Evolutionary Insight into the Association between New Jersey Polyomavirus and Humans.

Advances in viral discovery techniques have led to the identification of numerous novel viruses in human samples. However, the low prevalence of certain viruses in humans raises doubts about their association with our species. To ascertain the authenticity of a virus as a genuine human-infecting agent, it can be useful to investigate the diversification of its lineage within hominines, the group encompassing humans and African great apes. Building upon this rationale, we examined the case of the New Jersey polyomavirus (NJPyV; Alphapolyomavirus terdecihominis), which has only been detected in a single patient thus far. In this study, we obtained and analyzed sequences from closely related viruses infecting all African great ape species. We show that NJPyV nests within the diversity of these viruses and that its lineage placement is compatible with an ancient origin in humans, despite its apparent rarity in human populations.

Comparative life history patterns of female gorillas.

OBJECTIVES: Several theories have been proposed to explain the impact of ecological conditions on differences in life history variables within and between species. Here we compare female life history parameters of one western lowland gorilla population (Gorilla gorilla gorilla) and two mountain gorilla populations (Gorilla beringei beringei). MATERIALS AND METHODS: We compared the age of natal dispersal, age of first birth, interbirth interval, and birth rates using long-term demographic datasets from Mbeli Bai (western gorillas), Bwindi Impenetrable National Park and the Virunga Massif (mountain gorillas). RESULTS: The Mbeli western gorillas had the latest age at first birth, longest interbirth interval, and slowest surviving birth rate compared to the Virunga mountain gorillas. Bwindi mountain gorillas were intermediate in their life history patterns. DISCUSSION: These patterns are consistent with differences in feeding ecology across sites. However, it is not possible to determine the evolutionary mechanisms responsible for these differences, whether a consequence of genetic adaptation to fluctuating food supplies ("ecological risk aversion hypothesis") or phenotypic plasticity in response to the abundance of food ("energy balance hypothesis"). Our results do not seem consistent with the extrinsic mortality risks at each site, but current conditions for mountain gorillas are unlikely to match their evolutionary history. Not all traits fell along the expected fast-slow continuum, which illustrates that they can vary independently from each other ("modularity model"). Thus, the life history traits of each gorilla population may reflect a complex interplay of multiple ecological influences that are operating through both genetic adaptations and phenotypic plasticity.

Association patterns of female gorillas.

Social interactions ultimately impact health and fitness in gregarious mammals. However, research focusing on the strength of affiliative interactions has primarily been conducted on female philopatric species. Gorillas provide an interesting counterpoint to previous research as females emigrate multiple times throughout their lives. We compare female-female association strength, duration and consistency in wild mountain (Gorilla beringei beringei) and western gorillas (Gorilla gorilla gorilla). Additionally, we examine whether the alpha male influences female association strength and if these associations are an artefact of both females concurrently in spatial proximity of the alpha male. In this between-species comparison, female gorillas had differentiated association patterns that were consistent on average for 2 years. The alpha males did not influence female association strength, with associations being similar in his presence or absence. Finally, we found more variability in association patterns among mountain gorillas with higher average association scores and higher proportion of 'preferred associates' than western gorillas. The rare dispersal pattern in the Gorilla genus may lead to greater flexibility in female association patterns than in species exhibiting female philopatry and strong kinship bonds. This may echo ancestral human society and provide new evidence to help us understand the evolution of modern human society. This article is part of the theme issue 'Cooperation among women: evolutionary and cross-cultural perspectives'.

Population dynamics of western gorillas at Mbeli Bai.

