The deep trabecular structure of first metacarpals in extant hominids

OBJECTIVES

Recent studies have associated subarticular trabecular bone distribution in the extant hominid first metacarpal (Mc1) with observed thumb use, to infer fossil hominin thumb use. Here, we analyze the entire Mc1 to test for interspecific differences in: (1) the absolute volume of trabecular volume fraction, (2) the distribution of the deeper trabecular network, and (3) the distribution of trabeculae in the medullary cavity, especially beneath the Mc1 disto-radial flange.

MATERIALS AND METHODS

Trabecular bone was imaged using micro-computed tomography in a sample of Homo sapiens (n = 11), Pan paniscus (n = 10), Pan troglodytes (n = 11), Gorilla gorilla (n = 10) and Pongo sp., (n = 7). Using Canonical Holistic Morphometric Analysis (cHMA), we tested for interspecific differences in the trabecular bone volume fraction (BV/TV) and its relative distribution (rBV/TV) throughout the Mc1, including within the head, medullary cavity, and base.

RESULTS

P. paniscus had the highest, and H. sapiens the lowest, BV/TV relative to other species. rBV/TV distribution statistically distinguished the radial concentrations and lack of medullary trabecular bone in the H. sapiens Mc1 from all other hominids. H. sapiens and, to a lesser extent, G. gorilla also had a significantly higher trabecular volume beneath the disto-radial flange relative to other hominids.

DISCUSSION

These results are consistent with differences in observed thumb use in these species and may also reflect systemic differences in bone volume fraction. The trabecular bone extension into the medullary cavity and concentrations beneath the disto-radial flange may represent crucial biomechanical signals that will aid in the inference of fossil hominin thumb use.

An overview of nutritional factors in the aetiopathogenesis of myocardial fibrosis in great apes

The main cause of mortality in great apes in zoological settings is cardiovascular disease (CVD), affecting all four taxa: chimpanzee (Pan troglodytes), bonobo (Pan paniscus), gorilla (Gorilla spp.) and orangutan (Pongo spp.). Myocardial fibrosis, the most typical histological characterisation of CVD in great apes, is non-specific, making it challenging to understand the aetiopathogenesis. A multifactorial origin of disease is assumed whereby many potential causative factors are directly or indirectly related to the diet, which in wild-living great apes mainly consists of high-fibre, low-carbohydrate and very low-sodium components. Diets of great apes housed in zoological settings are often different compared with the situation in the wild. Moreover, low circulating vitamin D levels have recently been recognised in great apes housed in more northern regions. Evaluation of current supplementation guidelines shows that, despite implementation of different dietary strategies, animals stay vitamin D insufficient. Therefore, recent hypotheses designate vitamin D deficiency as a potential underlying factor in the pathogenesis of myocardial fibrosis. The aim of this literature review is to: (i) examine important differences in nutritional factors between zoological and wild great ape populations; (ii) explain the potential detrimental effects of the highlighted dietary discrepancies on cardiovascular function in great apes; and (iii) elucidate specific nutrition-related pathophysiological mechanisms that may underlie the development of myocardial fibrosis. This information may contribute to understanding the aetiopathogenesis of myocardial fibrosis in great apes and pave the way for future clinical studies and a more preventive approach to great ape CVD management.

Recursive self-embedded vocal motifs in wild orangutans

Recursive procedures that allow placing a vocal signal inside another of a similar kind provide a neuro-computational blueprint for syntax and phonology in spoken language and human song. There are, however, no known vocal sequences among nonhuman primates arranged in self-embedded patterns that evince vocal recursion or potential incipient or evolutionary transitional forms thereof, suggesting a neuro-cognitive transformation exclusive to humans. Here, we uncover that wild flanged male orangutan long calls feature rhythmically isochronous call sequences nested within isochronous call sequences, consistent with two hierarchical strata. Remarkably, three temporally and acoustically distinct call rhythms in the lower stratum were not related to the overarching rhythm at the higher stratum by any low multiples, which suggests that these recursive structures were neither the result of parallel non-hierarchical procedures nor anatomical artifacts of bodily constraints or resonances. Findings represent a case of temporally recursive hominid vocal combinatorics in the absence of syntax, semantics, phonology, or music. Second-order combinatorics, 'sequences within sequences', involving hierarchically organized and cyclically structured vocal sounds in ancient hominids may have preluded the evolution of recursion in modern language-able humans.

Evaluating the Presence of Disgust in Animals

The emotion of disgust in humans is widely considered to represent a continuation of the disease-avoidance behavior ubiquitous in animals. The extent to which analogs of human disgust are evident in nonhuman animals, however, remains unclear. The scant research explicitly investigating disgust in animals has predominantly focused on great apes and suggests that disgust might be present in a highly muted form. In this review, we outline the main approaches to disgust. We then briefly discuss disease-avoidance behavior in nonhuman animals, proposing a set of criteria against which evidence for the presence or absence of disgust in animals can be evaluated. The resultant decision tree takes into account other plausible causes of avoidance and aversion when evaluating whether it is likely that the behavior represents disgust. We apply this decision tree to evaluate evidence of disgust-like behavior (e.g., avoidance of carrion and avoidance of feces-contaminated food) in several examples, including nonhuman great apes. Finally, we consider the large disparity between disgust in humans compared to muted disgust in other great apes, examining the possibility that heightened disgust in humans is a relatively recent cultural acquisition.

Whither dominance? An enduring evolutionary legacy of primate sociality

This article discusses dominance personality dimensions found in primates, particularly in the great apes, and how they compare to dominance in humans. Dominance traits are seen in virtually all primate species, and these dimensions reflect how adept an individual is at ascending within a social hierarchy. Among great apes, dominance is one of the most prominent personality factors but, in humans, dominance is usually modeled as a facet of extraversion. Social, cultural, and cognitive differences between humans and our closest ape relatives are explored, alongside humanity's hierarchical and egalitarian heritage. The basic characteristics of dominance in humans and nonhuman great apes are then described, alongside the similarities and differences between great apes. African apes live in societies each with its own hierarchical organization. Humans were a possible exception for some of our history, but more recently, hierarchies have dominated. The general characteristics of high-dominance humans, particularly those living in industrialized nations, are described. Dominance itself can be subdivided into correlated subfactors: domineering, prestige, and leadership. Various explanations have been posed for why dominance has declined in prominence within human personality factor structures, and several possibilities are evaluated. The value of dominance in personality research is discussed: dominance has links to, for instance, age, sex, aggression, self-esteem, locus of control, stress, health, and multiple socioeconomic status indicators. The piece concludes with recommendations for researchers who wish to assess dominance in personality.

Specimens as individuals: Four interventions and recommendations for great ape skeletal collections research and curation

Extensive discourse surrounds the ethics of human skeletal research and curation, but there has yet to be a similar discussion of the treatment of great ape skeletal remains, despite the clear interest in their ethical treatment when alive. Here we trace the history of apes who were killed and collected for natural history museums during the early 20th century and showcase how the guiding research questions of the colonial era continue to influence scholarship. We discuss best practices for improving industry and academic standards of research on, and the curation of, ape remains. The suggested interventions involve restoring individual identity and narrative to great apes while engaging with contextual reflexivity and decolonial theory. The resulting recommendations include contextualizing the individual, piecing individuals back together, challenging/questioning the captive-wild dichotomy, and collaborative international conversations. Our objective is to encourage a conversation regarding ethical and theoretical considerations in great ape skeletal remains research.

Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes

Y chromosomal ampliconic genes (YAGs) are important for male fertility, as they encode proteins functioning in spermatogenesis. The variation in copy number and expression levels of these multicopy gene families has been studied in great apes; however, the diversity of splicing variants remains unexplored. Here, we deciphered the sequences of polyadenylated transcripts of all nine YAG families (BPY2, CDY, DAZ, HSFY, PRY, RBMY, TSPY, VCY, and XKRY) from testis samples of six great ape species (human, chimpanzee, bonobo, gorilla, Bornean orangutan, and Sumatran orangutan). To achieve this, we enriched YAG transcripts with capture probe hybridization and sequenced them with long (Pacific Biosciences) reads. Our analysis of this data set resulted in several findings. First, we observed evolutionarily conserved alternative splicing patterns for most YAG families except for BPY2 and PRY. Second, our results suggest that BPY2 transcripts and proteins originate from separate genomic regions in bonobo versus human, which is possibly facilitated by acquiring new promoters. Third, our analysis indicates that the PRY gene family, having the highest representation of noncoding transcripts, has been undergoing pseudogenization. Fourth, we have not detected signatures of selection in the five YAG families shared among great apes, even though we identified many species-specific protein-coding transcripts. Fifth, we predicted consensus disorder regions across most gene families and species, which could be used for future investigations of male infertility. Overall, our work illuminates the YAG isoform landscape and provides a genomic resource for future functional studies focusing on infertility phenotypes in humans and critically endangered great apes.

The reconstructed cranium of Pierolapithecus and the evolution of the great ape face

Pierolapithecus catalaunicus (~12 million years ago, northeastern Spain) is key to understanding the mosaic nature of hominid (great ape and human) evolution. Notably, its skeleton indicates that an orthograde (upright) body plan preceded suspensory adaptations in hominid evolution. However, there is ongoing debate about this species, partly because the sole known cranium, preserving a nearly complete face, suffers from taphonomic damage. We 1) carried out a micro computerized tomography (CT) based virtual reconstruction of the Pierolapithecus cranium, 2) assessed its morphological affinities using a series of two-dimensional (2D) and three-dimensional (3D) morphometric analyses, and 3) modeled the evolution of key aspects of ape face form. The reconstruction clarifies many aspects of the facial morphology of Pierolapithecus. Our results indicate that it is most similar to great apes (fossil and extant) in overall face shape and size and is morphologically distinct from other Middle Miocene apes. Crown great apes can be distinguished from other taxa in several facial metrics (e.g., low midfacial prognathism, relatively tall faces) and only some of these features are found in Pierolapithecus, which is most consistent with a stem (basal) hominid position. The inferred morphology at all ancestral nodes within the hominoid (ape and human) tree is closer to great apes than to hylobatids (gibbons and siamangs), which are convergent with other smaller anthropoids. Our analyses support a hominid ancestor that was distinct from all extant and fossil hominids in overall facial shape and shared many features with Pierolapithecus. This reconstructed ancestral morphotype represents a testable hypothesis that can be reevaluated as new fossils are discovered.

Origins and Evolution of Novel Bacteroides in Captive Apes

Bacterial strains evolve in response to the gut environment of their hosts, with genomic changes that influence their interactions with hosts as well as with other members of the gut community. Great apes in captivity have acquired strains of Bacteroides xylanisolvens, which are common within gut microbiome of humans but not typically found other apes, thereby enabling characterization of strain evolution following colonization. Here, we isolate, sequence and reconstruct the history of gene gain and loss events in numerous captive-ape-associated strains since their divergence from their closest human-associated strains. We show that multiple captive-ape-associated B. xylanisolvens lineages have independently acquired gene complexes that encode functions related to host mucin metabolism. Our results support the finding of high genome fluidity in Bacteroides, in that several strains, in moving from humans to captive apes, have rapidly gained large genomic regions that augment metabolic properties not previously present in their relatives.

Empirical challenges from the comparative and developmental literature to the Shared Intentionality Theory - a review of alternative data on recursive mind reading, prosociality, imitation and cumulative culture

Humans have an irresistible inclination to coordinate actions with others, leading to species-unique forms of cooperation. According to the highly influential Shared Intentionality Theory (SITh), human cooperation is made possible by shared intentionality (SI), typically defined as a suite of socio-cognitive and motivational traits for sharing psychological states with others, thereby enabling individuals to engage in joint action in the mutually aware pursuit of shared goals. SITh theorises that SI evolved as late as 400,000 years ago, when our ancestors (in particular, Homo heidelbergensis) turned to a kind of food procurement that obligatorily required joint coordinated action. SI is, thus, hypothesized to be absent in other extant species, including our closest genetic relatives, the nonhuman great apes ("apes"). According to SITh, ape psychology is exclusively driven by individualistic motivations, as opposed to human psychology which is uniquely driven by altruistic motivations. The evolutionary scenario proposed by SITh builds on a series of findings from socio-cognitive research with apes and human children, and on the assumption that abilities expressed early in human development are human universals, unlikely to have been shaped by socio-cultural influences. Drawing on the primatological and developmental literature, we provide a systematic - albeit selective - review of SITh-inconsistent findings concerning psychological and behavioural traits theorised to be constitutive of SI. The findings we review pertain to all three thematic clusters typically addressed in SITh: (i) recursive mind reading; (ii) prosociality; (iii) imitation and cumulative culture. We conclude that such alternative data undermine two core SITh claims: the late evolutionary emergence of SI and the radical divide between ape and human psychology. We also discuss several conceptual and methodological limitations that currently hamper reliable comparative research on SI, in particular those engendered by Western-centric biases in the social sciences, where an overreliance on Western samples has promoted the formulation of Western-centric conceptualisations, operationalisations and methodologies.

Feeling a bit peckish: Seasonal and opportunistic insectivory for wild gorillas

OBJECTIVES

Insectivory likely contributed to survival of early humans in diverse conditions and influenced human cognitive evolution through the need to develop harvesting tools. In living primates, insectivory is a widespread behavior and frequently seasonal, although previous studies do not always agree on reasons behind this. Since western gorillas (Gorilla gorilla) diet is largely affected by seasonal variation in fruit availability, we aimed to test three non-mutually exclusive hypotheses (habitat use, frugivory and rainfall) to explain seasonality in termite feeding across age/sex classes in three habituated groups (Nindividuals  = 27) in Central Africa.

MATERIALS AND METHODS

We used 4 years of ranging, scan and continuous focal sampling records of gorillas (Nranging days  = 883, Nscans  = 12,384; Nhours  = 891) in addition to 116 transects recording vegetation and termite mound distribution.

RESULTS

Depending on the age/sex classes, we found support for all three hypotheses. Time spent in termite-rich vegetation positively impacted termite consumption in all age/sex classes, but subadults. Lengthier travels increased termite feeding in females but decreased it in subadults. Frugivory decreased termite consumption in adults. Daily rainfall had a positive effect on termite feeding and foraging in silverbacks and juveniles, but a negative effect in subadults. For females, rainfall had a positive effect on termite feeding, but a negative effect for termite foraging.

DISCUSSION

In great apes, seasonal insectivory seems to be multifactorial and primarily opportunistic with important differences among age/sex classes. While insectivory has potentials to be traditional, it likely played a crucial role during primate evolution (including ours), allowing diet flexibility in changing environments.

Comparative Genomic Analysis Identifies Great-Ape-Specific Structural Variants and Their Evolutionary Relevance

During the origin of great apes about 14 million years ago, a series of phenotypic innovations emerged, such as the increased body size, the enlarged brain volume, the improved cognitive skill, and the diversified diet. Yet, the genomic basis of these evolutionary changes remains unclear. Utilizing the high-quality genome assemblies of great apes (including human), gibbon, and macaque, we conducted comparative genome analyses and identified 15,885 great ape-specific structural variants (GSSVs), including eight coding GSSVs resulting in the creation of novel proteins (e.g., ACAN and CMYA5). Functional annotations of the GSSV-related genes revealed the enrichment of genes involved in development and morphogenesis, especially neurogenesis and neural network formation, suggesting the potential role of GSSVs in shaping the great ape-shared traits. Further dissection of the brain-related GSSVs shows great ape-specific changes of enhancer activities and gene expression in the brain, involving a group of GSSV-regulated genes (such as NOL3) that potentially contribute to the altered brain development and function in great apes. The presented data highlight the evolutionary role of structural variants in the phenotypic innovations during the origin of the great ape lineage.

