It is about time: Conceptual and experimental evaluation of the temporal cognitive mechanisms in mental time travel

Mental time travel (MTT) is the ability that allows humans to mentally project themselves backwards in time to remember past events (i.e., episodic memory) or forwards in time to imagine future events (i.e., future thinking). Despite empirical evidence showing that animals might possess MTT abilities, some still claim that this ability is uniquely human. Recent debates have suggested that it is the temporal cognitive mechanism (i.e., ability to represent the sense of past and future) that makes MTT uniquely human. Advances in the field have been constrained by a lack of comparative data, methodological shortcomings that prevent meaningful comparisons, and a lack of clear conceptualizations of the temporal cognitive mechanism. Here I will present a comprehensive review into MTT in humans and animals-with a particular focus on great apes. I will examine three of the most prominent and influential theoretical models of human MTT. Drawing on these accounts, I suggest that a basic way of understanding time might be shared across species, however culture and language will play a critical role at shaping the way we elaborate mental representations about past and future events. This article is categorized under: Cognitive Biology > Evolutionary Roots of Cognition Psychology > Comparative Psychology.

Implicit Measures Help Demonstrate the Value of Conservation Education in the Democratic Republic of the Congo

Biodiversity is being lost at unprecedented rates. Limited conservation resources must be prioritized strategically to maximize impact. Here we introduce novel methods to assess a small-scale conservation education program in the Democratic Republic of Congo. Lola ya Bonobo is the world's only sanctuary for one of humans' two closest living relatives, bonobos, orphaned by the illegal trade in bushmeat and exotic pets. The sanctuary is situated on the edge of the country's capital, Kinshasa, its most densely populated region and a hub for the illegal wildlife trade that is imperiling bonobos and other endangered species. Lola ya Bonobo implements an education program specifically designed to combat this trade. Previous evaluation demonstrated the program's efficacy in transmitting conservation knowledge to children. In Study 1, we use novel implicit tests to measure conservation attitudes before and after an educational visit and document a significant increase in children's pro-conservation attitudes following direct exposure to bonobos and the education program. In Study 2, we show that adults exhibit high levels of conservation knowledge even before visiting the sanctuary, likely due to the sanctuary's longstanding education efforts in Kinshasa. In Study 3, we explored adults' empathetic attitudes toward bonobos before and after the sanctuary tour. Our results support the conservation education hypothesis that conservation education has improved relevant knowledge and attitudes in Kinshasa. Crucially, the present study validates new methods for implicitly assessing attitudes about environmental and social issues. These methods overcome typical biases in survey sampling and can be employed in diverse populations, including those with low literacy rates.

Understanding Language Evolution: Beyond Pan-Centrism

Language does not fossilize but this does not mean that the language's evolutionary timeline is lost forever. Great apes provide a window back in time on our last prelinguistic ancestor's communication and cognition. Phylogeny and cladistics implicitly conjure Pan (chimpanzees, bonobos) as a superior (often the only) model for language evolution compared with earlier diverging lineages, Gorilla and Pongo (orangutans). Here, in reviewing the literature, it is shown that Pan do not surpass other great apes along genetic, cognitive, ecologic, or vocal traits that are putatively paramount for language onset and evolution. Instead, revived herein is the idea that only by abandoning single-species models and learning about the variation among great apes, there might be a chance to retrieve lost fragments of the evolutionary timeline of language.

THE USE OF CITALOPRAM HYDROBROMIDE TO MANAGE AGGRESSION IN A MALE CHIMPANZEE (PAN TROGLODYTES)

At times severe, and occasionally fatal, aggression plays an intrinsic role in chimpanzee behavior and social dynamics, particularly among male chimpanzees in both managed and free-ranging troops. At the Los Angeles Zoo, one adult male's natural aggressive behavior developed into unmanageable violence during a period of social and emotional instability consequent to the lack of an established alpha male in the colony. The severity and duration of resulting attacks on a subdominant member of the community, despite environmental and behavioral modification, indicated the need for psychopharmaceutical intervention. Prior treatment of this animal with haloperidol and gabapentin had produced undesirable side effects. Administration of citalopram hydrobromide, a selective serotonin reuptake inhibitor, successfully reduced both the intensity and duration of this male chimpanzee's attacks upon a conspecific animal with minimal observable side effects or adverse behavioral changes.