Long-term studies of population dynamics can provide insights into life history theory, population ecology, socioecology, conservation biology and wildlife management. Here we examine 25 years of population dynamics of western gorillas at Mbeli Bai, a swampy forest clearing in Nouabalé-Ndoki National Park, the Republic of Congo. The Mbeli population more than doubled from 101 to 226 gorillas during the study. After adjusting for a net influx of gorillas into the study population, the increase represents an inherent growth rate of 0.7% per year, with 95% confidence limits between -0.7% and 2.6%. The influx of gorillas mainly involved immigration of individuals into existing study groups (social dispersal), but it also included the appearance of a few previously unknown groups (locational dispersal). The average group size did not change significantly during the study, which is consistent with the possibility that western gorillas face socioecological constraints on group size, even when the population is increasing. We found no significant evidence of density dependence on female reproductive success or male mating competition. The distribution of gorillas among age/sex categories also did not change significantly, which suggests that the population had a stable age structure. Our results provide evidence of population stability or growth for some western gorillas (albeit within a small area). The results highlight the value of law enforcement, long-term monitoring, and protected areas; but they do not diminish the importance of improving conservation for this critically endangered species.

Dietary variability of western gorillas (Gorilla gorilla gorilla).

Spatial and temporal variability in the availability of food resources will lead to variation in a species' diet, which can then influence patterns of space use, sociality, and life history characteristics. Despite such potential impacts, little information is available about dietary variability for some species with large geographical ranges. Here we quantify the diet and nutritional content of plants consumed by western lowland gorillas (Gorilla gorilla gorilla) in Loango National Park, Gabon over a 2.6 year period and make comparisons with two study sites located 800 km away. The major foods consumed by the Loango gorillas differed greatly from the other two study sites, but gorillas at all three locations spent a similar proportion of feeding time consuming herbaceous vegetation and tree leaves (~ 50%) and fruit (35%). The Loango gorillas spent approximately 10% of feeding time eating nuts, which were not consumed at the other two study sites. Gorillas at those sites spent about 5% of feeding time eating insects, which were not consumed by Loango gorillas. Even though the species composition of the diet differed among the three sites, the nutritional composition of the major food items differed very little, suggesting that western gorillas consume foods of similar nutritional values to meet their dietary needs. This study shows the flexibility of diet of a species with a wide geographic distribution, which has implications for understanding variation in life history characteristics and can be useful for conservation management plans.

The complex Y-chromosomal history of gorillas.

Studies of the evolutionary relationships among gorilla populations using autosomal and mitochondrial sequences suggest that male-mediated gene flow may have been important in the past, but data on the Y-chromosomal relationships among the gorilla subspecies are limited. Here, we genotyped blood and noninvasively collected fecal samples from 12 captives and 257 wild male gorillas of known origin representing all four subspecies (Gorilla gorilla gorilla, G. g. diehli, G. beringei beringei, and G. b. graueri) at 10 Y-linked microsatellite loci resulting in 102 unique Y-haplotypes for 224 individuals. We found that western lowland gorilla (G. g. gorilla) haplotypes were consistently more diverse than any other subspecies for all measures of diversity and comprised several genetically distinct groups. However, these did not correspond to geographical proximity and some closely related haplotypes were found several hundred kilometers apart. Similarly, our broad sampling of eastern gorillas revealed that mountain (G. b. beringei) and Grauer's (G. b. graueri) gorilla Y-chromosomal haplotypes did not form distinct clusters. These observations suggest structure in the ancestral population with subsequent mixing of differentiated haplotypes by male dispersal for western lowland gorillas, and postisolation migration or incomplete lineage sorting due to short divergence times for eastern gorillas.

Dissecting the two mechanisms of scramble competition among the Virunga mountain gorillas.