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.

Long-term home range stability provides foraging benefits in western gorillas

OBJECTIVES

Long-term home range stability presumably emerges because familiarity with an area improves fitness through increased foraging efficiency, reduced predation risk, or reduced costs of intergroup aggression. While the use of spatial memory by primates has been widely demonstrated, few studies have examined whether long-term space use creates opportunities for interannual reuse of spatial knowledge. Here we examine the ranging behavior of western gorillas (Gorilla gorilla) to assess the degree of long-term site fidelity and the foraging consequences of reuse of space.

METHODS

We measured interannual home range overlap over a 10-year period for a single group of gorillas at the Mondika Research Center, using both grid-based and kernel density estimation. By plotting the total area used over time, we identified periods of home-range stability and expansion. We compared foraging and ranging behavior in familiar versus unfamiliar areas, considering fruit trees visited, dietary diversity, and daily path length, to determine whether the lack of spatial knowledge in unfamiliar areas was associated with foraging costs.

RESULTS

Average interannual home range overlap by the group remained high throughout the study. During periods of home range expansion, daily path lengths increased but not the number of fruit trees visited, suggesting that reduced familiarity with the area led to decreased foraging efficiency because individuals lacked prior knowledge of where to find resources.

DISCUSSION

Western gorillas at Mondika exhibit long-term home range stability, presumably reflecting a strategy that relies on the use of spatial memory to increase foraging efficiency that is favored by their reliance on ephemeral fruit resources.

Life of p: A consonant older than speech

Which sounds composed the first spoken languages? Archetypal sounds are not phylogenetically or archeologically recoverable, but comparative linguistics and primatology provide an alternative approach. Labial articulations are the most common speech sound, being virtually universal across the world's languages. Of all labials, the plosive 'p' sound, as in 'Pablo Picasso', transcribed /p/, is the most predominant voiceless sound globally and one of the first sounds to emerge in human infant canonical babbling. Global omnipresence and ontogenetic precocity imply that /p/-like sounds could predate the first major linguistic diversification event(s) in humans. Indeed, great ape vocal data support this view, namely, the only cultural sound shared across all great ape genera is articulatorily homologous to a rolling or trilled /p/, the 'raspberry'. /p/-like labial sounds represent an 'articulatory attractor' among living hominids and are likely among the oldest phonological features to have ever emerged in linguistic systems.

Surgical placement of implantable cardiac loop recorders in great apes

Cardiovascular disease is the leading cause of morbidity and mortality in zoologically managed adult great apes, accounting for 29%-77% of adult deaths in the North American population depending on the species. In an effort to better understand the underlying causes of heart disease, implantable loop recorders (ILRs) have been used in some cases to monitor great apes with suspected or known cases of arrhythmia. This is a 10-year review of the Great Ape Heart Project's experience of implanting 21 ILRs in 7 gorillas (Gorilla gorilla gorilla; 9 total ILR devices), 5 chimpanzees (Pan troglodytes, 11 total ILR devices), and 1 orangutan (Pongo abelii, 1 ILR device) in an effort to develop effective methods for surgical implantation and remote collection of the data for analysis.

Evaluating individual biomarkers for predicting health risks in zoo-housed chimpanzees (Pan troglodytes) and bonobos (Pan paniscus)

Although biomarkers are often used for predicting morbidity and mortality in humans, similar data are lacking in our closest relatives. This study analyzed 16 biomarkers in zoo-housed chimpanzees and bonobos from serum samples collected during both routine and nonroutine veterinary immobilizations. Generalized linear and generalized linear mixed models were used to determine the efficacy of each biomarker to predict all-cause morbidity, defined as the presence of at least one chronic condition, or cardiac disease as a subset of all-cause morbidity. Cox proportional hazards models were used to examine associations between biomarkers and mortality risk from any cause. Analyses were conducted using two data sets for each species, one with all values retained (chimpanzees: n = 148; bonobos: n = 33) and the other from samples collected during routine immobilizations only (chimpanzees: n = 95; bonobos: n = 23). Consistent results across both data sets in chimpanzees included associations of higher cortisol with all-cause morbidity risk, lower creatinine with cardiac disease risk, and higher creatinine with mortality risk, and in bonobos were increased cardiac disease risk with higher cortisol and lower dehydroepiandrosterone-sulfate, fructosamine, and triglycerides. However, there were some inconsistencies between data sets, such as tumor necrosis factor-α predicting mortality risk positively in chimpanzees when all values were retained, but negatively for routine values only. Despite the close evolutionary relationships between chimpanzees and bonobos, the only result observed in both species was a negative association between albumin and mortality risk in the all values retained data sets. Thus, data suggest some biomarkers may be useful predictors of future health outcomes, although a better understanding of both individual and species variation in biomarkers and their contribution to health risks is needed.

Arboreal origin of consonants and thus, ultimately, speech

The world's spoken languages are universally composed of vowels and consonants, but the primate prototypical call repertoire is almost exclusively composed of vowel-like calls. What was the origin of consonant-like calls? Their prevalence across great apes suggests that an arboreal lifestyle and extractive foraging were ecological preconditions for speech evolution.

Bringing trees back into the human evolutionary story: recent evidence from extant great apes

Hypotheses have historically linked the emergence and evolution of defining human characteristics such as bipedal walking to ground-dwelling, envisioning our earliest ancestors as living in treeless savannahs (i.e. the traditional savannah hypothesis). However, over the last two decades, evidence from the fossil record combined with comparative studies of extant apes have challenged this hypothesis, instead favoring the importance of arboreality during key phases of hominin evolutionary history. Here we review some of these studies, including a recent study of savannah chimpanzees that provides the first model of how bipedalism could have been adaptive as an arboreal locomotor behavior in early hominins, even after the forests receded during the early Miocene-Pliocene transition. We suggest that whilst a shift to exploiting open habitats catalyzed hominin divergence from great apes, adaptations to arboreal living have been key in shaping what defines humans today, in counter to the traditional savannah hypothesis. Future comparative studies within and between great ape species will be instrumental to understanding variation in arboreality in extant apes, and thus the processes shaping human evolution over the last 3-7 million years.

Testing for personality consistency across naturally occurring behavioral contexts in sanctuary chimpanzees (Pan troglodytes)

Personality is both a reflection of the bio-behavioral profile of individuals and a summary of how they typically interact with their physical and social world. Personality is usually defined as having distinct behavioral characteristics, which are assumed to be consistent over time and across contexts. Like other mammals, primates have individual differences in personality. Although temporal consistency is sometimes measured in primates, and contextual consistency is sometimes measured across experimental contexts, it is rare to measure both in the same individuals and outside of experimental settings. Here, we aim to measure both temporal and contextual consistency in chimpanzees, assessing their personality with behavioral observations from naturally occurring contexts (i.e., real-life settings). We measured personality-based behaviors in 22 sanctuary chimpanzees, in the contexts of feeding, affiliation, resting, and solitude, across two time periods, spanning 4 years. Of the 22 behaviors recorded, about 64% were consistent across two to four contexts and 50% were consistent over time. Ten behaviors loaded significantly onto three trait components: explorativeness, boldness-sociability, and anxiety-sociability, as revealed by factor analysis. Like others, we documented individual differences in the personality of chimpanzees based on reliably measured observations in real-life contexts. Furthermore, we demonstrated relatively strong, but not absolute, temporal, and contextual consistency in personality-based behaviors. We also found another aspect of individual differences in personality, specifically, the extent to which individual chimpanzees show consistency. Some individuals showed contextual and temporal consistency, whereas others show significant variation across behaviors, contexts, and/or time. We speculate that the relative degree of consistency in personality may vary within chimpanzees. It may be that different primate species vary in the extent to which individuals show consistency of personality traits. Our behavioral-based assessment can be used with wild populations, increasing the validity of personality studies, facilitating comparative studies and potentially being applicable to conservation efforts.

