Publications

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the mobile element locator tool (melt): population-scale mobile element discovery and biology.mobile element insertions (meis) represent ~25% of all structural variants in human genomes. moreover, when they disrupt genes, meis can influence human traits and diseases. therefore, meis should be fully discovered along with other forms of genetic variation in whole genome sequencing (wgs) projects involving population genetics, human diseases, and clinical genomics. here, we describe the mobile element locator tool (melt), which was developed as part of the 1000 genomes project to perform me ...201728855259
comparative genomics of human stem cell factor (scf).stem cell factor (scf) is a critical protein with key roles in the cell such as hematopoiesis, gametogenesis and melanogenesis. in the present study a comparative analysis on nucleotide sequences of scf was performed in humanoids using bioinformatics tools including ncbi-blast, mega6, and jbrowse. our analysis of nucleotide sequences to find closely evolved organisms with high similarity by ncbi-blast tools and mega6 showed that human and chimpanzee (pan troglodytes) were placed into the same cl ...201728447043
elucidating the origin of hla-b*73 allelic lineage: did modern humans benefit by archaic introgression?a previous study reported that some of the human leukocyte antigen (hla) alleles and haplotypes in present-day humans were acquired by admixture with archaic humans; specifically, an exceptionally diverged hla-b*73 allele was proposed to be transmitted from denisovans, although the dna sequence of hla-b*73 has not been detected in the denisovan genome. here, we argue against the hypothesis that hla-b*73 introgressed from denisovans into early modern humans. a phylogenetic analysis revealed that ...201727695917
fire usage and ancient hominin detoxification genes: protective ancestral variants dominate while additional derived risk variants appear in modern humans.studies of the defence capacity of ancient hominins against toxic substances may contribute importantly to the reconstruction of their niche, including their diets and use of fire. fire usage implies frequent exposure to hazardous compounds from smoke and heated food, known to affect general health and fertility, probably resulting in genetic selection for improved detoxification. to investigate whether such genetic selection occurred, we investigated the alleles in neanderthals, denisovans and ...201727655273
from play to proficiency: the ontogeny of stone-tool use in coastal-foraging long-tailed macaques (macaca fascicularis) from a comparative perception-action perspective.macaques crack shellfish in coastal environments with specialized stone-hammering techniques. i provide the first examination of skill development from 866 object-manipulation and 7,400 tool-use bouts, collected over 15 months, using longitudinal analyses of infants' object manipulation (n = 7) and cross-sectional comparisons of manipulative and tool-use behavior (n = 69). i adopt a perception-action approach, examining how the emergence of actions on objects relate to the spatial-relational and ...201728318292
the laminar organization of the motor cortex in monodactylous mammals: a comparative assessment based on horse, chimpanzee, and macaque.the architecture of the neocortex classically consists of six layers, based on cytological criteria and on the layout of intra/interlaminar connections. yet, the comparison of cortical cytoarchitectonic features across different species proves overwhelmingly difficult, due to the lack of a reliable model to analyze the connection patterns of neuronal ensembles forming the different layers. we first defined a set of suitable morphometric cell features, obtained in digitized nissl-stained sections ...201728210850
pharmacokinetics of the novel echinocandin cd101 in multiple animal species.cd101 is a novel semisynthetic echinocandin with antifungal activity against candida and aspergillus spp. the pharmacokinetics (pk) of cd101 administered intravenously to mice, rats, dogs, cynomolgus monkeys, and chimpanzees are presented. cd101 consistently exhibited very low clearance, a modest volume of distribution at steady state (vss), and a long half-life (t1/2) across all species tested. in mouse, rat, dog, cynomolgus monkey, and chimpanzee, cd101 clearance was 0.10, 0.47, 0.30, 0.41, an ...201728137817
analysis of sea almond (terminalia catappa) cracking sites used by wild burmese long-tailed macaques (macaca fascicularis aurea).nut-cracking is shared by all non-human primate taxa that are known to habitually use percussive stone tools in the wild: robust capuchins (sapajus spp.), western chimpanzees (pan troglodytes verus), and burmese long-tailed macaques (macaca fascicularis aurea). despite opportunistically processing nuts, burmese long-tailed macaques predominantly use stone tools to process mollusks in coastal environments. here, we present the first comprehensive survey of sea almond (terminalia catappa) nut-crac ...201728056164
