Potentially Zoonotic Enteric Infections in Gorillas and Chimpanzees, Cameroon and Tanzania.

Despite zoonotic potential, data are lacking on enteric infection diversity in wild apes. We employed a novel molecular diagnostic platform to detect enteric infections in wild chimpanzees and gorillas. Prevalent Cryptosporidium parvum, adenovirus, and diarrheagenic Escherichia coli across divergent sites and species demonstrates potential widespread circulation among apes in Africa.

Barriers to chimpanzee gene flow at the south-east edge of their distribution.

Populations on the edge of a species' distribution may represent an important source of adaptive diversity, yet these populations tend to be more fragmented and are more likely to be geographically isolated. Lack of genetic exchanges between such populations, due to barriers to animal movement, can not only compromise adaptive potential but also lead to the fixation of deleterious alleles. The south-eastern edge of chimpanzee distribution is particularly fragmented, and conflicting hypotheses have been proposed about population connectivity and viability. To address this uncertainty, we generated both mitochondrial and MiSeq-based microsatellite genotypes for 290 individuals ranging across western Tanzania. While shared mitochondrial haplotypes confirmed historical gene flow, our microsatellite analyses revealed two distinct clusters, suggesting two populations currently isolated from one another. However, we found evidence of high levels of gene flow maintained within each of these clusters, one of which covers an 18,000 km2 ecosystem. Landscape genetic analyses confirmed the presence of barriers to gene flow with rivers and bare habitats highly restricting chimpanzee movement. Our study demonstrates how advances in sequencing technologies, combined with the development of landscape genetics approaches, can resolve ambiguities in the genetic history of critical populations and better inform conservation efforts of endangered species.

Widespread extinctions of co-diversified primate gut bacterial symbionts from humans.

Humans and other primates harbour complex gut bacterial communities that influence health and disease, but the evolutionary histories of these symbioses remain unclear. This is partly due to limited information about the microbiota of ancestral primates. Here, using phylogenetic analyses of metagenome-assembled genomes (MAGs), we show that hundreds of gut bacterial clades diversified in parallel (that is, co-diversified) with primate species over millions of years, but that humans have experienced widespread losses of these ancestral symbionts. Analyses of 9,460 human and non-human primate MAGs, including newly generated MAGs from chimpanzees and bonobos, revealed significant co-diversification within ten gut bacterial phyla, including Firmicutes, Actinobacteriota and Bacteroidota. Strikingly, ~44% of the co-diversifying clades detected in African apes were absent from available metagenomic data from humans and ~54% were absent from industrialized human populations. In contrast, only ~3% of non-co-diversifying clades detected in African apes were absent from humans. Co-diversifying clades present in both humans and chimpanzees displayed consistent genomic signatures of natural selection between the two host species but differed in functional content from co-diversifying clades lost from humans, consistent with selection against certain functions. This study discovers host-species-specific bacterial symbionts that predate hominid diversification, many of which have undergone accelerated extinctions from human populations.

A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes.

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 ecology and epidemiology of malaria parasitism in wild chimpanzee reservoirs.

Chimpanzees (Pan troglodytes) harbor rich assemblages of malaria parasites, including three species closely related to P. falciparum (sub-genus Laverania), the most malignant human malaria parasite. Here, we characterize the ecology and epidemiology of malaria infection in wild chimpanzee reservoirs. We used molecular assays to screen chimpanzee fecal samples, collected longitudinally and cross-sectionally from wild populations, for malaria parasite mitochondrial DNA. We found that chimpanzee malaria parasitism has an early age of onset and varies seasonally in prevalence. A subset of samples revealed Hepatocystis mitochondrial DNA, with phylogenetic analyses suggesting that Hepatocystis appears to cross species barriers more easily than Laverania. Longitudinal and cross-sectional sampling independently support the hypothesis that mean ambient temperature drives spatiotemporal variation in chimpanzee Laverania infection. Infection probability peaked at ~24.5 °C, consistent with the empirical transmission optimum of P. falciparum in humans. Forest cover was also positively correlated with spatial variation in Laverania prevalence, consistent with the observation that forest-dwelling Anophelines are the primary vectors. Extrapolating these relationships across equatorial Africa, we map spatiotemporal variation in the suitability of chimpanzee habitat for Laverania transmission, offering a hypothetical baseline indicator of human exposure risk.