Impact of Mutation Rate and Selection at Linked Sites on DNA Variation across the Genomes of Humans and Other Homininae

DNA diversity varies across the genome of many species. Variation in diversity across a genome might arise from regional variation in the mutation rate, variation in the intensity and mode of natural selection, and regional variation in the recombination rate. We show that both noncoding and nonsynonymous diversity are positively correlated to a measure of the mutation rate and the recombination rate and negatively correlated to the density of conserved sequences in 50 kb windows across the genomes of humans and nonhuman homininae. Interestingly, we find that although noncoding diversity is equally affected by these three genomic variables, nonsynonymous diversity is mostly dominated by the density of conserved sequences. The positive correlation between diversity and our measure of the mutation rate seems to be largely a direct consequence of regions with higher mutation rates having more diversity. However, the positive correlation with recombination rate and the negative correlation with the density of conserved sequences suggest that selection at linked sites also affect levels of diversity. This is supported by the observation that the ratio of the number of nonsynonymous to noncoding polymorphisms is negatively correlated to a measure of the effective population size across the genome. We show these patterns persist even when we restrict our analysis to GC-conservative mutations, demonstrating that the patterns are not driven by GC biased gene conversion. In conclusion, our comparative analyses describe how recombination rate, gene density, and mutation rate interact to produce the patterns of DNA diversity that we observe along the hominine genomes.

Quantifying GC-Biased Gene Conversion in Great Ape Genomes Using Polymorphism-Aware Models

As multi-individual population-scale data become available, more complex modeling strategies are needed to quantify genome-wide patterns of nucleotide usage and associated mechanisms of evolution. Recently, the multivariate neutral Moran model was proposed. However, it was shown insufficient to explain the distribution of alleles in great apes. Here, we propose a new model that includes allelic selection. Our theoretical results constitute the basis of a new Bayesian framework to estimate mutation rates and selection coefficients from population data. We apply the new framework to a great ape dataset, where we found patterns of allelic selection that match those of genome-wide GC-biased gene conversion (gBGC). In particular, we show that great apes have patterns of allelic selection that vary in intensity-a feature that we correlated with great apes' distinct demographies. We also demonstrate that the AT/GC toggling effect decreases the probability of a substitution, promoting more polymorphisms in the base composition of great ape genomes. We further assess the impact of GC-bias in molecular analysis, and find that mutation rates and genetic distances are estimated under bias when gBGC is not properly accounted for. Our results contribute to the discussion on the tempo and mode of gBGC evolution, while stressing the need for gBGC-aware models in population genetics and phylogenetics.

Humans and Chimpanzees Display Opposite Patterns of Diversity in Arylamine N-Acetyltransferase Genes

Among the many genes involved in the metabolism of therapeutic drugs, human arylamine N-acetyltransferases (NATs) genes have been extensively studied, due to their medical importance both in pharmacogenetics and disease epidemiology. One member of this small gene family, NAT2, is established as the locus of the classic human acetylation polymorphism in drug metabolism. Current hypotheses hold that selective processes favoring haplotypes conferring lower NAT2 activity have been operating in modern humans’ recent history as an adaptation to local chemical and dietary environments. To shed new light on such hypotheses, we investigated the genetic diversity of the three members of the NAT gene family in seven hominid species, including modern humans, Neanderthals and Denisovans. Little polymorphism sharing was found among hominids, yet all species displayed high NAT diversity, but distributed in an opposite fashion in chimpanzees and bonobos (Pan genus) compared to modern humans, with higher diversity in Pan species at NAT1 and lower at NAT2, while the reverse is observed in humans. This pattern was also reflected in the results returned by selective neutrality tests, which suggest, in agreement with the predicted functional impact of mutations detected in non-human primates, stronger directional selection, presumably purifying selection, at NAT1 in modern humans, and at NAT2 in chimpanzees. Overall, the results point to the evolution of divergent functions of these highly homologous genes in the different primate species, possibly related to their specific chemical/dietary environment (exposome) and we hypothesize that this is likely linked to the emergence of controlled fire use in the human lineage.

