Persistent anthrax as a major driver of wildlife mortality in a tropical rainforest.

Anthrax is a globally important animal disease and zoonosis. Despite this, our current knowledge of anthrax ecology is largely limited to arid ecosystems, where outbreaks are most commonly reported. Here we show that the dynamics of an anthrax-causing agent, Bacillus cereus biovar anthracis, in a tropical rainforest have severe consequences for local wildlife communities. Using data and samples collected over three decades, we show that rainforest anthrax is a persistent and widespread cause of death for a broad range of mammalian hosts. We predict that this pathogen will accelerate the decline and possibly result in the extirpation of local chimpanzee (Pan troglodytes verus) populations. We present the epidemiology of a cryptic pathogen and show that its presence has important implications for conservation.

Discovery of Novel Herpes Simplexviruses in Wild Gorillas, Bonobos, and Chimpanzees Supports Zoonotic Origin of HSV-2.

Viruses closely related to human pathogens can reveal the origins of human infectious diseases. Human herpes simplexvirus type 1 (HSV-1) and type 2 (HSV-2) are hypothesized to have arisen via host-virus codivergence and cross-species transmission. We report the discovery of novel herpes simplexviruses during a large-scale screening of fecal samples from wild gorillas, bonobos, and chimpanzees. Phylogenetic analysis indicates that, contrary to expectation, simplexviruses from these African apes are all more closely related to HSV-2 than to HSV-1. Molecular clock-based hypothesis testing suggests the divergence between HSV-1 and the African great ape simplexviruses likely represents a codivergence event between humans and gorillas. The simplexviruses infecting African great apes subsequently experienced multiple cross-species transmission events over the past 3 My, the most recent of which occurred between humans and bonobos around 1 Ma. These findings revise our understanding of the origins of human herpes simplexviruses and suggest that HSV-2 is one of the earliest zoonotic pathogens.

The bean method as a tool to measure sensitive behavior.

Conservationists need to measure human behavior to guide decisions and evaluate their impact. However, activities can be misreported and reporting accuracy may change following conservation interventions, making it hard to verify any apparent changes. Techniques for asking sensitive questions are increasingly integrated into survey designs to improve data quality, but some can be costly or hard for nonexperts to implement. We demonstrate a straightforward, low-cost approach, the bean method in which respondents give anonymous answers by adding a colored bean to a jar to denote a yes or no response. We applied the bean method to measure wild-meat hunting and trading over 2 years at a conservation-project (hunting reduction) site in Gola Forest, Liberia. We extended the technique to accommodate questions about hunting and meat-selling frequency. We compared responses given using the bean method and direct questioning for groups that did and did not participate in conservation interventions. Results from the bean method corresponded to those from direct questioning, and there was no indication of change in question sensitivity following conservation interventions. Estimates from both methods indicated that wild-meat trading decreased in project and nonproject households (from 36% to 20%) and that hunting decreased in 1 project group (38-28%). Where inconsistent answers were given (2-6% of respondents), differences were in both directions and were most likely attributable to measurement error. The bean method was quick and straightforward to administer in a low-literacy setting. We showed how it can be modified for answers of more than 2 categories and consider it a valuable tool that could be adapted for a wide range of conservation settings.