ABSTRACT: Two mechanisms have been proposed to explain why scramble competition can increase the travel requirements of individuals within larger groups. Firstly, individuals in larger groups may be more likely to encounter food sites where other group members have already eaten, leading to greater asynchronous "individual" travel to find fresh sites. Secondly, when food sites are aggregated into patches, larger groups may need to visit more patches to obtain the same amount of food per capita, leading to greater synchronous "group" travel between patches. If the first mechanism can be mitigated by increasing group spread, then we expect the second mechanism to be more sensitive to group size. Here, we examine the individual travel and group travel of the Virunga mountain gorillas, along with potential implications for the two mechanisms of scramble competition. Asynchronous individual travel accounted for 67% of the total travel time, and the remainder arose from group travel. Group spread increased significantly for larger groups, but not enough to prevent an increase in individual travel. Contrary to expectations, group travel decreased with size among most groups, and we found only limited evidence of patch depletion that would cause the second mechanism of scramble competition. Collectively, our results illustrate how the influence of group size can differ for individual travel versus group travel, just as it differs among species for overall travel. Studies that distinguish between the two mechanisms of scramble competition may enhance our understanding of ecological constraints upon group size, including potential differences between frugivores and folivores. SIGNIFICANCE STATEMENT: Feeding competition provides insight into how group size can influence the foraging patterns of social animals, but two key mechanisms are not typically compared. Firstly, larger groups may visit more patches to access the same amount of food per capita (group travel). Secondly, their individuals may also need to move past more spots where another member has already eaten (individual travel). Contrary to expectations, we found that group travel decreased with size for most groups of mountain gorillas, which may reflect extra travel by smaller groups to avoid larger groups. Individual travel increased with size in most groups, even though gorillas in larger groups compensated by spreading out over a broader area. The two mechanisms revealed patterns that were not apparent in our previous study of overall travel. Our approach may help to explain potential differences between folivores and frugivores.

Dominance style is a key predictor of vocal use and evolution across nonhuman primates.

Animal communication has long been thought to be subject to pressures and constraints associated with social relationships. However, our understanding of how the nature and quality of social relationships relates to the use and evolution of communication is limited by a lack of directly comparable methods across multiple levels of analysis. Here, we analysed observational data from 111 wild groups belonging to 26 non-human primate species, to test how vocal communication relates to dominance style (the strictness with which a dominance hierarchy is enforced, ranging from 'despotic' to 'tolerant'). At the individual-level, we found that dominant individuals who were more tolerant vocalized at a higher rate than their despotic counterparts. This indicates that tolerance within a relationship may place pressure on the dominant partner to communicate more during social interactions. At the species-level, however, despotic species exhibited a larger repertoire of hierarchy-related vocalizations than their tolerant counterparts. Findings suggest primate signals are used and evolve in tandem with the nature of interactions that characterize individuals' social relationships.

The long lives of primates and the 'invariant rate of ageing' hypothesis.

Is it possible to slow the rate of ageing, or do biological constraints limit its plasticity? We test the 'invariant rate of ageing' hypothesis, which posits that the rate of ageing is relatively fixed within species, with a collection of 39 human and nonhuman primate datasets across seven genera. We first recapitulate, in nonhuman primates, the highly regular relationship between life expectancy and lifespan equality seen in humans. We next demonstrate that variation in the rate of ageing within genera is orders of magnitude smaller than variation in pre-adult and age-independent mortality. Finally, we demonstrate that changes in the rate of ageing, but not other mortality parameters, produce striking, species-atypical changes in mortality patterns. Our results support the invariant rate of ageing hypothesis, implying biological constraints on how much the human rate of ageing can be slowed.

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.

Chest beats as an honest signal of body size in male mountain gorillas (Gorilla beringei beringei).

Acoustic signals that reliably indicate body size, which usually determines competitive ability, are of particular interest for understanding how animals assess rivals and choose mates. Whereas body size tends to be negatively associated with formant dispersion in animal vocalizations, non-vocal signals have received little attention. Among the most emblematic sounds in the animal kingdom is the chest beat of gorillas, a non-vocal signal that is thought to be important in intra and inter-sexual competition, yet it is unclear whether it reliably indicates body size. We examined the relationship among body size (back breadth), peak frequency, and three temporal characteristics of the chest beat: duration, number of beats and beat rate from sound recordings of wild adult male mountain gorillas. Using linear mixed models, we found that larger males had significantly lower peak frequencies than smaller ones, but we found no consistent relationship between body size and the temporal characteristics measured. Taken together with earlier findings of positive correlations among male body size, dominance rank and reproductive success, we conclude that the gorilla chest beat is an honest signal of competitive ability. These results emphasize the potential of non-vocal signals to convey important information in mammal communication.