Spatio-temporal changes in chimpanzee density and abundance in the Greater Mahale Ecosystem, Tanzania

Species conservation and management require reliable information about animal distribution and population size. Better management actions within a species' range can be achieved by identifying the location and timing of population changes. In the Greater Mahale Ecosystem (GME), western Tanzania, deforestation due to the expansion of human settlements and agriculture, annual burning, and logging are known threats to wildlife. For one of the most charismatic species, the endangered eastern chimpanzee (Pan troglodytes schweinfurthii), approximately 75% of the individuals are distributed outside national park boundaries, requiring monitoring and protection efforts over a vast landscape of various protection statuses. These efforts are especially challenging when we lack data on trends in density and population size. To predict spatio-temporal chimpanzee density and abundance across the GME, we used density surface modeling, fitting a generalized additive model to a 10-year time-series data set of nest counts based on line-transect surveys. The chimpanzee population declined at an annual rate of 2.41%, including declines of 1.72% in riparian forests (from this point forward, forests), 2.05% in miombo woodlands (from this point forward, woodlands) and 3.45% in nonforests. These population declines were accompanied by ecosystem-wide declines in vegetation types of 1.36% and 0.32% per year for forests and woodlands, respectively; we estimated an annual increase of 1.35% for nonforests. Our model predicted the highest chimpanzee density in forests (0.86 chimpanzees/km² , 95% confidence intervals (CIs) 0.60-1.23; as of 2020), followed by woodlands (0.19, 95% CI 0.12-0.30) and nonforests (0.18, 95% CI 0.10-1.33). Although forests represent only 6% of the landscape, they support nearly one-quarter of the chimpanzee population (769 chimpanzees, 95% CI 536-1103). Woodlands dominate the landscape (71%) and therefore support more than a half of the chimpanzee population (2294; 95% CI 1420-3707). The remaining quarter of the landscape is represented by nonforests and supports another quarter of the chimpanzee population (750; 95% CI 408-1381). Given the pressures on the remaining suitable habitat in Tanzania, and the need of chimpanzees to access both forest and woodland vegetation to survive, we urge future management actions to increase resources and expand the efforts to protect critical forest and woodland habitat and promote strategies and policies that more effectively prevent irreversible losses. We suggest that regular monitoring programs implement a systematic random design to effectively inform and allocate conservation actions and facilitate interannual comparisons for trend monitoring, measuring conservation success, and guiding adaptive management.

Coordinating social action: a primer for the cross-species investigation of communicative repair

Human joint action is inherently cooperative, manifested in the collaborative efforts of participants to minimize communicative trouble through interactive repair. Although interactive repair requires sophisticated cognitive abilities, it can be dissected into basic building blocks shared with non-human animal species. A review of the primate literature shows that interactionally contingent signal sequences are at least common among species of non-human great apes, suggesting a gradual evolution of repair. To pioneer a cross-species assessment of repair this paper aims at (i) identifying necessary precursors of human interactive repair; (ii) proposing a coding framework for its comparative study in humans and non-human species; and (iii) using this framework to analyse examples of interactions of humans (adults/children) and non-human great apes. We hope this paper will serve as a primer for cross-species comparisons of communicative breakdowns and how they are repaired. This article is part of the theme issue 'Revisiting the human 'interaction engine': comparative approaches to social action coordination'.

Eye-tracking as a window into primate social cognition

Over the past decade, noninvasive, restraint-free eye-tracking research with primates has transformed our understanding of primate social cognition. The use of this technology with many primate species allows for the exploration and comparison of how these species attend to and understand social agents and interactions. The ability to compare and contrast the cognitive capacities of various primate species, including humans, provides insight into the evolutionary mechanisms and selective pressures that have likely shaped social cognition in similar and divergent ways across the primate order. In this review, we begin by discussing noninvasive behavioral methods used to measure primate gaze and attention before the introduction of noninvasive, restraint-free eye-tracking methodologies. Next, we focus on findings from recent eye-tracking research on primate social cognition, beginning with simple visual and search mechanisms. We then discuss the results that have built on this basic understanding of how primates view images and videos, exploring discrimination and knowledge of social agents, following social cues, tracking perspectives and predicting behavior, and the combination of eye-tracking and other behavioral and physiological methods. Finally, we discuss some future directions of noninvasive eye-tracking research on primate social cognition and current eye-tracking work-in-progress that builds on these previous studies, investigating underexplored socio-cognitive capacities and utilizing new methodologies.

Great ape health watch: Enhancing surveillance for emerging infectious diseases in great apes

Infectious diseases have the potential to extirpate populations of great apes. As the interface between humans and great apes expands, zoonoses pose an increasingly severe threat to already endangered great ape populations. Despite recognition of the threat posed by human pathogens to great apes, health monitoring is only conducted for a small fraction of the world's wild great apes (and mostly those that are habituated) meaning that outbreaks of disease often go unrecognized and therefore unmitigated. This lack of surveillance (even in sites where capacity to conduct surveillance is present) is the most significant limiting factor in our ability to quickly detect and respond to emerging infectious diseases in great apes when they first appear. Accordingly, we must create a surveillance system that links disease outbreaks in humans and great apes in time and space, and enables veterinarians, clinicians, conservation managers, national decision makers, and the global health community to respond quickly to these events. Here, we review existing great ape health surveillance programs in African range habitats to identify successes, gaps, and challenges. We use these findings to argue that standardization of surveillance across sites and geographic scales, that monitors primate health in real-time and generates early warnings of disease outbreaks, is an efficient, low-cost step to conserve great ape populations. Such a surveillance program, which we call "Great Ape Health Watch" would lead to long-term improvements in outbreak preparedness, prevention, detection, and response, while generating valuable data for epidemiological research and sustainable conservation planning. Standardized monitoring of great apes would also make it easier to integrate with human surveillance activities. This approach would empower local stakeholders to link wildlife and human health, allowing for near real-time, bidirectional surveillance at the great ape-human interface.

Chromosome size affects sequence divergence between species through the interplay of recombination and selection

The structure of the genome shapes the distribution of genetic diversity and sequence divergence. To investigate how the relationship between chromosome size and recombination rate affects sequence divergence between species, we combined empirical analyses and evolutionary simulations. We estimated pairwise sequence divergence among 15 species from three different mammalian clades-Peromyscus rodents, Mus mice, and great apes-from chromosome-level genome assemblies. We found a strong significant negative correlation between chromosome size and sequence divergence in all species comparisons within the Peromyscus and great apes clades but not the Mus clade, suggesting that the dramatic chromosomal rearrangements among Mus species may have masked the ancestral genomic landscape of divergence in many comparisons. Our evolutionary simulations showed that the main factor determining differences in divergence among chromosomes of different sizes is the interplay of recombination rate and selection, with greater variation in larger populations than in smaller ones. In ancestral populations, shorter chromosomes harbor greater nucleotide diversity. As ancestral populations diverge, diversity present at the onset of the split contributes to greater sequence divergence in shorter chromosomes among daughter species. The combination of empirical data and evolutionary simulations revealed that chromosomal rearrangements, demography, and divergence times may also affect the relationship between chromosome size and divergence, thus deepening our understanding of the role of genome structure in the evolution of species divergence.

Great apes and human children rationally monitor their decisions

Several species can detect when they are uncertain about what decision to make-revealed by opting out of the choice, or by seeking more information before deciding. However, we do not know whether any nonhuman animals recognize when they need more information to make a decision because new evidence contradicts an already-formed belief. Here, we explore this ability in great apes and human children. First, we show that after great apes saw new evidence contradicting their belief about which of two rewards was greater, they stopped to recheck the evidence for their belief before deciding. This indicates the ability to keep track of the reasons for their decisions, or 'rational monitoring' of the decision-making process. Children did the same at 5 years of age, but not at 3 years. In a second study, participants formed a belief about a reward's location, but then a social partner contradicted them, by picking the opposite location. This time even 3-year-old children rechecked the evidence, while apes ignored the disagreement. While apes were sensitive only to the conflict in physical evidence, the youngest children were more sensitive to peer disagreement than conflicting physical evidence.