El Método del Frijol como Herramienta para Medir los Comportamientos Sensibles Resumen Los conservacionistas necesitan medir el comportamiento humano para dirigir las decisiones tomadas y evaluar su impacto. Sin embargo, las actividades pueden estar mal reportadas y la fiabilidad de los reportes puede cambiar después de implementadas las intervenciones de conservación, lo cual complica la verificación de cualquier cambio aparente. Las técnicas para realizar preguntas sensibles cada vez se integran más al diseño de los censos y así mejorar la calidad de los datos, aunque algunas pueden ser caras o complicadas de implementar para quienes no son expertos. Demostramos una estrategia directa y de bajo costo, el método del frijol, en el cual los respondientes proporcionan respuestas anónimas al añadir un frijol pintado dentro de un frasco y así indicar una respuesta de sí o no. Aplicamos el método del frijol para medir la cacería y el mercado de carne silvestre durante dos años dentro de un proyecto de conservación (reducción de la cacería) en el bosque Gola, Liberia. Extendimos la técnica para acomodar preguntas sobre la frecuencia de la caza y la venta de carne. Comparamos las respuestas dadas usando el método del frijol y aquellas dadas en el cuestionamiento directo a grupos que participaban o no en las intervenciones de conservación. Los resultados obtenidos con el método del frijol correspondieron a aquellos obtenidos con los cuestionamientos directos y no hubo indicación de cambios en la sensibilidad de las preguntas después de las intervenciones de conservación. Las estimaciones de ambos métodos indicaron que el mercado de carne silvestre disminuyó en los hogares participantes o no en el proyecto (de 36% a 20%) y que la cacería disminuyó en un grupo del proyecto (38% a 28%). En donde se dieron respuestas contradictorias (2-6% de los respondientes), las diferencias fueron en ambas direcciones y en su mayoría probablemente eran atribuibles al error en la medición. El método del frijol fue rápido y directo para administrarlo en un ambiente de bajo alfabetismo. Mostramos cómo puede modificarse para respuestas con más de dos categorías y lo consideramos una herramienta valiosa que podría adaptarse para una gama amplia de escenarios de conservación.

Open-access platform to synthesize knowledge of ape conservation across sites.

Despite the large body of literature on ape conservation, much of the data needed for evidence-based conservation decision-making is still not readily accessible and standardized, rendering cross-site comparison difficult. To support knowledge synthesis and to complement the IUCN SSC Ape Populations, Environments and Surveys database, we created the A.P.E.S. Wiki (https://apeswiki.eva.mpg.de), an open-access platform providing site-level information on ape conservation status and context. The aim of this Wiki is to provide information and data about geographical ape locations, to curate information on individuals and organizations active in ape research and conservation, and to act as a tool to support collaboration between conservation practitioners, scientists, and other stakeholders. To illustrate the process and benefits of knowledge synthesis, we used the momentum of the update of the conservation action plan for western chimpanzees (Pan troglodytes verus) and began with this critically endangered taxon. First, we gathered information on 59 sites in West Africa from scientific publications, reports, and online sources. Information was compiled in a standardized format and can thus be summarized using a web scraping approach. We then asked experts working at those sites to review and complement the information (20 sites have been reviewed to date). We demonstrate the utility of the information available through the Wiki, for example, for studying species distribution. Importantly, as an open-access platform and based on the well-known wiki layout, the A.P.E.S. Wiki can contribute to direct and interactive information sharing and promote the efforts invested by the ape research and conservation community. The Section on Great Apes and the Section on Small Apes of the IUCN SSC Primate Specialist Group will guide and support the expansion of the platform to all small and great ape taxa. Similar collaborative efforts can contribute to extending knowledge synthesis to all nonhuman primate species.

Quantitative estimates of glacial refugia for chimpanzees (Pan troglodytes) since the Last Interglacial (120,000 BP).

Paleoclimate reconstructions have enhanced our understanding of how past climates have shaped present-day biodiversity. We hypothesize that the geographic extent of Pleistocene forest refugia and suitable habitat fluctuated significantly in time during the late Quaternary for chimpanzees (Pan troglodytes). Using bioclimatic variables representing monthly temperature and precipitation estimates, past human population density data, and an extensive database of georeferenced presence points, we built a model of changing habitat suitability for chimpanzees at fine spatio-temporal scales dating back to the Last Interglacial (120,000 BP). Our models cover a spatial resolution of 0.0467° (approximately 5.19 km2 grid cells) and a temporal resolution of between 1000 and 4000 years. Using our model, we mapped habitat stability over time using three approaches, comparing our modeled stability estimates to existing knowledge of Afrotropical refugia, as well as contemporary patterns of major keystone tropical food resources used by chimpanzees, figs (Moraceae), and palms (Arecacae). Results show habitat stability congruent with known glacial refugia across Africa, suggesting their extents may have been underestimated for chimpanzees, with potentially up to approximately 60,000 km2 of previously unrecognized glacial refugia. The refugia we highlight coincide with higher species richness for figs and palms. Our results provide spatio-temporally explicit insights into the role of refugia across the chimpanzee range, forming the empirical foundation for developing and testing hypotheses about behavioral, ecological, and genetic diversity with additional data. This methodology can be applied to other species and geographic areas when sufficient data are available.

