Functional host-specific adaptation of the intestinal microbiome in hominids

Fine-scale knowledge of the changes in composition and function of the human gut microbiome compared that of our closest relatives is critical for understanding the evolutionary processes underlying its developmental trajectory. To infer taxonomic and functional changes in the gut microbiome across hominids at different timescales, we perform high-resolution metagenomic-based analyzes of the fecal microbiome from over two hundred samples including diverse human populations, as well as wild-living chimpanzees, bonobos, and gorillas. We find human-associated taxa depleted within non-human apes and patterns of host-specific gut microbiota, suggesting the widespread acquisition of novel microbial clades along the evolutionary divergence of hosts. In contrast, we reveal multiple lines of evidence for a pervasive loss of diversity in human populations in correlation with a high Human Development Index, including evolutionarily conserved clades. Similarly, patterns of co-phylogeny between microbes and hosts are found to be disrupted in humans. Together with identifying individual microbial taxa and functional adaptations that correlate to host phylogeny, these findings offer insights into specific candidates playing a role in the diverging trajectories of the gut microbiome of hominids. We find that repeated horizontal gene transfer and gene loss, as well as the adaptation to transient microaerobic conditions appear to have played a role in the evolution of the human gut microbiome.

Wild chimpanzees' use of single and combined vocal and gestural signals

ABSTRACT

We describe the individual and combined use of vocalizations and gestures in wild chimpanzees. The rate of gesturing peaked in infancy and, with the exception of the alpha male, decreased again in older age groups, while vocal signals showed the opposite pattern. Although gesture-vocal combinations were relatively rare, they were consistently found in all age groups, especially during affiliative and agonistic interactions. Within behavioural contexts rank (excluding alpha-rank) had no effect on the rate of male chimpanzees' use of vocal or gestural signals and only a small effect on their use of combination signals. The alpha male was an outlier, however, both as a prolific user of gestures and recipient of high levels of vocal and gesture-vocal signals. Persistence in signal use varied with signal type: chimpanzees persisted in use of gestures and gesture-vocal combinations after failure, but where their vocal signals failed they tended to add gestural signals to produce gesture-vocal combinations. Overall, chimpanzees employed signals with a sensitivity to the public/private nature of information, by adjusting their use of signal types according to social context and by taking into account potential out-of-sight audiences. We discuss these findings in relation to the various socio-ecological challenges that chimpanzees are exposed to in their natural forest habitats and the current discussion of multimodal communication in great apes.

SIGNIFICANCE STATEMENT

All animal communication combines different types of signals, including vocalizations, facial expressions, and gestures. However, the study of primate communication has typically focused on the use of signal types in isolation. As a result, we know little on how primates use the full repertoire of signals available to them. Here we present a systematic study on the individual and combined use of gestures and vocalizations in wild chimpanzees. We find that gesturing peaks in infancy and decreases in older age, while vocal signals show the opposite distribution, and patterns of persistence after failure suggest that gestural and vocal signals may encode different types of information. Overall, chimpanzees employed signals with a sensitivity to the public/private nature of information, by adjusting their use of signal types according to social context and by taking into account potential out-of-sight audiences.

Urinary oxytocin and social bonding in related and unrelated wild chimpanzees

Animals that maintain cooperative relationships show gains in longevity and offspring survival. However, little is known about the cognitive or hormonal mechanisms involved in cooperation. Indeed, there is little support for a main hypothesis that non-human animals have the cognitive capacities required for bookkeeping of cooperative exchanges. We tested an alternative hypothesis that cooperative relationships are facilitated by an endocrinological mechanism involving oxytocin, a hormone required for bonding in parental and sexual relationships across mammals. We measured urinary oxytocin after single bouts of grooming in wild chimpanzees. Oxytocin levels were higher after grooming with bond partners compared with non-bond partners or after no grooming, regardless of genetic relatedness or sexual interest. We ruled out other possible confounds, such as grooming duration, grooming direction or sampling regime issues, indicating that changes in oxytocin levels were mediated by social bond strength. Oxytocin, which is thought to act directly on neural reward and social memory systems, is likely to play a key role in keeping track of social interactions with multiple individuals over time. The evolutionary linkage of an ancestral hormonal system with complex social cognition may be the primary mechanism through which long-term cooperative relationships develop between both kin and non-kin in mammals.

The use of fruiting synchrony by foraging mangabey monkeys: a 'simple tool' to find fruit

Previous research has shown that a considerable number of primates can remember the location and fruiting state of individual trees in their home range. This enables them to relocate fruit or predict whether previously encountered fruit has ripened. Recent studies, however, suggest that the ability of primates to cognitively map fruit-bearing trees is limited. In this study, we investigated an alternative and arguably simpler, more efficient strategy, the use of synchrony, a botanical characteristic of a large number of fruit species. Synchronous fruiting would allow the prediction of the fruiting state of a large number of trees without having to first check the trees. We studied whether rainforest primates, grey-cheeked mangabeys in the Kibale National Park, Uganda, used synchrony in fruit emergence to find fruit. We analysed the movements of adult males towards Uvariopsis congensis food trees, a strongly synchronous fruiting species with different local patterns of synchrony. Monkeys approached within crown distance, entered and inspected significantly more Uvariopsis trees when the percentage of trees with ripe fruit was high compared to when it was low. Since the effect was also found for empty trees, the monkeys likely followed a synchrony-based inspection strategy. We found no indication that the monkeys generalised this strategy to all Uvariopsis trees within their home range. Instead, they attended to fruiting peaks in local areas within the home range and adjusted their inspective behaviour accordingly revealing that non-human primates use botanical knowledge in a flexible way.