Implanted Radio Telemetry in Orangutan Reintroduction and Post-release Monitoring and its Application in Other Ape Species

Designed as a new method to facilitate the reintroduction and post-release monitoring of orangutans and other apes, implanted radio-telemetry (IRT) was developed and first deployed in 2009. Since that time, it has been necessary to collate and review information on its uptake and general efficacy to inform its ongoing development and that of other emerging tracking technologies. We present here technical specifications and the surgical procedure used to implant miniaturized radio transmitters, as well as a formal testing procedure for measuring detectable transmission distances of implanted devices. Feedback from IRT practitioners (veterinarians and field managers) was gathered through questionnaires and is also presented. To date, IRT has been used in at least 250 individual animals (mainly orangutans) from four species of ape in both Asia and Africa. Median surgical and wound healing times were 30 min and 15 days, respectively, with implants needing to be removed on at least 36 separate occasions. Confirmed failures within the first year of operation were 18.1%, while longer distances were reported from positions of higher elevation relative to the focal animal. IRT has been a transformational technology in facilitating the relocation of apes after their release, resulting in much larger amounts of post-release data collection than ever before. It is crucial however, that implant casings are strengthened to prevent the requirement for recapture and removal surgeries, especially for gradually adapting apes. As with all emerging technological solutions, IRT carries with it inherent risk, especially so due to the requirement for subcutaneous implantation. These risks must, however, be balanced with the realities of releasing an animal with no means of relocation, as has historically been, and is still, the case with orangutans and gorillas.

Infant handling by female mountain gorillas: Establishing its frequency, function, and (ir)relevance for life history evolution

OBJECTIVES

Infant handling describes cases in which youngsters are temporarily removed from the care of their mothers and "taken care of" (held, carried, etc.) by other conspecifics. Handlers may gain indirect fitness benefits from these actions and can practice mothering skills, thereby improving the odds of survival of their own infants. Great apes are notable for displaying little infant handling. Apart from anecdotal observations, no published data exist on infant handling in wild mountain gorillas. We tested two of the most pertinent explanations ("kin selection" and "learning to mother") in a wild population of mountain gorillas in Rwanda. We predicted that (a) nulliparous females would exhibit infant handling (i.e., carrying) more than parous females and (b) maternal kin would exhibit more infant handling than nonkin.

METHODS

We collated 8 years of data on infant carrying behavior collected in 13 groups monitored by the Dian Fossey Gorilla Fund's Karisoke Research Center.

RESULTS

Infant handling is an infrequent behavior (1,783 instances over 25,600 observation hours). A strong positive effect of relatedness and handler parity on the frequency of infant handling emerged.

CONCLUSIONS

While the nature of handler-infant interactions (affiliative, abusive, etc.) remains unstudied, they could constitute alloparental care and could therefore attenuate maternal energetic burden and ultimately allow increased birth rates. However, the rarity of this behavior makes it an unlikely contributor to mountain gorillas' relatively short interbirth intervals.

Differences in novel food response between Pongo and Pan

The diversity of great ape diets requires behavioral flexibility. Consequently, the exploration of potentially novel food sources is supposedly beneficial, but simultaneously, apes show high neophobia to prevent harmful and poisonous food intake. Social information, such as presence of group members or observations of non-naïve, experienced individuals have been demonstrated to affect the acceptance of novel food items in primates. Sociality may have evolutionary effects on the response of apes to novel foods. Here we assess the social information hypothesis, which predicts that selection favors higher neophobia in species where social information is abundant. We report the results from 134 great apes housed in multiple facilities from four closely related species that naturally differ in their degree of sociality: Pongo pygmaeus, Pongo abelii, Pan troglodytes and Pan paniscus. We examined individuals' reactions to novel foods when alone, which enabled us to detect any inherent differences and revealed significant distinctions between species. Chimpanzees and bonobos, that are naturally exposed to higher amounts of social information, were less likely to consume novel foods alone (showed higher neophobia) than the two more solitary orangutan species. Chimpanzees were especially cautious and showed higher explorative behaviors before tasting novel food than other species. Age influenced neophobia as younger individuals of all species took longer to taste novel foods than adults did.