Effectiveness of 20 years of conservation investments in protecting orangutans

Conservation strategies are rarely systematically evaluated, which reduces transparency, hinders the cost-effective deployment of resources, and hides what works best in different contexts. Using data on the iconic and critically endangered orangutan (Pongo spp.), we developed a novel spatiotemporal framework for evaluating conservation investments. We show that around USD 1 billion was invested between 2000 and 2019 into orangutan conservation by governments, nongovernmental organizations, companies, and communities. Broken down by allocation to different conservation strategies, we find that habitat protection, patrolling, and public outreach had the greatest return on investment for maintaining orangutan populations. Given the variability in threats, land-use opportunity costs, and baseline remunerations in different regions, there were differential benefits per dollar invested across conservation activities and regions. We show that although challenging from a data and analysis perspective, it is possible to fully understand the relationships between conservation investments and outcomes and the external factors that influence these outcomes. Such analyses can provide improved guidance toward a more effective biodiversity conservation. Insights into the spatiotemporal interplays between the costs and benefits driving effectiveness can inform decisions about the most suitable orangutan conservation strategies for halting population declines. Although our study focuses on the three extant orangutan species of Sumatra and Borneo, our findings have broad application for evidence-based conservation science and practice worldwide.

Facial asymmetry tracks genetic diversity among Gorilla subspecies

Mountain gorillas are particularly inbred compared to other gorillas and even the most inbred human populations. As mountain gorilla skeletal material accumulated during the 1970s, researchers noted their pronounced facial asymmetry and hypothesized that it reflects a population-wide chewing side preference. However, asymmetry has also been linked to environmental and genetic stress in experimental models. Here, we examine facial asymmetry in 114 crania from three Gorilla subspecies using 3D geometric morphometrics. We measure fluctuating asymmetry (FA), defined as random deviations from perfect symmetry, and population-specific patterns of directional asymmetry (DA). Mountain gorillas, with a current population size of about 1000 individuals, have the highest degree of facial FA (explaining 17% of total facial shape variation), followed by Grauer gorillas (9%) and western lowland gorillas (6%), despite the latter experiencing the greatest ecological and dietary variability. DA, while significant in all three taxa, explains relatively less shape variation than FA does. Facial asymmetry correlates neither with tooth wear asymmetry nor increases with age in a mountain gorilla subsample, undermining the hypothesis that facial asymmetry is driven by chewing side preference. An examination of temporal trends shows that stress-induced developmental instability has increased over the last 100 years in these endangered apes.

Symbolic Signal Use in Wild Chimpanzee Gestural Communication?: A Theoretical Framework

Symbolic communication is not obvious in the natural communicative repertoires of our closest living relatives, the great apes. However, great apes do show symbolic competencies in laboratory studies. This includes the understanding and the use of human-provided abstract symbols. Given this evidence for the underlying ability, the apparent failure to make use of it in the wild is puzzling. We provide a theoretical framework for identifying basic forms of symbolic signal use in chimpanzee natural communication. In line with the laboratory findings, we concentrate on the most promising domain to investigate, namely gesture, and we provide a case study in this area. We suggest that evidence for basic symbolic signal use would consist of the presence of two key characteristics of symbolic communication, namely arbitrariness and conventionalization. Arbitrariness means that the linkage between the form of the gesture and its meaning shows no obvious logical or otherwise motivated connection. Conventionalization means that the gesture is shared at the group-level and is thus socially learned, not innate. Further, we discuss the emergence and transmission of these gestures. Demonstrating this basic form of symbolic signal use would indicate that the symbolic capacities revealed by laboratory studies also find their expression in the natural gestural communication of our closest living relatives, even if only to a limited extent. This theoretical article thus aims to contribute to our understanding of the developmental origins of great ape gestures, and hence, arguably, of human symbolic communication. It also has a very practical aim in that by providing clear criteria and by pointing out potential candidates for symbolic communication, we give fieldworkers useful prerequisites for identifying and analyzing signals which may demonstrate the use of great apes' symbolic capacities in the wild.

Evidence of joint commitment in great apes' natural joint actions

Human joint action seems special, as it is grounded in joint commitment-a sense of mutual obligation participants feel towards each other. Comparative research with humans and non-human great apes has typically investigated joint commitment by experimentally interrupting joint actions to study subjects' resumption strategies. However, such experimental interruptions are human-induced, and thus the question remains of how great apes naturally handle interruptions. Here, we focus on naturally occurring interruptions of joint actions, grooming and play, in bonobos and chimpanzees. Similar to humans, both species frequently resumed interrupted joint actions (and the previous behaviours, like grooming the same body part region or playing the same play type) with their previous partners and at the previous location. Yet, the probability of resumption attempts was unaffected by social bonds or rank. Our data suggest that great apes experience something akin to joint commitment, for which we discuss possible evolutionary origins.

Orangutan information broadcast via consonant-like and vowel-like calls breaches mathematical models of linguistic evolution

The origin of language is one of the most significant evolutionary milestones of life on Earth, but one of the most persevering scientific unknowns. Two decades ago, game theorists and mathematicians predicted that the first words and grammar emerged as a response to transmission errors and information loss in language's precursor system, however, empirical proof is lacking. Here, we assessed information loss in proto-consonants and proto-vowels in human pre-linguistic ancestors as proxied by orangutan consonant-like and vowel-like calls that compose syllable-like combinations. We played back and re-recorded calls at increasing distances across a structurally complex habitat (i.e. adverse to sound transmission). Consonant-like and vowel-like calls degraded acoustically over distance, but no information loss was detected regarding three distinct classes of information (viz. individual ID, context and population ID). Our results refute prevailing mathematical predictions and herald a turning point in language evolution theory and heuristics. Namely, explaining how the vocal–verbal continuum was crossed in the hominid family will benefit from future mathematical and computational models that, in order to enjoy empirical validity and superior explanatory power, will be informed by great ape behaviour and repertoire.

Current Progress in Evolutionary Comparative Genomics of Great Apes

The availability of high-quality genome sequences of great ape species provides unprecedented opportunities for genomic analyses. Herein, we reviewed the recent progress in evolutionary comparative genomic studies of the existing great ape species, including human, chimpanzee, bonobo, gorilla, and orangutan. We elaborate discovery on evolutionary history, natural selection, structural variations, and new genes of these species, which is informative for understanding the origin of human-specific phenotypes.

Do we need to reclassify the social systems of gregarious apes?

Decades of research have led to a solid understanding of the social systems of gregarious apes: chimpanzees, bonobos, gorillas, and gibbons. As field studies have increasingly collected data from multiple neighboring habituated groups, genetic and social interconnections have been revealed. These findings provide a more nuanced picture of intergroup relations in apes, and have led to claims in the literature that some ape taxa have multilevel societies. A multilevel society is defined as a nested collection of social entities comprising at least two discernible levels of social integration between the individual and the population. We argue that the evidence for multilevel sociality sensu stricto in apes is currently inconclusive and that it is premature to abandon the traditional classification of ape social systems. However, available findings appear to be consistent with the existence of some degree of higher social grouping patterns. We propose the term supra-group organization which may adequately capture ape social systems when viewed from a top-down perspective.

Captive great apes tend to innovate simple tool behaviors quickly

Recent studies have highlighted the important role that individual learning mechanisms and different forms of enhancenment play in the acquisition of novel behaviors by naïve individuals. A considerable subset of these studies has focused on tool innovation by our closest living relatives, the great apes, to better undestand the evolution of technology in our own lineage. To be able to isolate the role that individual learning plays in great ape tool innovation, researchers usually employ what are known as baseline tests. Although these baselines are commonly used in behavioral studies in captivity, the length of these tests in terms of number of trials and duration remains unstandarized across studies. To address this methodological issue, we conducted a literature review of great ape tool innovation studies conducted in zoological institutions and compiled various methodological data including the timing of innovation. Our literature review revealed an early innovation tendency in great apes, which was particularly pronounced when simple forms of tool use were investigated. In the majority of experiments where tool innovation took place, this occurred within the first trial and/or the first hour of testing. We discuss different possible sources of variation in the latency to innovate such as testing setup, species and task. We hope that our literature review helps researchers design more data-informed, resource-efficient experiments on tool innovation in our closest living relatives.