Causal cognition in a non-human primate: field playback experiments with Diana monkeys

Crested guinea fowls (Guttera pucherani) living in West African rainforests give alarm calls to leopards (Panthera pardus) and sometimes humans (Homo sapiens), two main predators of sympatric Diana monkeys (Cercopithecus diana). When hearing these guinea fowl alarm calls, Diana monkeys respond as if a leopard were present, suggesting that by default the monkeys associate guinea fowl alarm calls with the presence of a leopard. To assess the monkeys' level of causal understanding, I primed monkeys to the presence of either a leopard or a human, before exposing them to playbacks of guinea fowl alarm calls. There were significant differences in the way leopard-primed groups and human-primed groups responded to guinea fowl alarm calls, suggesting that the monkeys' response was not directly driven by the alarm calls themselves but by the calls' underlying cause, i.e. the predator most likely to have caused the calls. Results are discussed with respect to three possible cognitive mechanisms - associative learning, specialized learning programs, and causal reasoning - that could have led to causal knowledge in Diana monkeys.

Referential labelling in Diana monkeys

Animal semantic communication has received considerable theoretical and empirical attention because of its relevance to human language. Advances have been made by studies of alarm-call behaviour in nonhumans. In monkeys, for example, there is evidence that recipients have a fairly sophisticated understanding of a call's meaning; that is, the predator type usually associated with a certain alarm call. Little is known, however, about the mental mechanisms that drive call production in nonhuman primates. In some nonprimate species, it has been found that signallers do not respond to a predator's physical features but instead seem to respond to its relative threat or direction of attack. In these species, therefore, alarm calls do not denote different predator categories but simply reflect different types or levels of danger. Because different predator categories typically impose different types and degrees of threat it is entirely possible that nonhuman primates also respond to threat rather than a predator's category. This study examined how wild Diana monkeys, Cercopithecus diana, of the Taï forest, Ivory Coast, label predation events. By altering playback stimuli and the position of a concealed speaker, I investigated whether Diana monkeys respond with acoustically different alarm calls depending on a predator's (1) distance (close versus far), (2) elevation (above versus below), or (3) category (eagle versus leopard). Analysis of male and female alarm-call behaviour showed that Diana monkeys consistently responded to predator category regardless of immediate threat or direction of attack. Data further suggested that, in addition to predator category, monkeys' alarm calls might also convey information about the predator's distance. Copyright 2000 The Association for the Study of Animal Behaviour.

Interspecies semantic communication in two forest primates

West African Diana monkeys (Cercopithecus diana) and Campbell's monkeys (Cercopithecus campbelli) frequently form mixed-species associations. Males of both species produce acoustically distinct alarm calls to crowned eagles (Stephanoaetus coronalus) and leopards (Panthera pardus), two of their main predators. Field playback experiments were conducted to investigate whether Diana monkeys respond to Campbell's alarm calls and whether they understand the calls' semantic content. Diana monkeys responded to playback of Campbell's leopard or eagle alarm calls as though the original predator were present. In a second experiment, Diana monkeys were primed with either Campbell's eagle or leopard alarm calls and then subsequently probed with the vocalizations of a crowned eagle or a leopard. Results showed that monkeys used the semantic information conveyed by the Campbell's alarm calls to predict the presence of a predator. The data are consistent with the hypothesis that non-human primates are able to use acoustic signals of diverse origin as labels for underlying mental representations.

Causal knowledge of predators' behaviour in wild Diana monkeys

Wild Diana monkeys, Cercopithecus diana, of Taï forest, Ivory Coast, are preyed upon by leopards, Panthera pardus, and chimpanzees, Pan troglodytes. These two predators differ in their main hunting tactic and Diana monkeys attempt to avoid predation with two distinct antipredator strategies: conspicuous alarm-calling behaviour to leopards and silent, cryptic behaviour to chimpanzees. However, the Diana monkeys' choice of the appropriate antipredator strategy is complicated by the fact that chimpanzees themselves also fall prey to leopards. Chimpanzees give loud and conspicuous alarm screams when they detect a leopard. When these chimpanzees' leopard alarm calls were played back to different groups of Diana monkeys, in about half of the cases recipients switched from a chimp-specific cryptic response to a leopard-specific conspicuous response, suggesting that some individuals assumed the presence of a leopard. Groups whose home range was in the core area of the resident chimpanzee community were more likely to respond this way than more peripheral groups, indicating between-group differences in semantic knowledge. In a follow-up experiment, the monkeys' understanding of the chimpanzee alarm calls was further assessed with a prime-probe technique. Monkeys were primed with chimpanzee alarm calls and then, 5 min later, tested with leopard growls to see whether they were able to anticipate the presence of a leopard. Results were consistent with the hypothesis that monkeys responding cryptically to chimpanzee alarm calls did so because they were not able to understand the calls' meaning. Data are discussed with respect to three possible cognitive mechanisms, associative learning, specialized learning programmes, and causal reasoning, that could have led to causal knowledge in some individuals but not others. Copyright 2000 The Association for the Study of Animal Behaviour.