that these chimpanzees may have an enhanced propensity to use tool sets that could be related to other aspects of their tool repertoire. Clearly, there is still much to be learned about the behavioral diversity of chimpanzees residing within the Congo Basin.

Societal Impact Statement Globally, the conservation value of big trees is linked to biodiversity and carbon sequestration. We studied trees, greater than 80 cm in diameter, in a forest in the Republic of Congo. We found that more than 100 species reach this size and the most abundant species is Sapele (Entandrophragma cylindricum), which is exploited for global timber markets. More than 40% of the large tree species are used by local people for food. Our results show that big trees are important to local people in the Congo Basin in addition to being the focus of industrial logging and in many areas the basis for the formal economy. Summary The main aim of this paper is to establish standard techniques for surveying the biggest trees in tropical rain forests. One hundred and thirty hectares (13 plots of 10 ha) of unlogged mixed species terra firma forest in the Republic of Congo were surveyed for trees greater than 80 cm in diameter. More than 100 species of tree exceed 80 cm in diameter and one species, Entandrophragma cylindricum (Sapele or Sapelli), dominates this size class. Obtaining comparable data of big trees from different sites across the tropics is a priority. We propose a standardised plot size of 10 ha, replicated 10 times for each forest type at different study sites and a minimum trunk diameter of 70 cm at breast height or above buttresses. Globally, the conservation value of big trees is linked to biodiversity and carbon sequestration. We studied trees, greater than 80 cm in diameter, in a forest in the Republic of Congo. We found that more than 100 species reach this size and the most abundant species is Sapele (Entandrophragma cylindricum), which is exploited for global timber markets. More than 40% of the large tree species are used by local people for food. Our results show that big trees are important to local people in the Congo Basin in addition to being the focus of industrial logging and in many areas the basis for the formal economy.

In 2006-2007 we observed an unusual mortality event among apes in northern Republic of Congo that, although not diagnostically confirmed, we believe to have been a disease outbreak. In 2007-2011 we conducted ape nest surveys in the region, recording 11,835 G. g. gorilla nests (2,262 groups) and 5,548 P. t. troglodytes nests (2,139 groups). We developed a statistical model to determine likely points of origin of the outbreak to help identify variables associated with disease emergence and spread. We modeled disease spread across the study area, using suitable habitat conditions for apes as proxy for local ape densities. Infectious status outputs from that spread model were then used alongside vegetation, temperature, precipitation and human impact factors as explanatory variables in a Generalized Linear Model framework to explain observed 2007-2011 ape nest trends in the region. The best models predicted emergence in the western region of Odzala-Kokoua National Park and north of the last confirmed Ebola virus disease epizootics. Roads were consistently associated with attenuation of modeled virus spread. As disease is amongst the leading threats to great apes, gaining a better understanding of disease transmission dynamics in these species is imperative. Identifying ecological drivers underpinning a disease emergence event and transmission dynamics in apes is critical to creating better predictive models to guide wildlife management, develop potential protective measures for wildlife and to reduce potential zoonotic transmission to humans. The results of our model represent an important step in understanding variables related to great ape disease ecology in Central Africa.

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.