the foxp2-driven network in developmental disorders and neurodegeneration.the transcription repressor foxp2 is a crucial player in nervous system evolution and development of humans and songbirds. in order to provide an additional insight into its functional role we compared target gene expression levels between human neuroblastoma cells (sh-sy5y) stably overexpressing foxp2 cdna of either humans or the common chimpanzee, rhesus monkey, and marmoset, respectively. rna-seq led to identification of 27 genes with differential regulation under the control of human foxp2, ...201728798667
automated face recognition of rhesus macaques.rhesus macaques are widely used in biomedical research. automated behavior monitoring can be useful in various fields (including neuroscience), as well as having applications to animal welfare but current technology lags behind that developed for other species. one difficulty facing developers is the reliable identification of individual macaques within a group especially as pair- and group-housing of macaques becomes standard. current published methods require either implantation or wearing of ...201728739161
comprehensive transcriptome analysis of neocortical layers in humans, chimpanzees and macaques.while human cognitive abilities are clearly unique, underlying changes in brain organization and function remain unresolved. here we characterized the transcriptome of the cortical layers and adjacent white matter in the prefrontal cortexes of humans, chimpanzees and rhesus macaques using unsupervised sectioning followed by rna sequencing. more than 20% of detected genes were expressed predominantly in one layer, yielding 2,320 human layer markers. while the bulk of the layer markers were conser ...201728414332
changes in lipidome composition during brain development in humans, chimpanzees, and macaque monkeys.lipids are essential components of the brain. here, we conducted a comprehensive mass spectrometry-based analysis of lipidome composition in the prefrontal cortex of 40 humans, 40 chimpanzees, and 40 rhesus monkeys over postnatal development and adulthood. of the 11,772 quantified lipid peaks, 7,589 change significantly along the lifespan. more than 60% of these changes occur prior to adulthood, with less than a quarter associated with myelination progression. evolutionarily, 36% of the age-depe ...201728158622
robust representations of individual faces in chimpanzees (pan troglodytes) but not monkeys (macaca mulatta).being able to recognize the faces of our friends and family members no matter where we see them represents a substantial challenge for the visual system because the retinal image of a face can be degraded by both changes in the person (age, expression, pose, hairstyle, etc.) and changes in the viewing conditions (direction and degree of illumination). yet most of us are able to recognize familiar people effortlessly. a popular theory for how face recognition is achieved has argued that the brain ...201727864643
the first smile: spontaneous smiles in newborn japanese macaques (macaca fuscata).spontaneous smiles are facial movements that are characterized by lip corner raises that occur during irregular sleep or drowsiness without known external or internal causes. they are shown by human infants and infant chimpanzees. these smiles are considered to be the developmental origin of smiling and laughter. there are some case studies showing that spontaneous smiles occur in japanese macaques. the goals of this study were to investigate whether newborn japanese macaques show a considerable ...201727485748
the evolutionary roots of prosociality: the case of instrumental helping.comparative studies with closely related primate species are crucial to understand the origins of human prosociality. one type of prosocial behaviour that probably relies on evolutionary ancient skills and motivations is instrumental helping. recent experimental studies have shown that bonobos and chimpanzees will help others achieve their action goals. chimpanzees have shown to help others picking up and giving objects to a recipient, opening locked doors for conspecifics struggling to open the ...201728850865
children, chimpanzees, and bonobos adjust the visibility of their actions for cooperators and competitors.chimpanzees and bonobos are highly capable of tracking other's mental states. it has been proposed, however, that in contrast to humans, chimpanzees are only able to do this in competitive interactions but this has rarely been directly tested. here, pairs of chimpanzees or bonobos (study 1) and 4-year-old children (study 2) were presented with two almost identical tasks differing only regarding the social context. in the cooperation condition, players' interests were matched: they had to make co ...201728819263
the development and flexibility of gaze alternations in bonobos and chimpanzees.infants' early gaze alternations are one of their first steps towards a sophisticated understanding of the social world. this ability, to gaze alternate between an object of interest and another individual also attending to that object, has been considered foundational to the development of many complex social-cognitive abilities, such as theory of mind and language. however, to understand the evolution of these abilities, it is important to identify whether and how gaze alternations are used an ...201728812318