Female reproductive aging in seven primate species: Patterns and consequences.

Age-related changes in fertility have increasingly been documented in wild animal populations: In many species the youngest and oldest reproducers are disadvantaged relative to prime adults. How do these effects evolve, and what explains their diversity across species? Tackling this question requires detailed data on patterns of age-related reproductive performance in multiple animal species. Here, we compare patterns and consequences of age-related changes in female reproductive performance in seven primate populations that have been subjects of long-term continuous study for 29 to 57 y. We document evidence of age effects on fertility and on offspring performance in most, but not all, of these primate species. Specifically, females of six species showed longer interbirth intervals in the oldest age classes, youngest age classes, or both, and the oldest females also showed relatively fewer completed interbirth intervals. In addition, five species showed markedly lower survival among offspring born to the oldest mothers, and two species showed reduced survival for offspring born to both the youngest and the oldest mothers. In contrast, we found mixed evidence that maternal age affects the age at which daughters first reproduce: Only in muriquis and to some extent in chimpanzees, the only two species with female-biased dispersal, did relatively young mothers produce daughters that tended to have earlier first reproduction. Our findings demonstrate shared patterns as well as contrasts in age-related changes in female fertility across species of nonhuman primates and highlight species-specific behavior and life-history patterns as possible explanations for species-level differences.

Drinking frequency in wild lactating chimpanzees (Pan troglodytes schweinfurthii) and their offspring.

Maintaining water balance is essential for organismal health, and lactating females must balance individual needs with milk production and offspring hydration. Primate milk is dilute and presumed to be the primary source for infant hydration for a considerable time period. Few studies have investigated the hydration burden that lactation may place on female primates. In this study, we investigated sources of variation in female and offspring drinking frequency among wild chimpanzees (Pan troglodytes). We hypothesized females would experience seasonal and lactation hydration burdens and adjust their drinking behavior to accommodate these, but this hydration burden would vary between females of different dominance ranks. We also predicted that parity would relate to maternal drinking frequency since primiparous females are still investing in their own growth. Finally, we predicted that offspring would drink more in the dry season and as they aged and lost milk as a water source, but that offspring of high-ranking females would be buffered from these effects. Using 41 years of long-term data on the behavior of mothers and offspring of Gombe National Park, we found that mothers drank more in the dry season, but there was no significant difference between mothers of different ranks during this period. Low-ranking females drank significantly more than mid- and high-ranking females during late lactation. Offspring also drank more in the dry season and as they aged, but there was no evidence of buffering for those with high-ranking mothers. While chimpanzees in our study population drank infrequently, they do demonstrate noticeable shifts in drinking behavior that suggests seasonal and reproductive hydration burdens.

The Gombe Ecosystem Health Project: 16 years of program evolution and lessons learned.

Infectious disease outbreaks pose a significant threat to the conservation of chimpanzees (Pan troglodytes) and all threatened nonhuman primates. Characterizing and mitigating these threats to support the sustainability and welfare of wild populations is of the highest priority. In an attempt to understand and mitigate the risk of disease for the chimpanzees of Gombe National Park, Tanzania, we initiated a long-term health-monitoring program in 2004. While the initial focus was to expand the ongoing behavioral research on chimpanzees to include standardized data on clinical signs of health, it soon became evident that the scope of the project would ideally include diagnostic surveillance of pathogens for all primates (including people) and domestic animals, both within and surrounding the National Park. Integration of these data, along with in-depth post-mortem examinations, have allowed us to establish baseline health indicators to inform outbreak response. Here, we describe the development and expansion of the Gombe Ecosystem Health project, review major findings from the research and summarize the challenges and lessons learned over the past 16 years. We also highlight future directions and present the opportunities and challenges that remain when implementing studies of ecosystem health in a complex, multispecies environment.

