Tandem NBPF 3mer HORs (Olduvai triplets) in Neanderthal and two novel HOR tandem arrays in human chromosome 1 T2T-CHM13 assembly.

It is known that the ~ 1.6 kb Neuroblastoma BreakPoint Family (NBPF) repeats are human specific and contributing to cognitive capabilities, with increasing frequency in higher order repeat 3mer HORs (Olduvai triplets). From chimpanzee to modern human there is a discontinuous jump from 0 to ~ 50 tandemly organized 3mer HORs. Here we investigate the structure of NBPF 3mer HORs in the Neanderthal genome assembly of Pääbo et al., comparing it to the results obtained for human hg38.p14 chromosome 1. Our findings reveal corresponding NBPF 3mer HOR arrays in Neanderthals with slightly different monomer structures and numbers of HOR copies compared to humans. Additionally, we compute the NBPF 3mer HOR pattern for the complete telomere-to-telomere human genome assembly (T2T-CHM13) by Miga et al., identifying two novel tandem arrays of NBPF 3mer HOR repeats with 5 and 9 NBPF 3mer HOR copies. We hypothesize that these arrays correspond to novel NBPF genes (here referred to as NBPFA1 and NBPFA2). Further improving the quality of the Neanderthal genome using T2T-CHM13 as a reference would be of great interest in determining the presence of such distant novel NBPF genes in the Neanderthal genome and enhancing our understanding of human evolution.

The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees.

BACKGROUND: Comparative gene expression studies in apes are fundamentally limited by the challenges associated with sampling across different tissues. Here, we used single-cell RNA sequencing of embryoid bodies to collect transcriptomic data from over 70 cell types in three humans and three chimpanzees. RESULTS: We find hundreds of genes whose regulation is conserved across cell types, as well as genes whose regulation likely evolves under directional selection in one or a handful of cell types. Using embryoid bodies from a human-chimpanzee fused cell line, we also infer the proportion of inter-species regulatory differences due to changes in cis and trans elements between the species. Using the cis/trans inference and an analysis of transcription factor binding sites, we identify dozens of transcription factors whose inter-species differences in expression are affecting expression differences between humans and chimpanzees in hundreds of target genes. CONCLUSIONS: Here, we present the most comprehensive dataset of comparative gene expression from humans and chimpanzees to date, including a catalog of regulatory mechanisms associated with inter-species differences.

Morphological evolution of language-relevant brain areas.

Human language is supported by a cortical network involving Broca's area, which comprises Brodmann Areas 44 and 45 (BA44 and BA45). While cytoarchitectonic homolog areas have been identified in nonhuman primates, it remains unknown how these regions evolved to support human language. Here, we use histological data and advanced cortical registration methods to precisely compare the morphology of BA44 and BA45 in humans and chimpanzees. We found a general expansion of Broca's areas in humans, with the left BA44 enlarging the most, growing anteriorly into a region known to process syntax. Together with recent functional and receptorarchitectural studies, our findings support the conclusion that BA44 evolved from an action-related region to a bipartite system, with a posterior portion supporting action and an anterior portion supporting syntactic processes. Our findings add novel insights to the longstanding debate on the relationship between language and action, and the evolution of Broca's area.

Viral evolution of SIV chimpanzee toward HIV-1 using humanized mice.

HIV-1 emerged from SIVcpz evolving in humans. Humanized mice are an effective tool for assessing viral evolution via measuring viral loads, CD4+ T cell decline, and analyzing genetic changes. Four serial passages showed many non-synonymous mutations important for the adaptation and evolution of SIVcpz to human immune cells.

The provisioned primate: patterns of obesity across lemurs, monkeys, apes and humans.