Multiple Genomic Events Altering Hominin SIGLEC Biology and Innate Immunity Predated the Common Ancestor of Humans and Archaic Hominins

Human-specific pseudogenization of the CMAH gene eliminated the mammalian sialic acid (Sia) Neu5Gc (generating an excess of its precursor Neu5Ac), thus changing ubiquitous cell surface “self-associated molecular patterns” that modulate innate immunity via engagement of CD33-related-Siglec receptors. The Alu-fusion-mediated loss-of-function of CMAH fixed ∼2–3 Ma, possibly contributing to the origins of the genus Homo. The mutation likely altered human self-associated molecular patterns, triggering multiple events, including emergence of human-adapted pathogens with strong preference for Neu5Ac recognition and/or presenting Neu5Ac-containing molecular mimics of human glycans, which can suppress immune responses via CD33-related-Siglec engagement. Human-specific alterations reported in some gene-encoding Sia-sensing proteins suggested a “hotspot” in hominin evolution. The availability of more hominid genomes including those of two extinct hominins now allows full reanalysis and evolutionary timing. Functional changes occur in 8/13 members of the human genomic cluster encoding CD33-related Siglecs, all predating the human common ancestor. Comparisons with great ape genomes indicate that these changes are unique to hominins. We found no evidence for strong selection after the Human–Neanderthal/Denisovan common ancestor, and these extinct hominin genomes include almost all major changes found in humans, indicating that these changes in hominin sialobiology predate the Neanderthal–human divergence ∼0.6 Ma. Multiple changes in this genomic cluster may also explain human-specific expression of CD33rSiglecs in unexpected locations such as amnion, placental trophoblast, pancreatic islets, ovarian fibroblasts, microglia, Natural Killer(NK) cells, and epithelia. Taken together, our data suggest that innate immune interactions with pathogens markedly altered hominin Siglec biology between 0.6 and 2 Ma, potentially affecting human evolution.

Ampliconic Genes on the Great Ape Y Chromosomes: Rapid Evolution of Copy Number but Conservation of Expression Levels

Multicopy ampliconic gene families on the Y chromosome play an important role in spermatogenesis. Thus, studying their genetic variation in endangered great ape species is critical. We estimated the sizes (copy number) of nine Y ampliconic gene families in population samples of chimpanzee, bonobo, and orangutan with droplet digital polymerase chain reaction, combined these estimates with published data for human and gorilla, and produced genome-wide testis gene expression data for great apes. Analyzing this comprehensive data set within an evolutionary framework, we, first, found high inter- and intraspecific variation in gene family size, with larger families exhibiting higher variation as compared with smaller families, a pattern consistent with random genetic drift. Second, for four gene families, we observed significant interspecific size differences, sometimes even between sister species—chimpanzee and bonobo. Third, despite substantial variation in copy number, Y ampliconic gene families’ expression levels did not differ significantly among species, suggesting dosage regulation. Fourth, for three gene families, size was positively correlated with gene expression levels across species, suggesting that, given sufficient evolutionary time, copy number influences gene expression. Our results indicate high variability in size but conservation in gene expression levels in Y ampliconic gene families, significantly advancing our understanding of Y-chromosome evolution in great apes.

Hand preference in unimanual and bimanual coordinated tasks in wild western lowland gorillas (Gorilla gorilla gorilla) feeding on African ginger (Zingiberaceae)

OBJECTIVES

Bimanual coordinated behaviors are critical for detecting robust individual hand preference in nonhuman primates but are particularly challenging to observe in the wild. This study focuses on spontaneous feeding behavior on African ginger (Aframomum sp. and Renealmia sp.), which involves a unimanual task (reaching and pulling out a ginger stem) and a bimanual coordinated task (extracting pith from a ginger stem) by wild western lowland gorillas.

MATERIALS AND METHODS

Study subjects were 21 gorillas in the Moukalaba-Doudou National Park, Gabon. We examined whether they exhibit significant hand preference at the individual and group levels for both tasks.

RESULTS

Sixteen gorillas showed significant hand preference in the unimanual task, whereas all 21 individuals showed significant hand preference in the bimanual coordinated task. Hand preference was significantly stronger in the bimanual coordinated task than in the unimanual task. It is noteworthy that gorillas showed a significant right-hand preference at the group level for the bimanual task (roughly 70% of the subjects).

DISCUSSION

This study confirmed that bimanual coordinated tasks are more sensitive in detecting hand preferences in nonhuman primates. In addition to the bimanual nature of the task, the precision grip for processing and the importance of African ginger as a food resource might influence the expression of hand preference. Evidence of a group-level right-hand preference may support the "postural origins theory." Because all wild African great apes feed on the pith of African ginger, comparing this task and its hand preferences can contribute toward a better understanding of the evolution of handedness in Hominidae.

Pathological lesions of the digestive tract in free-ranging mountain gorillas (Gorilla beringei beringei)

The finding of parasites and bacterial pathogens in mountain gorilla feces and oral lesions in gorilla skeletal remains has not been linked to pathological evidence of morbidity or mortality. In the current study, we conducted a retrospective study of digestive tracts including oral cavity, salivary glands, esophagus, stomach, intestines (gastrointestinal tract [GI]), liver, and pancreas of 60 free-ranging mountain gorillas from Uganda, Rwanda, and the Democratic Republic of Congo that died between 1985 and 2007. We reviewed clinical histories and gross pathology reports and examined histological sections. On histology, enteritis (58.6%), gastritis (37.3%), and colitis (29.3%) were the commonest lesions in the tracts. Enteritis and colitis were generally mild, and judged likely to have been subclinical. Gastritis was often chronic and proliferative or ulcerative, and associated with nematodiasis. A gastro-duodenal malignancy (carcinoid) was present in one animal. A number of incidental lesions were identified throughout the tract and cestodes and nematodes were frequently observed grossly and/or histologically. Pigmentation of teeth and tongue were a common finding, but periodontitis and dental attrition were less common than reported from past studies of skeletal remains. Despite observing numerous GI lesions and parasites in this study of deceased free-living mountain gorillas, we confirmed mortality attributable to gastroenteritis in just 8% (5/60) cases, which is less than that described in captive gorillas. Other deaths attributed to digestive tract lesions included cleft palate in an infant, periodontal disease causing systemic infection in an older adult and gastric cancer. Of all the parasitic infections observed, only hepatic capillariasis and gastric nematodiasis were significantly associated with lesions (hepatitis and gastritis, respectively). Understanding GI lesions in this endangered species is key in the management of morbidity associated with GI ailments.

Hybrid apes in the Anthropocene: Burden or asset for conservation?

Conservationists often view hybrid animals as problematic, at least if anthropogenic influence caused the intermixing to occur. However, critics propose that humans should respect non-human autonomy, reject and accept the creatures they have helped to create.Based on two case studies of our own ethological, genetic and ethnographic research about chimpanzee and orangutan subspecies hybrids, we assess what, if anything, should be done about such animals. We consider problems posed by cross-bred apes relating to: (a) Breeding-Do hybrids really experience reduced reproductive success? How are population-level concerns and welfare of individual animals balanced in conservation breeding? (b) Essentialism-Are anti-hybrid arguments based on essentialist or purist thinking? Does essentialism vary by conservation context? (c) Pragmatism-How do socio-economic circumstances influence whether hybrids are embraced or ignored? Does the erosion of 'untouched nature' render hybrids more important?We show that answers to these questions are complex and context-specific, and that therefore decisions should be made on a case-by-case basis. For example, we find that anti-hybrid arguments are essentialist in some cases (e.g. ape management in zoos) but not in others (e.g. ape reintroduction). Thus, rather than present recommendations, we conclude by posing nine questions that conservationists should ask themselves when making decisions about taxonomic hybrids. ​ A free Plain Language Summary can be found within the Supporting Information of this article.