Sleep and nesting behavior in primates: A review

Sleep is a universal behavior in vertebrate and invertebrate animals, suggesting it originated in the very first life forms. Given the vital function of sleep, sleeping patterns and sleep architecture follow dynamic and adaptive processes reflecting trade-offs to different selective pressures. Here, we review responses in sleep and sleep-related behavior to environmental constraints across primate species, focusing on the role of great ape nest building in hominid evolution. We summarize and synthesize major hypotheses explaining the proximate and ultimate functions of great ape nest building across all species and subspecies; we draw on 46 original studies published between 2000 and 2017. In addition, we integrate the most recent data brought together by researchers from a complementary range of disciplines in the frame of the symposium "Burning the midnight oil" held at the 26th Congress of the International Primatological Society, Chicago, August 2016, as well as some additional contributors, each of which is included as a "stand-alone" article in this "Primate Sleep" symposium set. In doing so, we present crucial factors to be considered in describing scenarios of human sleep evolution: (a) the implications of nest construction for sleep quality and cognition; (b) the tree-to-ground transition in early hominids; (c) the peculiarities of human sleep. We propose bridging disciplines such as neurobiology, endocrinology, medicine, and evolutionary ecology, so that future research may disentangle the major functions of sleep in human and nonhuman primates, namely its role in energy allocation, health, and cognition.

Evolutionary history of human Plasmodium vivax revealed by genome-wide analyses of related ape parasites

Wild-living African apes are endemically infected with parasites that are closely related to human Plasmodium vivax, a leading cause of malaria outside Africa. This finding suggests that the origin of P. vivax was in Africa, even though the parasite is now rare in humans there. To elucidate the emergence of human P. vivax and its relationship to the ape parasites, we analyzed genome sequence data of P. vivax strains infecting six chimpanzees and one gorilla from Cameroon, Gabon, and Côte d'Ivoire. We found that ape and human parasites share nearly identical core genomes, differing by only 2% of coding sequences. However, compared with the ape parasites, human strains of P. vivax exhibit about 10-fold less diversity and have a relative excess of nonsynonymous nucleotide polymorphisms, with site-frequency spectra suggesting they are subject to greatly relaxed purifying selection. These data suggest that human P. vivax has undergone an extreme bottleneck, followed by rapid population expansion. Investigating potential host-specificity determinants, we found that ape P. vivax parasites encode intact orthologs of three reticulocyte-binding protein genes (rbp2d, rbp2e, and rbp3), which are pseudogenes in all human P. vivax strains. However, binding studies of recombinant RBP2e and RBP3 proteins to human, chimpanzee, and gorilla erythrocytes revealed no evidence of host-specific barriers to red blood cell invasion. These data suggest that, from an ancient stock of P. vivax parasites capable of infecting both humans and apes, a severely bottlenecked lineage emerged out of Africa and underwent rapid population growth as it spread globally.

Studies of nonhuman primates: key sources of data on zoonoses and microbiota

The genetic and morphologic similarities between primates and humans means that much information obtained from primates may be applied to humans, and vice versa. However, habitat loss, hunting and the continued presence of humans have a negative effect on the biology and behaviour of almost all nonhuman primates. Noninvasive methods such as stool collection are among the safest alternative ways to study the multiple aspects of the biology of primates. Many epidemiologic issues (e.g. pathogen detection, microbiota studies) may be easily studied using stool samples from primates. Primates are undoubtedly among the first candidates suspected of becoming the source of one of the next emerging epidemic of zoonotic origin, as has already been observed with HIV, malaria and monkeypox. The Institut Hospitalo-Universitaire Méditerranée Infection in Marseille actively participates in the study, mostly epidemiologic, of nonhuman primates, using mostly stool samples.

Chimpanzees Consider Humans' Psychological States when Drawing Statistical Inferences

Great apes have been shown to be intuitive statisticians: they can use proportional information within a population to make intuitive probability judgments about randomly drawn samples [1, J.E., J.C., J.H., E.H., and H.R., unpublished data]. Humans, from early infancy onward, functionally integrate intuitive statistics with other cognitive domains to judge the randomness of an event [2-6]. To date, nothing is known about such cross-domain integration in any nonhuman animal, leaving uncertainty about the origins of human statistical abilities. We investigated whether chimpanzees take into account information about psychological states of experimenters (their biases and visual access) when drawing statistical inferences. We tested 21 sanctuary-living chimpanzees in a previously established paradigm that required subjects to infer which of two mixed populations of preferred and non-preferred food items was more likely to lead to a desired outcome for the subject. In a series of three experiments, we found that chimpanzees chose based on proportional information alone when they had no information about experimenters' preferences and (to a lesser extent) when experimenters had biases for certain food types but drew blindly. By contrast, when biased experimenters had visual access, subjects ignored statistical information and instead chose based on experimenters' biases. Lastly, chimpanzees intuitively used a violation of statistical likelihoods as indication for biased sampling. Our results suggest that chimpanzees have a random sampling assumption that can be overridden under the appropriate circumstances and that they are able to use mental state information to judge whether this is necessary. This provides further evidence for a shared statistical inference mechanism in apes and humans.