Audience segmentation to improve targeting of conservation interventions for hunters.

Audience segmentation could help improve the effectiveness of conservation interventions. Marketers use audience segmentation to define the target audience of a campaign. The technique involves subdividing a general population into groups that share similar profiles, such as sociodemographic or behavioral characteristics. Interventions are then designed to target the group or groups of interest. We explored the potential of audience segmentation for use in defining conservation target groups with a case study of hunters in Liberia. Using 2 data sets describing households (n = 476) and hunters (n = 205), we applied a clustering method in which infinite binomial mixture models group hunters and households according to livelihood and behavior variables and a simple method to define target groups based on hunting impact (hunting households and high-impact hunters). Clusters of hunters and households differed in their experiences with confiscation of catch at roadblocks and participation in livelihood-support programs, indicating that these interventions operate unevenly across subsets of the population. By contrast, the simple method masked these insights because profiles of hunting households and high-impact hunters were similar to those of the general population. Clustering results could be used to guide the development of livelihood and regulatory interventions. For example, a commonly promoted agricultural activity, cocoa farming, was practiced by only 2% (out of 87) of the largest hunter cluster of nonlocal gun hunters but was prevalent among local trappers, suggesting that assistance aimed at cocoa farmers is less appropriate for the former group. Our results support the use of audience segmentation across multiple variables to improve targeted intervention designs in conservation.

Segmentación del Público para Mejorar la Focalización de las Intervenciones de Conservación para los Cazadores Resumen La segmentación del público podría ayudar a mejorar la efectividad de las intervenciones de conservación. Los publicistas utilizan la segmentación del público para definir al público focal de una campaña. La técnica incluye la subdivisión de una población general en grupos que comparten perfiles similares, como las características socio-demográficas o de comportamiento. Después se diseñan las intervenciones para enfocarse en el grupo o los grupos de interés. Exploramos el potencial de la segmentación del público en el uso de la definición de grupos con objetivos de conservación usando el estudio de caso de los cazadores en Liberia. Con dos conjuntos de datos de descripciones de los hogares (n = 476) y de los cazadores (n = 205) aplicamos un método de agrupación en el cual los modelos de mezcla binomial infinita agruparon a los cazadores y a los hogares de acuerdo a las variables de sustento y de comportamiento. También aplicamos un método simple para definir los grupos focales con base en el impacto de la caza (hogares de cazadores y cazadores de alto impacto). Los grupos de cazadores y de hogares difirieron en experiencias con la confiscación de la caza en retenes y en participación dentro de programas de apoyo al sustento, lo que indica que estas intervenciones operan disparejamente en los subconjuntos de la población. En contraste, el método simple enmascaró estas percepciones ya que los perfiles de los hogares de cazadores y de los cazadores de alto impacto fueron similares a los de la población general. La agrupación de los resultados podría usarse para guiar el desarrollo del sustento y de las intervenciones regulatorias. Por ejemplo, el cultivo de cacao, una actividad agrícola que se promueve frecuentemente, sólo lo practicaba el 2% (de 87) del mayor grupo de cazadores de los cazadores armados no locales, pero fue prevaleciente entre los trampeadores locales, lo que sugiere que la asistencia enfocada hacia los cultivadores de cacao es menos apropiada para el primer grupo. Nuestros resultados respaldan el uso de la segmentación del público en múltiples variables para mejorar los diseños de intervenciones focalizadas en la conservación.

Nocturnal activity in wild chimpanzees (Pan troglodytes): Evidence for flexible sleeping patterns and insights into human evolution.

OBJECTIVES: We investigated occurrences and patterns of terrestrial nocturnal activity in wild chimpanzees (Pan troglodytes) and modelled the influence of various ecological predictors on nocturnal activity. METHODS: Data were extracted from terrestrial camera-trap footage and ecological surveys from 22 chimpanzee study sites participating in the Pan African Programme: The Cultured Chimpanzee. We described videos demonstrating nocturnal activity, and we tested the effects of the percentage of forest, abundance of predators (lions, leopards and hyenas), abundance of large mammals (buffalos and elephants), average daily temperature, rainfall, human activity, and percent illumination on the probability of nocturnal activity. RESULTS: We found terrestrial nocturnal activity to occur at 18 of the 22 study sites, at an overall average proportion of 1.80% of total chimpanzee activity, and to occur during all hours of the night, but more frequently during twilight hours. We found a higher probability of nocturnal activity with lower levels of human activity, higher average daily temperature, and at sites with a larger percentage of forest. We found no effect of the abundance of predators and large mammals, rainfall, or moon illumination. DISCUSSION: Chimpanzee terrestrial nocturnal activity appears widespread yet infrequent, which suggests a consolidated sleeping pattern. Nocturnal activity may be driven by the stress of high daily temperatures and may be enabled at low levels of human activity. Human activity may exert a relatively greater influence on chimpanzee nocturnal behavior than predator presence. We suggest that chimpanzee nocturnal activity is flexible, enabling them to respond to changing environmental factors.