Primate phageomes are structured by superhost phylogeny and environment.

Humans harbor diverse communities of microorganisms, the majority of which are bacteria in the gastrointestinal tract. These gut bacterial communities in turn host diverse bacteriophage (hereafter phage) communities that have a major impact on their structure, function, and, ultimately, human health. However, the evolutionary and ecological origins of these human-associated phage communities are poorly understood. To address this question, we examined fecal phageomes of 23 wild nonhuman primate taxa, including multiple representatives of all the major primate radiations. We find relatives of the majority of human-associated phages in wild primates. Primate taxa have distinct phageome compositions that exhibit a clear phylosymbiotic signal, and phage-superhost codivergence is often detected for individual phages. Within species, neighboring social groups harbor compositionally and evolutionarily distinct phageomes, which are structured by superhost social behavior. Captive nonhuman primate phageome composition is intermediate between that of their wild counterparts and humans. Phage phylogenies reveal replacement of wild great ape-associated phages with human-associated ones in captivity and, surprisingly, show no signal for the persistence of wild-associated phages in captivity. Together, our results suggest that potentially labile primate-phage associations have persisted across millions of years of evolution. Across primates, these phylosymbiotic and sometimes codiverging phage communities are shaped by transmission between groupmates through grooming and are dramatically modified when primates are moved into captivity.

A deepening understanding of animal culture suggests lessons for conservation.

A key goal of conservation is to protect biodiversity by supporting the long-term persistence of viable, natural populations of wild species. Conservation practice has long been guided by genetic, ecological and demographic indicators of risk. Emerging evidence of animal culture across diverse taxa and its role as a driver of evolutionary diversification, population structure and demographic processes may be essential for augmenting these conventional conservation approaches and decision-making. Animal culture was the focus of a ground-breaking resolution under the Convention on the Conservation of Migratory Species of Wild Animals (CMS), an international treaty operating under the UN Environment Programme. Here, we synthesize existing evidence to demonstrate how social learning and animal culture interact with processes important to conservation management. Specifically, we explore how social learning might influence population viability and be an important resource in response to anthropogenic change, and provide examples of how it can result in phenotypically distinct units with different, socially learnt behavioural strategies. While identifying culture and social learning can be challenging, indirect identification and parsimonious inferences may be informative. Finally, we identify relevant methodologies and provide a framework for viewing behavioural data through a cultural lens which might provide new insights for conservation management.

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.

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.

Variability of weaning age in mountain gorillas (Gorilla beringei beringei).

OBJECTIVES: Weaning is a key life history milestone for mammals that represents both the end of nutritional investment from the perspective of mothers and the start of complete nutritional independence for the infants. The age at weaning may vary depending on ecological, social, and demographic factors experienced by the mother and infant. Bwindi mountain gorillas live in different environmental conditions and have longer interbirth intervals than their counterparts in the Virunga Volcanoes, yet other life history characteristics of this population remain less well known. We use long-term data from Bwindi Impenetrable National Park, Uganda to examine factors related to weaning age. MATERIALS AND METHODS: We analyzed data on infants born in four mountain gorilla groups in Bwindi to quantify their age of weaning (defined as last nipple contact) and to test if the sex of offspring, parity, and dominance rank of mother influences age of weaning. We also compared the age at weaning and time to conception after resumption of mating in Bwindi and Virunga gorillas. RESULTS: Bwindi gorillas were weaned at an average age of 57.5 months. No difference was found between age of weaning for primiparous and multiparous mothers, nor did maternal dominance rank influence age of weaning, but sons were weaned at a later age than daughters. The majority of Bwindi mothers were still suckling when they resumed mating and mothers generally conceived before they weaned their previous offspring. The age of weaning was significantly later in Bwindi than in Virunga gorillas. After mothers resumed mating, the time to conceiving the next offspring was not significantly longer for Bwindi females than Virungas females (6 vs. 4 months). DISCUSSION: Later weaning age for sons than daughters is similar to findings of other studies of great apes. Bwindi mountain gorillas are weaned at approximately the same age as western gorillas and chimpanzees, which is more than a year later than Virunga mountain gorillas. The results of this study suggest that variation in ecological conditions of populations living in close geographic proximity can result in variation in life history patterns, which has implications for understanding the evolution of the unique life history patterns of humans.