Non-human primates are potentially informative but underutilized species for investigating obesity. I examined patterns of obesity across the Primate order, calculating the ratio of body mass in captivity to that in the wild. This index, relative body mass, for n = 40 non-human primates (mean ± s.d.: females: 1.28 ± 0.30, range 0.67-1.78, males: 1.24 ± 0.28, range 0.70-1.97) overlapped with a reference value for humans (women: 1.52, men: 1.44). Among non-human primates, relative body mass was unrelated to dietary niche, and was marginally greater among female cohorts of terrestrial species. Males and females had similar relative body masses, but species with greater sexual size dimorphism (male/female mass) in wild populations had comparatively larger female body mass in captivity. Provisioned populations in wild and free-ranging settings had similar relative body mass to those in research facilities and zoos. Compared to the wild, captive diets are unlikely to be low in protein or fat, or high in carbohydrate, suggesting these macronutrients are not driving overeating in captive populations. Several primate species, including chimpanzees, a sister-species to humans, had relative body masses similar to humans. Humans are not unique in the propensity to overweight and obesity. This article is part of a discussion meeting issue 'Causes of obesity: theories, conjectures and evidence (Part II)'.

Optimal path selection and secured data transmission in underwater acoustic sensor networks: LSTM-based energy prediction.

The Underwater Acoustic Sensor Network (UASN) is a large network in which the vicinity of a transmitting node is made up of numerous operational sensor nodes. The communication process may be substantially disrupted due to the underwater acoustic channel's time-varying and space-varying features. As a result, the underwater acoustic communication system faces the problems of reducing interference and enhancing communication effectiveness and quality through adaptive modulation. To overcome this issue, this paper intends to propose a model for optimal path selection and secured data transmission in UASN via Long Short-Term Memory (LSTM) based energy prediction. The proposed model of transmitting the secured data in UASN through the optimal path involves two major phases. Initially, the nodes are selected under the consideration of constraints like energy, distance and link quality in terms of throughput. Moreover, the energy is predicted with the aid of LSTM and the optimal path is selected with the proposed hybrid optimization algorithm termed as Pelican Updated Chimp Optimization Algorithm (PUCOA), which is the combination of two algorithms including the Pelican Optimization Algorithm (POA) and Chimp Optimization Algorithm (COA). Further, the data is transmitted via the optimal path securely by encrypting the data with the proposed improved blowfish algorithm (IBFA). At last, the developed LSTM+PUCOA model is validated with standard benchmark models and it proves that the performance of the proposed LSTM+PUCOA model attains 90.85% of accuracy, 92.78% of precision, 91.78% of specificity, 89.79% of sensitivity, 7.21% of FPR, 89.76% of F1 score, 89.77% of MCC, 10.20% of FNR, 92.45% of NPV, and 10.22% of FDR for Learning percentage 70.

Why do distractions sometimes aid self-control? Pigeons (Columba livia) highlight possible mechanisms underlying the distraction effect.

In this essay, the author explores the question of why distractions sometimes aid self-control. In a study with chimpanzees, Evans and Beran (2007) used two conditions with toys to address the possibility raised by Mueller et al. (2023) about toys as distractors. In the first, the accumulating rewards were within reach, and so chimpanzees had to inhibit taking rewards if more were to accumulate. The second condition was essential to this issue, as in that case toys also were available, but the delayed reward was out of reach (i.e., the chimpanzees were forced to wait to get the delayed reward). Because these trial types were intermixed, an explanation of the toys' effectiveness through conditioned association with the delayed reward would predict that the chimpanzees should have engaged the toys equally often in both conditions. However, three of four chimpanzees engaged the toys more when the accumulating reward was within reach compared to when it was not. Evans and Beran suggested that engagement with distractors in that study occurred when it was functionally effective in aiding delayed gratification, not solely as a result of toys being associated with delayed rewards, and thus was a cognitively controlled decision by the chimpanzees. The results of Evans and Beran (2007) have yet to be replicated in any other primate species. But, Mueller et al. (2023) noted that a study with a parrot (Koepke et al., 2015) showed that the parrot would use distractors and even move the smaller, sooner reward away from itself, perhaps matching the self-distraction techniques of children who hide their faces or talk to themselves. Thus, it remains to be determined whether those behaviors also can be explained by learned associations with reward or whether they reflect attention-based explanations. Mueller et al. (2023) have provided a creative experiment and a compelling argument that more careful analysis is needed of exactly what happens when an animal (or child) engages distractors and shows improved self-control, so that we can understand what role past reinforcement history may play and what possible attentional strategies or other cognitive strategies are at work in different self-control tasks. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

"Untying the knot": The primitive orofacial muscle architecture in the gorilla (Gorilla gorilla) as a key to the evolution of hominin facial movement.