ultrastructure of lingual papillae in common chimpanzee (pan troglodytes) foetus, newborn and adult specimens.among primates, the two recognized species of chimpanzees (common chimpanzee, pan troglodytes; pygmy chimpanzee, pan paniscus) are considered to be the most similar to humans. importantly, in mammals, the food intake behaviour largely determines the tongue morphology, including the type, proportion and distribution of gustatory and non-gustatory tongue papillae. the lingual papillae form during its development and mature in post-natal life depending on the different feeding. in this study, we ha ...201728726319
acquisition of terrestrial life by human ancestors influenced by forest microclimate.bipedalism, terrestriality and open habitat were thought to be linked to each other in the course of human evolution. however, recent paleontological evidence has revealed that early hominins evolved in a wooded, humid environment. did the evolutionary process from arboreal to terrestrial life actually require open habitat? here i report the seasonal change in forest utilization height of west african chimpanzees (pan troglodytes) and central african bonobos (pan paniscus), and show that the dif ...201728720889
male reproductive skew is higher in bonobos than chimpanzees.the two closest living relatives of humans, bonobos (pan paniscus) and chimpanzees (pan troglodytes), share many traits that are common in humans but rare in other mammals, including societies with high fission-fusion dynamics, male philopatry, female dispersal and extensive social bonding among unrelated individuals [1]. the major difference between these two species is that male aggression is more frequent and intense in male-dominated chimpanzees than in bonobos, where the highest-ranking ind ...201728697359
aids in chimpanzees: the role of mhc genes.the ancestral progenitor of common chimpanzees and bonobos experienced a selective sweep that ravaged its major histocompatibility complex (mhc) class i repertoire. the causative agent was probably an ancestral retrovirus, highly related to the contemporary hiv-1 strain, which initiated the acquired immunodeficiency syndrome pandemic in the human population. as a direct result, mhc class i allotypes with the capability of targeting conserved retroviral elements were enriched in the ancestral pro ...201728695283
significant differentiation in the apolipoprotein(a)/lipoprotein(a) trait between chimpanzees from western and central africa.elevated lipoprotein(a) (lp(a)) plasma concentrations are a risk factor for cardiovascular disease in humans, largely controlled by the lpa gene encoding apolipoprotein(a) (apo(a)). lp(a) is composed of low-density lipoprotein (ldl) and apo(a) and restricted to catarrhini. a variable number of kringle iv (kiv) domains in lpa lead to a size polymorphism of apo(a) that is inversely correlated with lp(a) concentrations. smaller apo(a) isoforms and higher lp(a) levels in central chimpanzees (pan tro ...201728671714
limited mhc class i intron 2 repertoire variation in bonobos.common chimpanzees (pan troglodytes) experienced a selective sweep, probably caused by a siv-like virus, which targeted their mhc class i repertoire. based on mhc class i intron 2 data analyses, this selective sweep took place about 2-3 million years ago. as a consequence, common chimpanzees have a skewed mhc class i repertoire that is enriched for allotypes that are able to recognise conserved regions of the siv proteome. the bonobo (pan paniscus) shared an ancestor with common chimpanzees appr ...201728623393
mhc class i diversity in chimpanzees and bonobos.major histocompatibility complex (mhc) class i genes are critically involved in the defense against intracellular pathogens. mhc diversity comparisons among samples of closely related taxa may reveal traces of past or ongoing selective processes. the bonobo and chimpanzee are the closest living evolutionary relatives of humans and last shared a common ancestor some 1 mya. however, little is known concerning mhc class i diversity in bonobos or in central chimpanzees, the most numerous and genetic ...201728623392
harassment of adults by immatures in bonobos (pan paniscus): testing the exploratory aggression and rank improvement hypotheses.the immatures of many primate species frequently pester adult group members with aggressive behaviors referred to as a type of harassment. although these behaviors are characteristic of immatures as they develop from infancy through adolescence, there have been few studies that specifically address the adaptive significance of harassment. two functional hypotheses have been generated from observations of the behavior in chimpanzees. the exploratory aggression hypothesis describes harassment as a ...201728612152
chimpanzees, bonobos and children successfully coordinate in conflict situations.social animals need to coordinate with others to reap the benefits of group-living even when individuals' interests are misaligned. we compare how chimpanzees, bonobos and children coordinate their actions with a conspecific in a snowdrift game, which provides a model for understanding how organisms coordinate and make decisions under conflict. in study 1, we presented pairs of chimpanzees, bonobos and children with an unequal reward distribution. in the critical condition, the preferred reward ...201728592680