Culture-enriched community profiling improves resolution of the vertebrate gut microbiota.

Vertebrates harbour gut microbial communities containing hundreds of bacterial species, most of which have never been cultivated or isolated in the laboratory. The lack of cultured representatives from vertebrate gut microbiotas limits the description and experimental interrogation of these communities. Here, we show that representatives from >50% of the bacterial genera detected by culture-independent sequencing in the gut microbiotas of fence lizards, house mice, chimpanzees, and humans were recovered in mixed cultures from frozen faecal samples plated on a panel of nine media under a single growth condition. In addition, culturing captured >100 rare bacterial genera overlooked by culture-independent sequencing, more than doubling the total number of bacterial sequence variants detected. Our approach recovered representatives from 23 previously uncultured candidate bacterial genera, 12 of which were not detected by culture-independent sequencing. Results identified strategies for both indiscriminate and selective culturing of the gut microbiota that were reproducible across vertebrate species. Isolation followed by whole-genome sequencing of 161 bacterial colonies from wild chimpanzees enabled the discovery of candidate novel species closely related to the opportunistic pathogens of humans Clostridium difficile and Hungatella hathewayi. This study establishes culturing methods that improve inventories and facilitate isolation of gut microbiota constituents from a wide diversity of vertebrate species.

Gregariousness is associated with parasite species richness in a community of wild chimpanzees.

Increased risk of pathogen transmission through proximity and contact is a well-documented cost of sociality. Affiliative social contact, however, is an integral part of primate group life and can benefit health. Despite its importance to the evolution and maintenance of sociality, the tradeoff between costs and benefits of social contact for group-living primate species remains poorly understood. To improve our understanding of this interplay, we used social network analysis to investigate whether contact via association in the same space and/or physical contact measured through grooming were associated with helminth parasite species richness in a community of wild chimpanzees (Pan troglodytes schweinfurthii). We identified parasite taxa in 381 fecal samples from 36 individuals from the Kasekela community of chimpanzees in Gombe National Park, Tanzania, from November 1, 2006 - October 31, 2012. Over the study period, eight environmentally transmitted helminth taxa were identified. We quantified three network metrics for association and grooming contact, including degree strength, betweenness, and closeness. Our findings suggest that more gregarious individuals - those who spent more time with more individuals in the same space - had higher parasite richness, while the connections in the grooming network were not related to parasite richness. The expected parasite richness in individuals increased by 1.13 taxa (CI: 1.04, 1.22; p = 0.02) per one standard deviation increase in degree strength of association contact. The results of this study add to the understanding of the role that different types of social contact plays in the parasite richness of group-living social primates.

In vivo deciduous dental eruption in LuiKotale bonobos and Gombe chimpanzees.

OBJECTIVES: Existing data on bonobo and chimpanzee dental eruption timing are derived predominantly from captive individuals or deceased wild individuals. However, recent advances in noninvasive photographic monitoring of living, wild apes have enabled researchers to characterize dental eruption in relatively healthy individuals under naturalistic conditions. At present, such data are available for only one population of wild chimpanzees. We report data for an additional population of wild chimpanzees and the first dental eruption data for wild bonobos. MATERIALS AND METHODS: We collected photographs and video footage of teeth from the open mouths of wild bonobos and East African chimpanzees of known age from LuiKotale, Democratic Republic of the Congo, and Gombe National Park, Tanzania, respectively. We scored the presence and absence of deciduous teeth from photographs and video footage to characterize deciduous dental eruption timing in these two populations. RESULTS: Deciduous dental eruption ages in our sample fall within the range of variation previously documented for captive chimpanzees, but eruption ages are later in wild than in captive contexts. We found substantial variation in deciduous canine eruption timing, particularly among bonobos. One bonobo had a deciduous canine present by 227 days old while another did not have a deciduous canine present at 477 days old. DISCUSSION: Our data indicate that deciduous teeth erupt later in wild individuals than in captive individuals. We also found that deciduous dental eruption timing varies considerably between individuals within our study populations, a pattern that is consistent with previous studies. Future studies should consider sources of variation in deciduous canine eruption timing and relationships with other aspects of life history as additional data become available.