Comparative primate obstetrics: Observations of 15 diurnal births in wild gelada monkeys (Theropithecus gelada) and their implications for understanding human and nonhuman primate birth evolution.

OBJECTIVES: The birth process has been studied extensively in many human societies, yet little is known about this essential life history event in other primates. Here, we provide the most detailed account of behaviors surrounding birth for any wild nonhuman primate to date. MATERIALS AND METHODS: Over a recent ∼10-year period, we directly observed 15 diurnal births (13 live births and 2 stillbirths) among geladas (Theropithecus gelada) at Guassa, Ethiopia. During each birth, we recorded the occurrence (or absence) of 16 periparturitional events, chosen for their potential to provide comparative evolutionary insights into the factors that shaped birth behaviors in humans and other primates. RESULTS: We found that several events (e.g., adopting standing crouched positions, delivering infants headfirst) occurred during all births, while other events (e.g., aiding the infant from the birth canal, licking infants following delivery, placentophagy) occurred during, or immediately after, most births. Moreover, multiparas (n = 9) were more likely than primiparas (n = 6) to (a) give birth later in the day, (b) isolate themselves from nearby conspecifics while giving birth, (c) aid the infant from the birth canal, and (d) consume the placenta. DISCUSSION: Our results suggest that prior maternal experience may contribute to greater competence or efficiency during the birth process. Moreover, face presentations (in which infants are born with their neck extended and their face appearing first, facing the mother) appear to be the norm for geladas. Lastly, malpresentations (in which infants are born in the occiput anterior position more typical of human infants) may be associated with increased mortality in this species. We compare the birth process in geladas to those in other primates (including humans) and discuss several key implications of our study for advancing understanding of obstetrics and the mechanism of labor in humans and nonhuman primates.

The Critically Endangered western chimpanzee declines by 80.

African large mammals are under extreme pressure from unsustainable hunting and habitat loss. Certain traits make large mammals particularly vulnerable. These include late age at first reproduction, long inter-birth intervals, and low population density. Great apes are a prime example of such vulnerability, exhibiting all of these traits. Here we assess the rate of population change for the western chimpanzee, Pan troglodytes verus, over a 24-year period. As a proxy for change in abundance, we used transect nest count data from 20 different sites archived in the IUCN SSC A.P.E.S. database, representing 25,000 of the estimated remaining 35,000 western chimpanzees. For each of the 20 sites, datasets for 2 different years were available. We estimated site-specific and global population change using Generalized Linear Models. At 12 of these sites, we detected a significant negative trend. The estimated change in the subspecies abundance, as approximated by nest encounter rate, yielded a 6% annual decline and a total decline of 80.2% over the study period from 1990 to 2014. This also resulted in a reduced geographic range of 20% (657,600 vs. 524,100 km2 ). Poverty, civil conflict, disease pandemics, agriculture, extractive industries, infrastructure development, and lack of law enforcement, are some of the many reasons for the magnitude of threat. Our status update triggered the uplisting of the western chimpanzee to "Critically Endangered" on the IUCN Red List. In 2017, IUCN will start updating the 2003 Action Plan for western chimpanzees and will provide a consensus blueprint for what is needed to save this subspecies. We make a plea for greater commitment to conservation in West Africa across sectors. Needed especially is more robust engagement by national governments, integration of conservation priorities into the private sector and development planning across the region and sustained financial support from donors.

Fitness impacts of tapeworm parasitism on wild gelada monkeys at Guassa, Ethiopia.