Multivariate analysis of variations in intrinsic foot musculature among hominoids

Comparative analysis of the foot muscle architecture among extant great apes is important for understanding the evolution of the human foot and, hence, human habitual bipedal walking. However, to our knowledge, there is no previous report of a quantitative comparison of hominoid intrinsic foot muscle dimensions. In the present study, we quantitatively compared muscle dimensions of the hominoid foot by means of multivariate analysis. The foot muscle mass and physiological cross-sectional area (PCSA) of five chimpanzees, one bonobo, two gorillas, and six orangutans were obtained by our own dissections, and those of humans were taken from published accounts. The muscle mass and PCSA were respectively divided by the total mass and total PCSA of the intrinsic muscles of the entire foot for normalization. Variations in muscle architecture among human and extant great apes were quantified based on principal component analysis. Our results demonstrated that the muscle architecture of the orangutan was the most distinctive, having a larger first dorsal interosseous muscle and smaller abductor hallucis brevis muscle. On the other hand, the gorilla was found to be unique in having a larger abductor digiti minimi muscle. Humans were distinguished from extant great apes by a larger quadratus plantae muscle. The chimpanzee and the bonobo appeared to have very similar muscle architecture, with an intermediate position between the human and the orangutan. These differences (or similarities) in architecture of the intrinsic foot muscles among humans and great apes correspond well to the differences in phylogeny, positional behavior, and locomotion.

Using geometric morphometric visualizations of directional selection gradients to investigate morphological differentiation

Researchers studying extant and extinct taxa are often interested in identifying the evolutionary processes that have lead to the morphological differences among the taxa. Ideally, one could distinguish the influences of neutral evolutionary processes (genetic drift, mutation) from natural selection, and in situations for which selection is implicated, identify the targets of selection. The directional selection gradient is an effective tool for investigating evolutionary process, because it can relate form (size and shape) differences between taxa to the variation and covariation found within taxa. However, although most modern morphometric analyses use the tools of geometric morphometrics (GM) to analyze landmark data, to date, selection gradients have mainly been calculated from linear measurements. To address this methodological gap, here we present a GM approach for visualizing and comparing between-taxon selection gradients with each other, associated difference vectors, and "selection" gradients from neutral simulations. To exemplify our approach, we use a dataset of 347 three-dimensional landmarks and semilandmarks recorded on the crania of 260 primate specimens (112 humans, 67 common chimpanzees, 36 bonobos, 45 gorillas). Results on this example dataset show how incorporating geometric information can provide important insights into the evolution of the human braincase, and serve to demonstrate the utility of our approach for understanding morphological evolution.

Comparing physical and social cognitive skills in macaque species with different degrees of social tolerance

Contemporary evolutionary theories propose that living in groups drives the selection of enhanced cognitive skills to face competition and facilitate cooperation between individuals. Being able to coordinate both in space and time with others and make strategic decisions are essential skills for cooperating within groups. Social tolerance and an egalitarian social structure have been proposed as one specific driver of cooperation. Therefore, social tolerance is predicted to be associated with enhanced cognitive skills that underpin communication and coordination. Social tolerance should also be associated with enhanced inhibition, which is crucial for suppressing automatic responses and permitting delayed gratification in cooperative contexts. We tested the performance of four closely related non-human primate species (genus Macaca) characterized by different degrees of social tolerance on a large battery of cognitive tasks covering physical and social cognition, and on an inhibitory control task. All species performed at a comparable level on the physical cognition tasks but the more tolerant species outperformed the less tolerant species at a social cognition task relevant to cooperation and in the inhibitory control task. These findings support the hypothesis that social tolerance is associated with the evolution of sophisticated cognitive skills relevant for cooperative social living.