Antimicrobial Resistance Creates Threat to Chimpanzee Health and Conservation in the Wild.

Infectious disease is recognized as the greatest threat to the endangered chimpanzees made famous by the groundbreaking work of Dr. Jane Goodall at Gombe National Park (GNP), Tanzania. The permeable boundary of this small protected area allows for regular wildlife-human and wildlife-domestic animal overlap, which may facilitate cross-species transmission of pathogens and antimicrobial resistance. Few studies have examined the prevalence of antimicrobial resistance in wild ape populations. We used molecular techniques to investigate the presence of genes conferring resistance to sulfonamides (often used to treat diarrheal illness in human settings in this region) and tetracycline (used in the past-though much less so now) in fecal specimens from humans, domestic animals, chimpanzees, and baboons in and around GNP. We also tested stream water used by these groups. Sulfonamide resistance was common in humans (74%), non-human primates (43%), and domestic animals (17%). Tetracycline resistance was less common in all groups: humans (14%), non-human primates (3%), and domestic animals (6%). Sul resistance genes were detected from 4/22 (18%) of streams sampled. Differences in sul gene frequencies did not vary by location in humans nor in chimpanzees.

Gregariousness, foraging effort, and affiliative interactions in lactating bonobos and chimpanzees.

Fission-fusion dynamics have evolved in a broad range of animal taxa and are thought to allow individuals to mitigate feeding competition. While this is the principal benefit of fission-fusion, few studies have evaluated its costs. We compared gregariousness, foraging budgets, and social budgets between lactating bonobos and chimpanzees from wild populations to evaluate potential costs. Both species exhibit fission-fusion dynamics, but chimpanzees, particularly in East African populations, appear to experience higher feeding competition than bonobos. We expected lactating chimpanzees to be less gregarious than lactating bonobos; reduced gregariousness should allow lactating chimpanzees to mitigate the costs of higher feeding competition without requiring more foraging effort. However, we expected the reduced gregariousness of lactating chimpanzees to limit their time available for affiliative interactions. Using long-term data from LuiKotale bonobos and Gombe chimpanzees, we found that lactating chimpanzees were indeed less gregarious than lactating bonobos, while feeding and travel time did not differ between species. Contrary to our predictions, lactating females did not differ in social interaction time, and lactating chimpanzees spent proportionately more time interacting with individuals other than their immature offspring. Our results indicate that lactating chimpanzees can maintain social budgets comparable to lactating bonobos despite reduced gregariousness and without incurring additional foraging costs. We discuss potential explanations for why lactating bonobos are more gregarious.

Wild chimpanzee offspring exhibit adult-like foraging patterns around the age of weaning.

OBJECTIVES: The prolonged juvenile period exhibited by primates is an evolutionary conundrum. Here we examine wild chimpanzee feeding development in the context of two hypotheses regarding prolonged development in primates: the needing-to-learn hypothesis and the expensive brain hypothesis. MATERIAL AND METHODS: We studied wild chimpanzee (Pan troglodytes schweinfurthii) offspring at Gombe National Park, Tanzania. We analyzed 41 years of observational behavioral data collected between 1975 and 2016 from 81 offspring. We characterized feeding development in the first 10 years of life via four different measures: (1) proportion of observation time spent feeding; (2) diet composition; (3) diet breadth; and (4) diet maturity as measured by similarity to maternal diet. We used mixed effects models to examine changes with age and by sex, while controlling for season. RESULTS: Feeding time, diet breadth, and diet maturity exhibited the most substantial increases with age in the first 6 years, with no significant change thereafter. Males and females showed different patterns of change in diet breadth by age, but did not differ by age 10. Diet composition did not change significantly with age and did not differ by sex. DISCUSSION: We found that chimpanzee offspring attained adult-like feeding behaviors between 4 and 6 years of age, concomitant with the completion of weaning. Thus, our data do not support the needing-to-learn feeding skills hypothesis of a prolonged juvenile period, but additional data are needed to evaluate how and when adolescent chimpanzees are able to make foraging decisions independent of their mothers. Existing data on growth provides support for the expensive brain hypothesis, however, these hypotheses are not necessarily mutually exclusive. As more studies across taxa accumulate sufficient datasets on a range of developmental metrics, we will be able to achieve a more robust understanding of prolonged development in primates.