The anatomical underpinnings of primate facial expressions are essential to exploring their evolution. Traditionally, it has been accepted that the primate face exhibits a "scala natura" morphocline, ranging from primitive to derived characteristics. At the primitive end, the face consists of undifferentiated muscular sheets, while at the derived end there is greater complexity with more muscles and insertion points. Among these, the role of the human modiolus ("knoten" in German) has been emphasized. Recent studies have challenged this view by revealing significant complexity in the faces of several non-human primates, thereby rejecting the linear notion of facial evolution. However, our knowledge of the facial architecture in gorillas, the second closest living relatives to modern humans, remains a significant gap in the literature. Here, we present new findings based on dissection and histological analysis of one gorilla craniofacial specimen, alongside 30 human hemifaces. Our results indicate that while the number and overall arrangement of facial muscles in the gorilla are comparable to those of chimpanzees and modern humans, several orofacial features distinguish the gorilla's anatomy from that of hominins. Among these are the absence of a modiolus, the continuity of muscular fibers over the region of the mouth corner, the flat (uncurving) sheet of the orbicularis oris muscle, and the insertion of direct labial tractors both anterior and posterior to it. Collectively, the anatomical characteristics observed in the gorilla suggest that the complex anatomy of the hominin face should be considered synapomorphic (shared-derived) within the Pan-Homo clade.

High diversity and sharing of strongylid nematodes in humans and great apes co-habiting an unprotected area in Cameroon.

Rapid increases in human populations and environmental changes of past decades have led to changes in rates of contact and spatial overlap with wildlife. Together with other historical, social and environmental processes, this has significantly contributed to pathogen transmission in both directions, especially between humans and non-human primates, whose close phylogenetic relationship facilitates cross-infections. Using high-throughput amplicon sequencing, we studied strongylid communities in sympatric western lowland gorillas, central chimpanzees and humans co-occurring in an unprotected area in the northern periphery of the Dja Faunal Reserve, Cameroon. At the genus level, we classified 65 strongylid ITS-2 amplicon sequencing variants (ASVs) in humans and great apes. Great apes exhibited higher strongylid diversity than humans. Necator and Oesophagostomum were the most prevalent genera, and we commonly observed mixed infections of more than one strongylid species. Human strongylid communities were dominated by the human hookworm N. americanus, while great apes were mainly infected with N. gorillae, O. stephanostomum and trichostrongylids. We were also able to detect rare strongylid taxa (such as Ancylostoma and Ternidens). We detected eight ASVs shared between humans and great apes (four N. americanus variants, two N. gorillae variants, one O. stephanostomum type I and one Trichostrongylus sp. type II variant). Our results show that knowledge of strongylid communities in primates, including humans, is still limited. Sharing the same habitat, especially outside protected areas (where access to the forest is not restricted), can enable mutual parasite exchange and can even override host phylogeny or conserved patterns. Such studies are critical for assessing the threats posed to all hosts by increasing human-wildlife spatial overlap. In this study, the term "contact" refers to physical contact, while "spatial overlap" refers to environmental contact.

Functional morphological integration related to feeding biomechanics in the hominine skull.

Quantifying and characterizing the pattern of trait covariances is crucial for understanding how population-level patterns of integration might constrain or facilitate craniofacial evolution related to the feeding system. This study addresses an important gap in our knowledge by investigating magnitudes and patterns of morphological integration of biomechanically informative traits in the skulls of Homo sapiens, Pan troglodytes, and Gorilla gorilla. We predicted a lower magnitude of integration among human biomechanical traits since humans eat a softer, less biomechanically challenging diet than apes. Indeed, compared to African apes, the magnitudes of integration were lower in H. sapiens skulls for form data (raw dimensions) but were similar or higher for shape data (raw dimensions scaled by geometric mean). Patterns of morphological integration were generally similar, but not identical, across the three species, particularly for the form data compared to the shape data. Traits that load heavily on the primary axis of variation in morphospace are generally associated with size and/or shape of the temporalis and masseter muscles and with dimensions related to the constrained lever model of jaw biomechanics. Given the conserved nature of morphological integration, skull adaptations for food processing in African apes and humans may have been constrained to occur along certain paths of high evolvability. The conserved pattern of functional integration also indicates that extant hominine species can operate as reasonable analogues for extinct hominins in studies that require population-level patterns of trait variance/covariance.