Parasitism is expected to impact host morbidity or mortality, although the fitness costs of parasitism have rarely been quantified for wildlife hosts. Tapeworms in the genus Taenia exploit a variety of vertebrates, including livestock, humans, and geladas (Theropithecus gelada), monkeys endemic to the alpine grasslands of Ethiopia. Despite Taenia's adverse societal and economic impacts, we know little about the prevalence of disease associated with Taenia infection in wildlife or the impacts of this disease on host health, mortality and reproduction. We monitored geladas at Guassa, Ethiopia over a continuous 6½ year period for external evidence (cysts or coenuri) of Taenia-associated disease (coenurosis) and evaluated the impact of coenurosis on host survival and reproduction. We also identified (through genetic and histological analyses) the tapeworms causing coenurosis in wild geladas at Guassa as Taenia serialis. Nearly 1/3 of adult geladas at Guassa possessed ≥1 coenurus at some point in the study. Coenurosis adversely impacted gelada survival and reproduction at Guassa and this impact spanned two generations: adults with coenuri suffered higher mortality than members of their sex without coenuri and offspring of females with coenuri also suffered higher mortality. Coenurosis also negatively affected adult reproduction, lengthening interbirth intervals and reducing the likelihood that males successfully assumed reproductive control over units of females. Our study provides the first empirical evidence that coenurosis increases mortality and reduces fertility in wild nonhuman primate hosts. Our research highlights the value of longitudinal monitoring of individually recognized animals in natural populations for advancing knowledge of parasite-host evolutionary dynamics and offering clues to the etiology and control of infectious disease.

Local genetic adaptation to habitat in wild chimpanzees.

How populations adapt to their environment is a fundamental question in biology. Yet we know surprisingly little about this process, especially for endangered species such as non-human great apes. Chimpanzees, our closest living relatives, are particularly interesting because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether genetic adaptation facilitates such habitat diversity remains unknown, despite having wide implications for evolutionary biology and conservation. Using 828 newly generated exomes from wild chimpanzees, we find evidence of fine-scale genetic adaptation to habitat. Notably, adaptation to malaria in forest chimpanzees is mediated by the same genes underlying adaptation to malaria in humans. This work demonstrates the power of non-invasive samples to reveal genetic adaptations in endangered populations and highlights the importance of adaptive genetic diversity for chimpanzees.

Population dynamics and genetic connectivity in recent chimpanzee history.

Knowledge on the population history of endangered species is critical for conservation, but whole-genome data on chimpanzees (Pan troglodytes) is geographically sparse. Here, we produced the first non-invasive geolocalized catalog of genomic diversity by capturing chromosome 21 from 828 non-invasive samples collected at 48 sampling sites across Africa. The four recognized subspecies show clear genetic differentiation correlating with known barriers, while previously undescribed genetic exchange suggests that these have been permeable on a local scale. We obtained a detailed reconstruction of population stratification and fine-scale patterns of isolation, migration, and connectivity, including a comprehensive picture of admixture with bonobos (Pan paniscus). Unlike humans, chimpanzees did not experience extended episodes of long-distance migrations, which might have limited cultural transmission. Finally, based on local rare variation, we implement a fine-grained geolocalization approach demonstrating improved precision in determining the origin of confiscated chimpanzees.

Death among geladas (Theropithecus gelada): a broader perspective on mummified infants and primate thanatology.

Despite intensive study in humans, responses to dying and death have been a neglected area of research in other social mammals, including nonhuman primates. Two recent reports [Anderson JR, Gillies A, Lock LC. 2010. Pan thanatology. Current Biology 20:R349-R351; Biro D, Humle T, Koops K, Souse C, Hayashi M, Matsuzawa T. 2010. Chimpanzee mothers at Bossou, Guinea carry the mummified remains of their dead infants. Current Biology 20:R351-R352] offered exciting new insights into behavior toward dying and dead conspecifics in our closest living relatives-chimpanzees. Here, we provide a comparative perspective on primate thanatology using observations from a more distant human relative-gelada monkeys (Theropithecus gelada)-and discuss how gelada reactions to dead and dying groupmates differ from those recently reported for chimpanzees. Over a 3.75-year study period, we observed 14 female geladas at Guassa, Ethiopia carrying dead infants from 1 hr to ≥48 days after death. Dead infants were carried by their mothers, other females in their group, and even by females belonging to other groups. Like other primate populations in which extended (>10 days) infant carrying after death has been reported, geladas at Guassa experience an extreme climate for primates, creating conditions which may favor slower rates of decomposition of dead individuals. We also witnessed the events leading up to the deaths of two individuals and the responses by groupmates to these dying individuals. Our results suggest that while chimpanzee mothers are not unique among primates in carrying their dead infants for long periods, seemingly "compassionate" caretaking behavior toward dying groupmates may be unique to chimpanzees among nonhuman primates (though it remains unknown whether such "compassionate" behavior occurs outside captivity).