Maternal death and offspring fitness in multiple wild primates.

Primate offspring often depend on their mothers well beyond the age of weaning, and offspring that experience maternal death in early life can suffer substantial reductions in fitness across the life span. Here, we leverage data from eight wild primate populations (seven species) to examine two underappreciated pathways linking early maternal death and offspring fitness that are distinct from direct effects of orphaning on offspring survival. First, we show that, for five of the seven species, offspring face reduced survival during the years immediately preceding maternal death, while the mother is still alive. Second, we identify an intergenerational effect of early maternal loss in three species (muriquis, baboons, and blue monkeys), such that early maternal death experienced in one generation leads to reduced offspring survival in the next. Our results have important implications for the evolution of slow life histories in primates, as they suggest that maternal condition and survival are more important for offspring fitness than previously realized.

Research and Conservation in the Greater Gombe Ecosystem: Challenges and Opportunities.

The study of chimpanzees in Gombe National Park, Tanzania, started by Jane Goodall in 1960, provided pioneering accounts of chimpanzee behavior and ecology. With funding from multiple sources, including the Jane Goodall Institute (JGI) and grants from private foundations and federal programs, the project has continued for sixty years, providing a wealth of information about our evolutionary cousins. These chimpanzees face two main challenges to their survival: infectious disease - including simian immunodeficiency virus (SIVcpz), which can cause Acquired Immune Deficiency Syndrome (AIDS) in chimpanzees - and the deforestation of land outside the park. A health monitoring program has increased understanding of the pathogens affecting chimpanzees and has promoted measures to characterize and reduce disease risk. Deforestation reduces connections between Gombe and other chimpanzee populations, which can cause loss of genetic diversity. To promote habitat restoration, JGI facilitated participatory village land use planning, in which communities voluntarily allocated land to a network of Village Land Forest Reserves. Expected benefits to people include stabilizing watersheds, improving water supplies, and ensuring a supply of forest resources. Surveys and genetic analyses confirm that chimpanzees persist on village lands and remain connected to the Gombe population. Many challenges remain, but the regeneration of natural forest on previously degraded lands provides hope that conservation solutions can be found that benefit both people and wildlife. Conservation work in the Greater Gombe Ecosystem has helped promote broader efforts to plan and work for conservation elsewhere in Tanzania and across Africa.

Why chimpanzees carry dead infants: an empirical assessment of existing hypotheses.

The study of non-human primate thanatology has expanded dramatically in recent years as scientists seek to understand the evolutionary roots of human death concepts and practices. However, observations of how conspecifics respond to dead individuals are rare and highly variable. Mothers of several species of primate have been reported to carry and continue to interact with dead infants. Such interactions have been proposed to be related to maternal condition, attachment, environmental conditions or reflect a lack of awareness that the infant has died. Here, we tested these hypotheses using a dataset of cases of infant corpse carrying by chimpanzees in Gombe National Park, Tanzania (n = 33), the largest dataset of such cases in chimpanzees. We found that mothers carried infant corpses at high rates, despite behavioural evidence that they recognize that death has occurred. Median duration of carriage was 1.83 days (interquartile range = 1.03-3.59). Using an information theoretic approach, we found no support for any of the leading hypotheses for duration of continued carriage. We interpret these data in the context of recent discussions regarding what non-human primates understand about death.