A non-invasive, concealed electrocardiogram and bioimpedance measurement system for captive primates.

Captive housed non-human primates, specifically great apes such as chimpanzees (Pan troglodytes) are frequently reported to have died from or are diagnosed with potentially fatal heart conditions that require the monitoring of physiological signals such as electrocardiogram (ECG) or respiratory rate. ECG screening must be conducted after applying full anaesthesia, causing potential physical and emotional stress as well as risk for the animal. Here, we present an electronic system that simultaneously measures the ECG and the electrical bioimpedance for the early detection of abnormal cardiovascular activity. Modified gloves whose fingers are equipped with electrodes enable the caregiver to obtain three cardiovascular signals (ECG, pulse rate and respiratory rate) by placing the fingertips on specific parts of the non-human primate without needing any prior physical preparations. Validation (ECG and bioimpedance) was performed both on humans and on captive housed chimpanzees, where all the signals of interest were correctly acquired.

Reciprocity and beyond: Explaining meat transfers in savanna-dwelling chimpanzees at Fongoli, Senegal.

OBJECTIVES: To understand the function of food sharing among our early hominin ancestors, we can turn to our nonhuman primate relatives for insight. Here, we examined the function of meat sharing by Fongoli chimpanzees, a community of western chimpanzees (Pan troglodytes verus) in southeastern Sénégal. MATERIALS AND METHODS: We tested three non-mutually exclusive hypotheses that have been used to explain patterns of food sharing: kin selection, generalized reciprocity, and meat-for-mating opportunities. We analyzed meat sharing events (n = 484) resulting from hunts, along with data on copulations, age-sex class, and kinship to determine which variables predict the likelihood of meat sharing during this study period (2006-2019). RESULTS: We found full or partial support for kin selection, direct reciprocity, and meat-for-mating-opportunities. However, the analyses reveal that reciprocity and a mother/offspring relationship were the strongest predictors of whether or not an individual shared meat. CONCLUSIONS: The results of this study emphasize the complexity of chimpanzee meat sharing behaviors, especially at a site where social tolerance offers increased opportunities for meat sharing by individuals other than dominant males. These findings can be placed in a referential model to inform hypotheses about the sensitivity of food sharing to environmental pressures, such as resource scarcity in savanna landscapes.

Ghost admixture in eastern gorillas.

Archaic admixture has had a substantial impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. In great apes, archaic admixture has been identified in chimpanzees and bonobos but the possibility of such events has not been explored in other species. Here, we address this question using high-coverage whole-genome sequences from all four extant gorilla subspecies, including six newly sequenced eastern gorillas from previously unsampled geographic regions. Using approximate Bayesian computation with neural networks to model the demographic history of gorillas, we find a signature of admixture from an archaic 'ghost' lineage into the common ancestor of eastern gorillas but not western gorillas. We infer that up to 3% of the genome of these individuals is introgressed from an archaic lineage that diverged more than 3 million years ago from the common ancestor of all extant gorillas. This introgression event took place before the split of mountain and eastern lowland gorillas, probably more than 40 thousand years ago and may have influenced perception of bitter taste in eastern gorillas. When comparing the introgression landscapes of gorillas, humans and bonobos, we find a consistent depletion of introgressed fragments on the X chromosome across these species. However, depletion in protein-coding content is not detectable in eastern gorillas, possibly as a consequence of stronger genetic drift in this species.

Intraspecific variation of long bone cross-sectional properties in Pan troglodytes troglodytes and Gorilla gorilla gorilla.