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.

Structure of Chimpanzee Gut Microbiomes across Tropical Africa.

Understanding variation in host-associated microbial communities is important given the relevance of microbiomes to host physiology and health. Using 560 fecal samples collected from wild chimpanzees (Pan troglodytes) across their range, we assessed how geography, genetics, climate, vegetation, and diet relate to gut microbial community structure (prokaryotes, eukaryotic parasites) at multiple spatial scales. We observed a high degree of regional specificity in the microbiome composition, which was associated with host genetics, available plant foods, and potentially with cultural differences in tool use, which affect diet. Genetic differences drove community composition at large scales, while vegetation and potentially tool use drove within-region differences, likely due to their influence on diet. Unlike industrialized human populations in the United States, where regional differences in the gut microbiome are undetectable, chimpanzee gut microbiomes are far more variable across space, suggesting that technological developments have decoupled humans from their local environments, obscuring regional differences that could have been important during human evolution. IMPORTANCE Gut microbial communities are drivers of primate physiology and health, but the factors that influence the gut microbiome in wild primate populations remain largely undetermined. We report data from a continent-wide survey of wild chimpanzee gut microbiota and highlight the effects of genetics, vegetation, and potentially even tool use at different spatial scales on the chimpanzee gut microbiome, including bacteria, archaea, and eukaryotic parasites. Microbial community dissimilarity was strongly correlated with chimpanzee population genetic dissimilarity, and vegetation composition and consumption of algae, honey, nuts, and termites were potentially associated with additional divergence in microbial communities between sampling sites. Our results suggest that host genetics, geography, and climate play a far stronger role in structuring the gut microbiome in chimpanzees than in humans.

Geographically structured genomic diversity of non-human primate-infecting Treponema pallidum subsp. pertenue.

Many non-human primate species in sub-Saharan Africa are infected with Treponema pallidum subsp. pertenue, the bacterium causing yaws in humans. In humans, yaws is often characterized by lesions of the extremities and face, while T. pallidum subsp. pallidum causes venereal syphilis and is typically characterized by primary lesions on the genital, anal or oral mucosae. It remains unclear whether other T. pallidum subspecies found in humans also occur in non-human primates and how the genomic diversity of non-human primate T. pallidum subsp. pertenue lineages is distributed across hosts and space. We observed orofacial and genital lesions in sooty mangabeys (Cercocebus atys) in Taï National Park, Côte d'Ivoire and collected swabs and biopsies from symptomatic animals. We also collected non-human primate bones from 8 species in Taï National Park and 16 species from 11 other sites across sub-Saharan Africa. Samples were screened for T. pallidum DNA using polymerase chain reactions (PCRs) and we used in-solution hybridization capture to sequence T. pallidum genomes. We generated three nearly complete T. pallidum genomes from biopsies and swabs and detected treponemal DNA in bones of six non-human primate species in five countries, allowing us to reconstruct three partial genomes. Phylogenomic analyses revealed that both orofacial and genital lesions in sooty mangabeys from Taï National Park were caused by T. pallidum subsp. pertenue. We showed that T. pallidum subsp. pertenue has infected non-human primates in Taï National Park for at least 28 years and has been present in two non-human primate species that had not been described as T. pallidum subsp. pertenue hosts in this ecosystem, western chimpanzees (Pan troglodytes verus) and western red colobus (Piliocolobus badius), complementing clinical evidence that started accumulating in Taï National Park in 2014. More broadly, simian T. pallidum subsp. pertenue strains did not form monophyletic clades based on host species or the symptoms caused, but rather clustered based on geography. Geographical clustering of T. pallidum subsp. pertenue genomes might be compatible with cross-species transmission of T. pallidum subsp. pertenue within ecosystems or environmental exposure, leading to the acquisition of closely related strains. Finally, we found no evidence for mutations that confer antimicrobial resistance.