Assessing attitudes towards gorilla conservation via employee interviews.

To determine the effectiveness of conservation strategies, not only should we monitor biological variables, such as population size and levels of illegal activity, but also we should examine changes in attitudes and behavior of local community members. Here, I use semistructured interviews of employees at two field sites, in Bwindi Impenetrable National Park, Uganda and Loango National Park, Gabon, to understand if their employment influenced their attitude towards gorillas and conservation and led to behavior change. In contrast to western views of gorillas as "gentle giants," staff viewed gorillas as dangerous animals before working for these projects. Overall, employment leads to viewing conservation and gorillas more positively, and in many cases, viewing the gorillas as kin. The most common value attributed to the gorillas was economic, yet intrinsic and non-use existence values were frequently mentioned. Loango staff, but not Bwindi staff, reported behavior change related to hunting and bushmeat consumption, which likely is related to bushmeat consumption being commonplace in Gabon but not in Uganda. The Bwindi staff seemed to have a more positive and broader outlook toward conservation than the Loango staff, possibly because they had more years of formal education, they worked with gorillas longer, there is more history of conservation activities in Bwindi, and/or they have been less directly affected by negative consequences of conservation (e.g., crop raiding). This study shows the importance of explaining that gorillas are not dangerous if not provoked and using their human-like characteristics as a means to change conservation values and interest of local communities, while concurrently recognizing that providing economic benefits and reducing negative effects of wildlife are a reality for conservation buy-in.

Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments.

Noninvasive samples as a source of DNA are gaining interest in genomic studies of endangered species. However, their complex nature and low endogenous DNA content hamper the recovery of good quality data. Target capture has become a productive method to enrich the endogenous fraction of noninvasive samples, such as faeces, but its sensitivity has not yet been extensively studied. Coping with faecal samples with an endogenous DNA content below 1% is a common problem when prior selection of samples from a large collection is not possible. However, samples classified as unfavourable for target capture sequencing might be the only representatives of unique specific geographical locations, or to answer the question of interest. To explore how library complexity may be increased without repeating DNA extractions and generating new libraries, in this study we captured the exome of 60 chimpanzees (Pan troglodytes) using faecal samples with very low proportions of endogenous content (<1%). Our results indicate that by performing additional hybridizations of the same libraries, the molecular complexity can be maintained to achieve higher coverage. Also, whenever possible, the starting DNA material for capture should be increased. Finally, we specifically calculated the sequencing effort needed to avoid exhausting the library complexity of enriched faecal samples with low endogenous DNA content. This study provides guidelines, schemes and tools for laboratories facing the challenges of working with noninvasive samples containing extremely low amounts of endogenous DNA.

An exploration of Menzerath's law in wild mountain gorilla vocal sequences.

Menzerath's law, traditionally framed as a negative relationship between the size of a structure and its constituent parts (e.g. sentences with more clauses have shorter clauses), is widespread across information-coding systems ranging from human language and the vocal and gestural sequences of primates and birds, to the building blocks of DNA, genes and proteins. Here, we analysed an extensive dataset of 'close-call' sequences produced by wild mountain gorillas (Gorilla beringei beringei, no. individuals = 10, no. sequences = 2189) to determine whether, in accordance with Menzerath's law, a negative relationship existed between the number of vocal units in a sequence and the duration of its constituent units. We initially found positive evidence for this but, on closer inspection, the negative relationship was driven entirely by the difference between single- and multi-unit (two to six unit) sequences. Once single-unit sequences were excluded from the analysis, we identified a relationship in the opposite direction, with longer sequences generally composed of longer units. The close-call sequences of mountain gorillas therefore represent an intriguing example of a non-human vocal system that only partially conforms to the predictions of Menzerath's law.