Early Socioemotional Intervention Mediates Long-Term Effects of Atypical Rearing on Structural Covariation in Gray Matter in Adult Chimpanzees

Atypical rearing has deleterious effects on chimpanzee behavior during development, some of which can be ameliorated with a responsive care intervention (RCI). Here, we obtained in vivo magnetic resonance images of adult brains of 27 chimpanzees given institutional care, with and without RCI, and compared them with those of 16 chimpanzees mother-reared from birth. We found significant long-term rearing effects on structural covariation and gray matter volume, specifically in the basal forebrain (i.e., caudate, putamen, nucleus accumbens, rectus gyrus, and orbital prefrontal cortex), indicating that RCI prevented brain changes due to atypical rearing. A significant correlation between covariation in these brain areas and caregiver nurturing, experienced in the first month of life, suggests a possible developmental mechanism for the effect of early experience on brain networks. We identified an early intervention that prevents changes in the basal forebrain that otherwise emerge as a consequence of institutionalized rearing without species-typical socioemotional experiences.

Incremental distribution of strontium and zinc in great ape and fossil hominin cementum using synchrotron X-ray fluorescence mapping

Cementum and the incremental markings it contains have been widely studied as a means of ageing animals and retrieving information about diet and nutrition. The distribution of trace elements in great ape and fossil hominin cementum has not been studied previously. Synchrotron X-ray fluorescence (SXRF) enables rapid scanning of large tissue areas with high resolution of elemental distributions. First, we used SXRF to map calcium, phosphorus, strontium and zinc distributions in great ape dentine and cementum. At higher resolution, we compared zinc and strontium distributions in cellular and acellular cementum in regions where clear incremental markings were expressed. We then mapped trace element distributions in fossil hominin dentine and cementum from the 1.55-1.65 million year old site of Koobi Fora, Kenya. Zinc, in particular, is a precise marker of cementum increments in great apes, and is retained in fossil hominin cementum, but does not correspond well with the more diffuse fluctuations observed in strontium distribution. Cementum is unusual among mineralized tissues in retaining so much zinc. This is known to reduce the acid solubility of hydroxyapatite and so may confer resistance to resorption by osteoclasts in the dynamic remodelling environment of the periodontal ligament and alveolar bone.

Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species

Six extant species of non-human great apes are currently recognized: Sumatran and Bornean orangutans, eastern and western gorillas, and chimpanzees and bonobos [1]. However, large gaps remain in our knowledge of fine-scale variation in hominoid morphology, behavior, and genetics, and aspects of great ape taxonomy remain in flux. This is particularly true for orangutans (genus: Pongo), the only Asian great apes and phylogenetically our most distant relatives among extant hominids [1]. Designation of Bornean and Sumatran orangutans, P. pygmaeus (Linnaeus 1760) and P. abelii (Lesson 1827), as distinct species occurred in 2001 [1, 2]. Here, we show that an isolated population from Batang Toru, at the southernmost range limit of extant Sumatran orangutans south of Lake Toba, is distinct from other northern Sumatran and Bornean populations. By comparing cranio-mandibular and dental characters of an orangutan killed in a human-animal conflict to those of 33 adult male orangutans of a similar developmental stage, we found consistent differences between the Batang Toru individual and other extant Ponginae. Our analyses of 37 orangutan genomes provided a second line of evidence. Model-based approaches revealed that the deepest split in the evolutionary history of extant orangutans occurred ∼3.38 mya between the Batang Toru population and those to the north of Lake Toba, whereas both currently recognized species separated much later, about 674 kya. Our combined analyses support a new classification of orangutans into three extant species. The new species, Pongo tapanuliensis, encompasses the Batang Toru population, of which fewer than 800 individuals survive. VIDEO ABSTRACT.

Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data

Understanding when species diverged aids in identifying the drivers of speciation, but the end of gene flow between populations can be difficult to ascertain from genetic data. We explore the use of pairwise sequential Markovian coalescent (PSMC) modelling to infer the timing of divergence between species and populations. PSMC plots generated using artificial hybrid genomes show rapid increases in effective population size at the time when the two parent lineages diverge, and this approach has been used previously to infer divergence between human lineages. We show that, even without high coverage or phased input data, PSMC can detect the end of significant gene flow between populations by comparing the PSMC output from artificial hybrids to the output of simulations with known demographic histories. We then apply PSMC to detect divergence times among lineages within two real datasets: great apes and bears within the genus Ursus Our results confirm most previously proposed divergence times for these lineages, and suggest that gene flow between recently diverged lineages may have been common among bears and great apes, including up to one million years of continued gene flow between chimpanzees and bonobos after the formation of the Congo River.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.