Consistent differences in a virtual world model of ape societies.

Practical and ethical constraints limit our ability to experimentally test socioecological theory in wild primates. We took an alternate approach to model this, allowing groups of humans to interact in a virtual world in which they had to find food and interact with both ingroup and outgroup avatars to earn rewards. We altered ratios and distributions of high- and low-value foods to test the hypothesis that hominoids vary with regards to social cohesion and intergroup tolerance due to their feeding ecology. We found larger nesting clusters and decreased attacks on outgroup competitors in the Bonobo condition versus the Chimpanzee condition, suggesting a significant effect of feeding competition alone on social structure. We also demonstrate that virtual worlds are a robust mechanism for testing hypotheses that are impossible to study in the wild.

Wild bonobo and chimpanzee females exhibit broadly similar patterns of behavioral maturation but some evidence for divergence.

OBJECTIVES: Primates exhibit variation in rates of growth and development. Variation in female growth and development across ape species appears to be explained by the Ecological Risk Aversion Hypothesis (ERAH). Indeed, existing data on variation in somatic growth and reproductive maturation between humans' closest living ape relatives, bonobos and chimpanzees, appear to be consistent with this hypothesis. However, existing data on behavioral maturation between the two species appear to contradict this hypothesis. We present novel behavioral data on infant and juvenile females from wild populations of both species in order to further evaluate predictions of the ERAH as it relates to the speed of behavioral maturation. MATERIALS AND METHODS: We analyzed 3 years of behavioral data on 17 female bonobos (<8 years of age) from LuiKotale, Democratic Republic of the Congo and 40 years of behavioral data on 30 age-matched female chimpanzees from Gombe, Tanzania. We compared the timing of (a) the attainment of independence from mothers and (b) the development of social skills using the following proxies: proximity between females and their mothers and the time that females spent engaged in eating, suckling, social play, social grooming, and riding on their mothers. RESULTS: We did not find species differences in the proportion of time that females spent in contact with their mothers or engaged in eating, suckling, social play, or social grooming. Female bonobos spent more time riding on their mothers than did female chimpanzees. Female bonobos spent more time at distances greater than 5 m from their mothers during the ages of 3-8 years, but females did not differ during the ages of 0-3 years. DISCUSSION: Behavioral maturation is largely similar between females of the two species based on the ages and proxies considered herein. We propose alternative explanations for the differences that we found in proximity and riding that do not invoke differences in underlying rates of maturation.

Sources of variation in weaned age among wild chimpanzees in Gombe National Park, Tanzania.

OBJECTIVES: A key feature of human life history evolution is that modern humans wean their infants 2-4 years earlier on average than African apes. However, our understanding of weaning variation in apes remains limited. Here we provide the first such report in chimpanzees by examining weaned age variation using long-term data from Gombe National Park, Tanzania. MATERIAL AND METHODS: We analyzed 41 years of observational behavioral data from 65 offspring of 29 mothers to examine the relationships between weaned age (defined as cessation of suckling) in wild chimpanzees and maternal age, dominance rank and parity, and offspring sex. We used Cox proportional hazards regression with mixed effects to model time to weaning and to examine potential sources of variation in offspring weaned age. RESULTS: We found that male offspring were less likely than female offspring to wean by a given age and that weaned age of males varied more than weaned age of females. In addition, maternal dominance rank interacted with offspring age, such that low-ranking mothers were less likely to wean offspring early, but this effect decreased with offspring age. DISCUSSION: We found that male offspring and offspring of low-ranking females were less likely to wean early, but did not find evidence for variable weaning according to maternal age or parity. As more data accumulate, we will be better able to disentangle the effects of maternal dominance rank, age and parity. Such studies will not only provide a richer understanding of living ape life history characteristics, but will also provide an important framework for understanding the evolution of early weaning in humans.