Environmental variability supports chimpanzee behavioural diversity.

Large brains and behavioural innovation are positively correlated, species-specific traits, associated with the behavioural flexibility animals need for adapting to seasonal and unpredictable habitats. Similar ecological challenges would have been important drivers throughout human evolution. However, studies examining the influence of environmental variability on within-species behavioural diversity are lacking despite the critical assumption that population diversification precedes genetic divergence and speciation. Here, using a dataset of 144 wild chimpanzee (Pan troglodytes) communities, we show that chimpanzees exhibit greater behavioural diversity in environments with more variability - in both recent and historical timescales. Notably, distance from Pleistocene forest refugia is associated with the presence of a larger number of behavioural traits, including both tool and non-tool use behaviours. Since more than half of the behaviours investigated are also likely to be cultural, we suggest that environmental variability was a critical evolutionary force promoting the behavioural, as well as cultural diversification of great apes.

Human impact erodes chimpanzee behavioral diversity.

Chimpanzees possess a large number of behavioral and cultural traits among nonhuman species. The "disturbance hypothesis" predicts that human impact depletes resources and disrupts social learning processes necessary for behavioral and cultural transmission. We used a dataset of 144 chimpanzee communities, with information on 31 behaviors, to show that chimpanzees inhabiting areas with high human impact have a mean probability of occurrence reduced by 88%, across all behaviors, compared to low-impact areas. This behavioral diversity loss was evident irrespective of the grouping or categorization of behaviors. Therefore, human impact may not only be associated with the loss of populations and genetic diversity, but also affects how animals behave. Our results support the view that "culturally significant units" should be integrated into wildlife conservation.

Cytomegalovirus distribution and evolution in hominines.

Herpesviruses are thought to have evolved in very close association with their hosts. This is notably the case for cytomegaloviruses (CMVs; genus Cytomegalovirus) infecting primates, which exhibit a strong signal of co-divergence with their hosts. Some herpesviruses are however known to have crossed species barriers. Based on a limited sampling of CMV diversity in the hominine (African great ape and human) lineage, we hypothesized that chimpanzees and gorillas might have mutually exchanged CMVs in the past. Here, we performed a comprehensive molecular screening of all 9 African great ape species/subspecies, using 675 fecal samples collected from wild animals. We identified CMVs in eight species/subspecies, notably generating the first CMV sequences from bonobos. We used this extended dataset to test competing hypotheses with various degrees of co-divergence/number of host switches while simultaneously estimating the dates of these events in a Bayesian framework. The model best supported by the data involved the transmission of a gorilla CMV to the panine (chimpanzee and bonobo) lineage and the transmission of a panine CMV to the gorilla lineage prior to the divergence of chimpanzees and bonobos, more than 800,000 years ago. Panine CMVs then co-diverged with their hosts. These results add to a growing body of evidence suggesting that viruses with a double-stranded DNA genome (including other herpesviruses, adenoviruses, and papillomaviruses) often jumped between hominine lineages over the last few million years.

Chimpanzee accumulative stone throwing.

The study of the archaeological remains of fossil hominins must rely on reconstructions to elucidate the behaviour that may have resulted in particular stone tools and their accumulation. Comparatively, stone tool use among living primates has illuminated behaviours that are also amenable to archaeological examination, permitting direct observations of the behaviour leading to artefacts and their assemblages to be incorporated. Here, we describe newly discovered stone tool-use behaviour and stone accumulation sites in wild chimpanzees reminiscent of human cairns. In addition to data from 17 mid- to long-term chimpanzee research sites, we sampled a further 34 Pan troglodytes communities. We found four populations in West Africa where chimpanzees habitually bang and throw rocks against trees, or toss them into tree cavities, resulting in conspicuous stone accumulations at these sites. This represents the first record of repeated observations of individual chimpanzees exhibiting stone tool use for a purpose other than extractive foraging at what appear to be targeted trees. The ritualized behavioural display and collection of artefacts at particular locations observed in chimpanzee accumulative stone throwing may have implications for the inferences that can be drawn from archaeological stone assemblages and the origins of ritual sites.