Non-goal-directed recall of specific events in apes after long delays

We examined if apes spontaneously remember one-time, distinctive events across long delays when probed by discriminant cues. Apes witnessed an experimenter hide a cache of food, which they could then retrieve. They retrieved one of two food types; one more distinctive than the other. Two, 10 or 50 weeks later, the apes returned to the same enclosure and found a piece of the previously hidden food on the ground. An experimenter who had not hidden the food was also present. Apes immediately searched the location where the food was previously hidden (no food was here), showing recall of the event. One week later, apes returned to the same enclosure, with the same food on the ground, but now the experimenter that had hidden the food was present. Again, apes immediately searched the hiding location. Apes that had not witnessed the hiding event did not search. There was no significant effect of food type, and retention declined from exposure to the two-week delay, then levelled, consistent with the forgetting curve in humans (Ebbinghaus, H. 1964 Memory: a contribution to experimental psychology (transl. H.A. Ruger & C.E. Bussenvis). New York, NY: Dover. (Original work published 1885.)). This is the first study to show apes can recall a one-time, non-goal-directed event longer than two weeks ago and that apes' recall declines in accordance with a standard retention function.

Hepatic expression of cytochrome P450 enzymes in non-human primate species

Cytochromes P450 (P450) largely remain to be characterized in great apes. Comparative immunochemical detection of drug metabolizing forms of P450s 1A, 2A, 2B, 2C, 2D, 2E, 2J, 3A, 4A, and 4F in liver microsomes from chimpanzees, gorillas, orangutans, gibbons, cynomolgus and rhesus macaques, and common marmosets were carried out.

Unexplored Archaeal Diversity in the Great Ape Gut Microbiome

Our findings show that Archaea are a habitual and vital component of human and great ape gut microbiomes but are largely ignored on account of the failure of previous studies to realize their full diversity. Here we report unprecedented levels of archaeal diversity in great ape gut microbiomes, exceeding that detected by conventional 16S rRNA gene surveys. Paralleling what has been reported for bacteria, there is a vast reduction of archaeal diversity in humans. Our study demonstrates that archaeal diversity in the great ape gut microbiome greatly exceeds that reported previously and provides the basis for further studies on the role of archaea in the gut microbiome.

Archaea are habitual residents of the human gut flora but are detected at substantially lower frequencies than bacteria. Previous studies have indicated that each human harbors very few archaeal species. However, the low diversity of human-associated archaea that has been detected could be due to the preponderance of bacteria in these communities, such that relatively few sequences are classified as Archaea even when microbiomes are sampled deeply. Moreover, the universal prokaryotic primer pair typically used to interrogate microbial diversity has low specificity to the archaeal domain, potentially leaving vast amounts of diversity unobserved. As a result, the prevalence, diversity, and distribution of archaea may be substantially underestimated. Here we evaluate archaeal diversity in gut microbiomes using an approach that targets virtually all known members of this domain. Comparing microbiomes across five great ape species allowed us to examine the dynamics of archaeal lineages over evolutionary time scales. These analyses revealed hundreds of gut-associated archaeal lineages, indicating that upwards of 90% of the archaeal diversity in the human and great ape gut microbiomes has been overlooked. Additionally, these results indicate a progressive reduction in archaeal diversity in the human lineage, paralleling the decline reported for bacteria.

IMPORTANCE Our findings show that Archaea are a habitual and vital component of human and great ape gut microbiomes but are largely ignored on account of the failure of previous studies to realize their full diversity. Here we report unprecedented levels of archaeal diversity in great ape gut microbiomes, exceeding that detected by conventional 16S rRNA gene surveys. Paralleling what has been reported for bacteria, there is a vast reduction of archaeal diversity in humans. Our study demonstrates that archaeal diversity in the great ape gut microbiome greatly exceeds that reported previously and provides the basis for further studies on the role of archaea in the gut microbiome.