No evidence for female kin association, indications for extragroup paternity, and sex-biased dispersal patterns in wild western gorillas

Characterizing animal dispersal patterns and the rational behind individuals' transfer choices is a long-standing question of interest in evolutionary biology. In wild western gorillas (Gorilla gorilla), a one-male polygynous species, previous genetic findings suggested that, when dispersing, females might favor groups with female kin to promote cooperation, resulting in higher-than-expected within-group female relatedness. The extent of male dispersal remains unclear with studies showing conflicting results. To investigate male and female dispersal patterns and extragroup paternity, we analyzed long-term field observations, including female spatial proximity data, together with genetic data (10 autosomal microsatellites) on individuals from a unique set of four habituated western gorilla groups, and four additional extragroup males (49 individuals in total). The majority of offspring (25 of 27) were sired by the group male. For two offspring, evidence for extragroup paternity was found. Contrarily to previous findings, adult females were not significantly more related within groups than across groups. Consistently, adult female relatedness within groups did not correlate with their spatial proximity inferred from behavioral data. Adult females were similarly related to adult males from their group than from other groups. Using R ST statistics, we found significant genetic structure and a pattern of isolation by distance, indicating limited dispersal in this species. Comparing relatedness among females and among males revealed that males disperse farer than females, as expected in a polygamous species. Our study on habituated western gorillas shed light on the dispersal dynamics and reproductive behavior of this polygynous species and challenge some of the previous results based on unhabituated groups.

Positive Selection in Gene Regulatory Factors Suggests Adaptive Pleiotropic Changes During Human Evolution

Gene regulatory factors (GRFs), such as transcription factors, co-factors and histone-modifying enzymes, play many important roles in modifying gene expression in biological processes. They have also been proposed to underlie speciation and adaptation. To investigate potential contributions of GRFs to primate evolution, we analyzed GRF genes in 27 publicly available primate genomes. Genes coding for zinc finger (ZNF) proteins, especially ZNFs with a Krüppel-associated box (KRAB) domain were the most abundant TFs in all genomes. Gene numbers per TF family differed between all species. To detect signs of positive selection in GRF genes we investigated more than 3,000 human GRFs with their more than 70,000 orthologs in 26 non-human primates. We implemented two independent tests for positive selection, the branch-site-model of the PAML suite and aBSREL of the HyPhy suite, focusing on the human and great ape branch. Our workflow included rigorous procedures to reduce the number of false positives: excluding distantly similar orthologs, manual corrections of alignments, and considering only genes and sites detected by both tests for positive selection. Furthermore, we verified the candidate sites for selection by investigating their variation within human and non-human great ape population data. In order to approximately assign a date to positively selected sites in the human lineage, we analyzed archaic human genomes. Our work revealed with high confidence five GRFs that have been positively selected on the human lineage and one GRF that has been positively selected on the great ape lineage. These GRFs are scattered on different chromosomes and have been previously linked to diverse functions. For some of them a role in speciation and/or adaptation can be proposed based on the expression pattern or association with human diseases, but it seems that they all contributed independently to human evolution. Four of the positively selected GRFs are KRAB-ZNF proteins, that induce changes in target genes co-expression and/or through arms race with transposable elements. Since each positively selected GRF contains several sites with evidence for positive selection, we suggest that these GRFs participated pleiotropically to phenotypic adaptations in humans.

From stem and progenitor cells to neurons in the developing neocortex: key differences among hominids

Comparing the biology of humans to that of other primates, and notably other hominids, is a useful path to learn more about what makes us human. Some of the most interesting differences among hominids are closely related to brain development and function, for example behaviour and cognition. This makes it particularly interesting to compare the hominid neural cells of the neocortex, a part of the brain that plays central roles in those processes. However, well-preserved tissue from great apes is usually extremely difficult to obtain. A variety of new alternative tools, for example brain organoids, are now beginning to make it possible to search for such differences and analyse their potential biological and biomedical meaning. Here, we present an overview of recent findings from comparisons of the neural stem and progenitor cells (NSPCs) and neurons of hominids. In addition to differences in proliferation and differentiation of NSPCs, and maturation of neurons, we highlight that the regulation of the timing of these processes is emerging as a general foundational difference in the development of the neocortex of hominids.

Comparing semi-landmarking approaches for analyzing three-dimensional cranial morphology

OBJECTIVES

Increased use of three-dimensional (3D) imaging data has led to a need for methods capable of capturing rich shape descriptions. Semi-landmarks have been demonstrated to increase shape information but placement in 3D can be time consuming, computationally expensive, or may introduce artifacts. This study implements and compares three strategies to more densely sample a 3D image surface.

MATERIALS AND METHODS

Three dense sampling strategies: patch, patch-thin-plate spline (TPS), and pseudo-landmark sampling, are implemented to analyze skulls from three species of great apes. To evaluate the shape information added by each strategy, the semi or pseudo-landmarks are used to estimate a transform between an individual and the population average template. The average mean root squared error between the transformed mesh and the template is used to quantify the success of the transform.

RESULTS

The landmark sets generated by each method result in estimates of the template that on average were comparable or exceeded the accuracy of using manual landmarks alone. The patch method demonstrates the most sensitivity to noise and missing data, resulting in outliers with large deviations in the mean shape estimates. Patch-TPS and pseudo-landmarking provide more robust performance in the presence of noise and variability in the dataset.

CONCLUSIONS

Each landmarking strategy was capable of producing shape estimations of the population average templates that were generally comparable to manual landmarks alone while greatly increasing the density of the shape information. This study highlights the potential trade-offs between correspondence of the semi-landmark points, consistent point spacing, sample coverage, repeatability, and computational time.

Elevated diversity in loci linked to facial morphology is consistent with the hypothesis that individual facial recognition is important across hominoids

OBJECTIVES

The ability to use visual signals to identify individuals is an important feature of primate social groups, including humans. Sheehan and Nachman (2014) showed that loci linked to facial morphology had elevated levels of diversity and interpreted this as evidence that the human face is under frequency-dependent selection to enhance individual recognition (Nature Communications 5). In our study, we tested whether this pattern is found in non-human ape species, to help understand whether individual recognition might also play a role in species other than humans.

MATERIALS AND METHODS

We examined levels of genetic diversity in an available population genomic dataset of humans, chimpanzees, bonobos, gorillas, and orangutans for three sets of loci, (1) loci linked to facial morphology, (2) loci linked to height, and (3) neutrally evolving regions. We tested whether loci linked to facial morphology were more variable than loci linked to height or neutrally evolving loci in each of these species.

RESULTS

We found significantly elevated diversity in loci linked to facial morphology in chimpanzees, gorillas, and Sumatran and Bornean orangutans.

DISCUSSION

Our findings closely parallel those of Sheehan and Nachman and are consistent with the idea that selection for facial diversity and individual recognition has not only shaped the evolution of the human face, but it has similarly shaped the evolution of most of our closest primate relatives. We also discuss alternative hypotheses for this pattern.