OBJECTIVES: Morphological intraspecific variation is due to the balance between skeletal plasticity and genetic constraint on the skeleton. Osteogenic responses to external stimuli, such as locomotion, have been well documented interspecifically across the primate order, but less so at the intraspecific level. Here, we examine the differences in cross-sectional variability of the femur, humerus, radius, and tibia in Pan troglodytes troglodytes versus Gorilla gorilla gorilla. We investigate whether there are sex, species, bone, and trait differences in response to variable body size and locomotion. MATERIALS AND METHODS: Adult male and female P. t. troglodytes and G. g. gorilla long bones from the Cleveland Museum of Natural History were scanned with a peripheral quantitative computer tomography system. Scans were taken at the midshaft of each bone according to functional bone length. Coefficients of variation were used to provide a size-independent measure of variation. We applied a Bonferroni correction to account for the multiple pairwise tests. RESULTS: There were limited significant differences between males and females, however, females tended to be more variable than males. Variation in Gorilla, when significant, was greater than in Pan, although significant differences were limited. There were no differences between bone variability in male and female Gorilla, and female Pan. DISCUSSION: Increased female variability may be due to more variable locomotor behavior, particularly during periods of pregnancy, lactation, and caring for an offspring compared to consistent locomotion over the life course by males. Body size may be a contributing factor to variability; more work is needed to understand this relationship.

Visually assessed body condition shows high heritability in a pedigreed great ape population.

Body condition, a measure for relative fat mass, is associated with primate health, fitness, and overall welfare. Body condition is often influenced by dietary factors, age, and/or sex, but several body condition measures (body weight, weight-to-height ratios, and so on) also show high heritability across primate species, indicating a role of genetic effects. Although different measures for body condition exist, many require direct handling of animals, which is invasive, time-consuming, and expensive, making them impractical in wild and captive settings. Therefore, noninvasive visual body condition score (BCS) systems were developed for various animal species, including macaques and chimpanzees, to visually assess relative fat mass. Here we evaluate the utility of a visual BCS system in bonobos by assessing (1) inter-rater reliability, (2) links with body mass, a traditional hands-on measure of condition, and (3) the factors driving individual variation in BCS. We adapted the chimpanzee BCS system to rate 76 bonobos in 11 European zoos (92% of the adult population). Inter-rater reliability was high (s* = 0.948), BCSs were positively associated with body mass (ß = 0.075) and not predicted by diet, sex, or age, nor were they associated with a higher abundance of obesity-related diseases. Instead, BCSs showed high levels of heritability (h2 = 0.637), indicating that a majority of body condition variation in bonobos is attributable to genetic similarity of the individuals. This is in line with reported h2 -values for traditional body condition measures in primates and provides support for the reliability of visual BCS systems in great apes. The results of this study emphasize an often unanticipated role of genetics in determining primate body fat and health that has implications for the management of captive primates. Application of this tool in wild populations would aid to unravel environmental from genetic drivers of body condition variation in primates.

The relevance of the unique anatomy of the human prefrontal operculum to the emergence of speech.

Identifying the evolutionary origins of human speech remains a topic of intense scientific interest. Here we describe a unique feature of adult human neuroanatomy compared to chimpanzees and other primates that may provide an explanation of changes that occurred to enable the capacity for speech. That feature is the Prefrontal extent of the Frontal Operculum (PFOp) region, which is located in the ventrolateral prefrontal cortex, adjacent and ventromedial to the classical Broca's area. We also show that, in chimpanzees, individuals with the most human-like PFOp, particularly in the left hemisphere, have greater oro-facial and vocal motor control abilities. This critical discovery, when combined with recent paleontological evidence, suggests that the PFOp is a recently evolved feature of human cortical structure (perhaps limited to the genus Homo) that emerged in response to increasing selection for cognitive and motor functions evident in modern speech abilities.

A human-specific motif facilitates CARD8 inflammasome activation after HIV-1 infection.