Assessing conservation attitudes and behaviors of Congolese children neighboring the world's first bonobo (Pan paniscus) release site

Poaching and habitat destruction in the Congo Basin threaten African great apes including the bonobo (Pan paniscus), chimpanzees (Pan troglodytes), and gorillas (Gorilla spp.) with extinction. One way to combat extinction is to reintroduce rescued and rehabilitated apes and repopulate native habitats. Reintroduction programs are only successful if they are supported by local populations. Ekolo ya Bonobo, located in Equateur province of the Democratic Republic of Congo (DRC), is the world's only reintroduction site for rehabilitated bonobos. Here we assess whether children, of the Ilonga-Pôo, living adjacent to Ekolo ya Bonobo demonstrate more pro-ape conservation attitudes than children living in, Kinshasa, the capital city. We examined children's attitudes toward great apes because children are typically the focus of conservation education programs. We used the Great Ape Attitude Questionnaire to test the Contact Hypothesis, which posits that proximity to great ape habitat influences pro-conservation attitudes toward great apes. Ilonga-Pôo children who live in closer contact with wild bonobos felt greater responsibility to protect great apes compared to those in Kinshasa who live outside the natural habitat of great apes. These results suggest that among participants in the DRC, spatial proximity to a species fosters a greater sense of responsibility to protect and conserve. These results have implications for the successful implementation of great ape reintroduction programs in the Congo Basin. The data analyzed in this study were collected in 2010 and therefore provide a baseline for longitudinal study of this reintroduction site.

Human and Nonhuman Primate Lineage-Specific Footprints in the Salivary Proteome

Proteins in saliva are needed for preprocessing food in the mouth, maintenance of tooth mineralization, and protection from microbial pathogens. Novel insights into human lineage-specific functions of salivary proteins and clues to their involvement in human disease can be gained through evolutionary studies, as recently shown for salivary amylase AMY1 and salivary agglutinin DMBT1/gp340. However, the entirety of proteins in saliva, the salivary proteome, has not yet been investigated from an evolutionary perspective. Here, we compared the proteomes of human saliva and the saliva of our closest extant evolutionary relatives, chimpanzees and gorillas, using macaques as an outgroup, with the aim to uncover features in saliva protein composition that are unique to each species. We found that humans produce a waterier saliva, containing less than half total protein than great apes and Old World monkeys. For all major salivary proteins in humans, we could identify counterparts in chimpanzee and gorilla saliva. However, we discovered unique protein profiles in saliva of humans that were distinct from those of nonhuman primates. These findings open up the possibility that dietary differences and pathogenic pressures may have shaped a distinct salivary proteome in the human lineage.

Enamel thickness variation in the deciduous dentition of extant large-bodied hominoids

OBJECTIVES

Enamel thickness features prominently in hominoid evolutionary studies. To date, however, studies of enamel thickness in humans, great apes, and their fossil relatives have focused on the permanent molar row. Comparatively little research effort has been devoted to tissue proportions within deciduous teeth. Here we attempt to fill this gap by documenting enamel thickness variation in the deciduous dentition of extant large-bodied hominoids.

MATERIALS AND METHODS

We used microcomputed tomography to image dental tissues in 80 maxillary and 78 mandibular deciduous premolars of Homo sapiens, Pan troglodytes, Gorilla, and Pongo. Two-dimensional virtual sections were created from the image volumes to quantify average (AET) and relative (RET) enamel thickness, as well as its distribution across the crown.

RESULTS

Our results reveal no significant differences in enamel thickness among the great apes. Unlike the pattern present in permanent molars, Pongo does not stand out as having relatively thicker-enameled deciduous premolars than P. troglodytes and Gorilla. Humans, on the other hand, possess significantly thicker deciduous premolar enamel in comparison to great apes. Following expectations from masticatory biomechanics, we also find that the "functional" side (protocone, protoconid) of deciduous premolars generally possesses thicker enamel than the "nonfunctional" side.

DISCUSSION

Our study lends empirical support to anecdotal observations that patterns of AET and RET observed for permanent molars of large-bodied apes do not apply to deciduous premolars. By documenting enamel thickness variation in hominoid deciduous teeth, this study provides the comparative context to interpret rates and patterns of wear of deciduous teeth and their utility in life history reconstructions.

Effects of a recurring late-night event on the behavior and welfare of a population of zoo-housed gorillas

The impact of visitors on the well-being of captive animals presents both positive and potentially negative consequences. While some amount of novelty through visitor stimulation offers the opportunity for a more complex captive environment, anecdotal evidence from primate staff observations at the Smithsonian's National Zoo and Conservation Biology Institute suggested that gorillas exhibited increased restlessness during the annual month-long late night ZooLights (ZL) event than before it. The current study compared activity budgets, aggression (interactions involving contact between conspecifics and displays toward visitors), and abnormal behaviors in two groups of socially housed gorillas for 1-month periods before, during, and after the 2015 ZL event. We also compared the fecal glucocorticoid metabolite profiles of all six gorillas across these same observation periods. Physiologically, most individuals appeared to cope appropriately with the increased visitor presence during the event. We saw little difference in contact aggression; however, abnormal behavior was observed in some gorillas during and after the event, which highlights the importance of individual analysis and data interpretation. As predicted, we found that the majority of gorillas rested less during ZL than during other observation periods, particularly adult females in the mixed sex troop. Preliminary results of this study aided the decision of zoo management to close initially the Great Ape House and subsequently most animal buildings during future ZL events to avoid the potential disruption of normal activity patterns. While the findings of this study were mixed as to the impact of the event on these gorillas, the results suggest that zoos should carefully consider the possible ramifications of keeping great ape buildings open for lengthy multi-night events.

Chimpanzee lip-smacks confirm primate continuity for speech-rhythm evolution

Speech is a human hallmark, but its evolutionary origins continue to defy scientific explanation. Recently, the open-close mouth rhythm of 2-7 Hz (cycles/second) characteristic of all spoken languages has been identified in the orofacial signals of several nonhuman primate genera, including orangutans, but evidence from any of the African apes remained missing. Evolutionary continuity for the emergence of speech is, thus, still inconclusive. To address this empirical gap, we investigated the rhythm of chimpanzee lip-smacks across four populations (two captive and two wild). We found that lip-smacks exhibit a speech-like rhythm at approximately 4 Hz, closing a gap in the evidence for the evolution of speech-rhythm within the primate order. We observed sizeable rhythmic variation within and between chimpanzee populations, with differences of over 2 Hz at each level. This variation did not result, however, in systematic group differences within our sample. To further explore the phylogenetic and evolutionary perspective on this variability, inter-individual and inter-population analyses will be necessary across primate species producing mouth signals at speech-like rhythm. Our findings support the hypothesis that speech recruited ancient primate rhythmic signals and suggest that multi-site studies may still reveal new windows of understanding about these signals' use and production along the evolutionary timeline of speech.

Comparison of 25-hydroxyvitamin D concentration in chimpanzee dried blood spots and serum

BACKGROUND

Dried blood spots (DBS) are used in human medicine to measure total 25-hydroxyvitamin D (25-OHD) in the blood. However, this easy and affordable sampling technique has not been evaluated in primates to measure vitamin D concentrations.

OBJECTIVES

We aimed to compare 25-OHD measurements in chimpanzee serum at two different laboratories and determine the precision and accuracy of the DBS method by comparing DBS and serum results.

METHODS

Blood samples from 17 captive chimpanzees were collected, and 25-OHD₃ and 25-OHD₂ were measured in serum at two accredited laboratories using liquid chromatography-tandem mass spectrometry. The same analytes were measured on DBS cards, and results were compared with that of serum. Data were assessed using the Spearman correlation, Deming regression, and Bland-Altman analyses.

RESULTS

The correlation coefficient between the two measurements in serum was r_s  = .51 (P = .04), and the mean bias was -1.25 ± 14.83. When comparing 25-OHD concentrations measured in DBS and serum at the same laboratory, the r_s was 0.7 (P = .002), and the mean bias was 1.42 ± 14.58. Estimated intra-assay and inter-assay coefficients of variation for DBS results were 6% and 12.6%, respectively.

CONCLUSIONS

Although substantial analytical variability was found in 25-OHD measurements regardless of the sample type, the identification of both constant and proportional error and wider limits of agreement with the DBS technique makes the interpretation of DBS results challenging, especially for values close to clinical cut-off points. The DBS and serum methods were not interchangeable, and further studies are needed to validate DBS samples for vitamin D measurements in chimpanzees.