Inflammasomes are cytosolic innate immune complexes that assemble upon detection of diverse pathogen-associated cues and play a critical role in host defense and inflammatory pathogenesis. Here, we find that the human inflammasome-forming sensor CARD8 senses HIV-1 infection via site-specific cleavage of the CARD8 N-terminus by the HIV protease (HIV-1PR). HIV-1PR cleavage of CARD8 induces pyroptotic cell death and the release of pro-inflammatory cytokines from infected cells, processes regulated by Toll-like receptor stimulation prior to viral infection. In acutely infected cells, CARD8 senses the activity of both de novo translated HIV-1PR and packaged HIV-1PR that is released from the incoming virion. Moreover, our evolutionary analyses reveal that the HIV-1PR cleavage site in human CARD8 arose after the divergence of chimpanzees and humans. Although chimpanzee CARD8 does not recognize proteases from HIV or simian immunodeficiency viruses from chimpanzees (SIVcpz), SIVcpz does cleave human CARD8, suggesting that SIVcpz was poised to activate the human CARD8 inflammasome prior to its cross-species transmission into humans. Our findings suggest a unique role for CARD8 inflammasome activation in response to lentiviral infection of humans.

Is it for real? Structural differences between play and real fighting in adult chimpanzees (Pan troglodytes).

In primates, as well as in other mammals, play fighting (PF) is a complex form of playful activity that is structurally similar to real fighting (RF) and may also be used in a competitive way. Here, we verify the structural key differences that can distinguish PF from RF in adult chimpanzees (Pan troglodytes). We collected 962 h of video recording on 30 adult individuals belonging to four chimpanzee groups (Mona Chimpanzee Sanctuary, Spain; La Vallée des Singes and ZooParc de Beauval, France). We applied different indices-two of which were borrowed from the ecological measures of biodiversity-to test for structural differences between PF (345 sessions) and RF (461 sessions) in the levels of behavior repetition (Repeatability of Same Behavior Index, RSBI), distribution uniformity (Pielou Index, J), variability (Shannon Index, H') and, symmetry (i.e., reciprocal exchange of offensive/defensive behaviors; Asymmetry Index, AI). Moreover, we compared the session duration between PF and RF. We found that duration and RSBI were higher in PF than RF while AI was higher in RF than PF. No difference was found between J and H'. Interestingly, both females and males maintained similar ranking positions (determined via Normalized David's scores) in RF and PF. Our study indicates that session duration, behavior repetition, and symmetry can be distinctive structural key features of PF whereas dominance role-reversal, behavior variability, and distribution uniformity were not. PF in adult chimpanzees may have elements of serious contexts (e.g., absence of role-reversal as in RF) which is in line with the view that play is a blended, multifunctional behavior deriving from the re-combination of different behavioral systems. Our findings highlight the need to investigate play structure and manifestation in a nuanced way to better understand the actual motivation that underlies what appears to be play.

Observational approaches to chimpanzee behavior in an African sanctuary: Implications for research, welfare, and capacity-building.

Research in African ape sanctuaries has emerged as an important context for our understanding of comparative cognition and behavior. While much of this work has focused on experimental studies of cognition, these animals semi-free-range in forest habitats and therefore can also provide important information about the behavior of primates in socioecologically-relevant naturalistic contexts. In this "New Approaches" article, we describe a project where we implemented a synthetic program of observational data collection at Ngamba Island Chimpanzee Sanctuary in Uganda, directly modeled after long-term data collection protocols at the Kibale Chimpanzee Project in Uganda, a wild chimpanzee field site. The foundation for this project was a strong partnership between sanctuary staff, field site staff, and external researchers. We describe how we developed a data-collection protocol through discussion and collaboration among these groups, and trained sanctuary caregivers to collect novel observational data using these protocols. We use these data as a case study to examine: (1) how behavioral observations in sanctuaries can inform primate welfare and care practices, such as by understanding aggression within the group; (2) how matched observational protocols across sites can inform our understanding of primate behavior across different contexts, including sex differences in social relationships; and (3) how more robust collaborations between foreign researchers and local partners can support capacity-building in primate range countries, along with mentoring and training students more broadly.