sex-specific association patterns in bonobos and chimpanzees reflect species differences in cooperation.in several group-living species, individuals' social preferences are thought to be influenced by cooperation. for some societies with fission-fusion dynamics, sex-specific association patterns reflect sex differences in cooperation in within- and between-group contexts. in our study, we investigated this hypothesis further by comparing sex-specific association patterns in two closely related species, chimpanzees and bonobos, which differ in the level of between-group competition and in the degre ...201728573000
comparison of male conflict behavior in chimpanzees (pan troglodytes) and bonobos (pan paniscus), with specific regard to coalition and post-conflict behavior.coalitions among males during within group conflicts have a strong influence on the competitive and social environment within social groups. to evaluate possible variation in the occurrence of such coalitions in our closest relatives, chimpanzees and bonobos, we compared male aggression and coalitionary behavior in two natural communities, one of each species, with a similar size and composition. furthermore we compared affiliative behavior that might be related to coalition formation among male ...201728543664
great apes distinguish true from false beliefs in an interactive helping task.understanding the behavior of others in a wide variety of circumstances requires an understanding of their psychological states. humans' nearest primate relatives, the great apes, understand many psychological states of others, for example, perceptions, goals, and desires. however, so far there is little evidence that they possess the key marker of advanced human social cognition: an understanding of false beliefs. here we demonstrate that in a nonverbal (implicit) false-belief test which is pas ...201728379987
bonobo anatomy reveals stasis and mosaicism in chimpanzee evolution, and supports bonobos as the most appropriate extant model for the common ancestor of chimpanzees and humans.common chimps and bonobos are our closest living relatives but almost nothing is known about bonobo internal anatomy. we present the first phylogenetic analysis to include musculoskeletal data obtained from a recent dissection of bonobos. notably, chimpanzees, and in particular bonobos, provide a remarkable case of evolutionary stasis for since the chimpanzee-human split c.8 ma among >120 head-neck (hn) and forelimb (fl) muscles there were only four minor changes in the chimpanzee clade, and a ...201728377592
bonobos maintain immune system diversity with three functional types of mhc-b.fast-evolving mhc class i polymorphism serves to diversify nk cell and cd8 t cell responses in individuals, families, and populations. because only chimpanzee and bonobo have strict orthologs of all hla class i, their study gives unique perspectives on the human condition. we defined polymorphism of papa-b, the bonobo ortholog of hla-b, for six wild bonobo populations. sequences for papa-b exon 2 and 3 were determined from the genomic dna in 255 fecal samples, minimally representing 110 individu ...201728348269
gorilla mhc class i gene and sequence variation in a comparative context.comparisons of mhc gene content and diversity among closely related species can provide insights into the evolutionary mechanisms shaping immune system variation. after chimpanzees and bonobos, gorillas are humans' closest living relatives; but in contrast, relatively little is known about the structure and variation of gorilla mhc class i genes (gogo). here, we combined long-range amplifications and long-read sequencing technology to analyze full-length mhc class i genes in 35 gorillas. we obta ...201728332079
"giving" and "responding" differences in gestural communication between nonhuman great ape mothers and infants.in the first comparative analysis of its kind, we investigated gesture behavior and response patterns in 25 captive ape mother-infant dyads (six bonobos, eight chimpanzees, three gorillas, and eight orangutans). we examined (i) how frequently mothers and infants gestured to each other and to other group members; and (ii) to what extent infants and mothers responded to the gestural attempts of others. our findings confirmed the hypothesis that bonobo mothers were more proactive in their gesturing ...201728323346
the y chromosomes of the great apes.the great apes (orangutans, gorillas, chimpanzees, bonobos and humans) descended from a common ancestor around 13 million years ago, and since then their sex chromosomes have followed very different evolutionary paths. while great-ape x chromosomes are highly conserved, their y chromosomes, reflecting the general lability and degeneration of this male-specific part of the genome since its early mammalian origin, have evolved rapidly both between and within species. understanding great-ape y chro ...201728265767
validation of a method for the assessment of urinary neopterin levels to monitor health status in non-human-primate species.determining individual health status is of great importance for a better understanding of life history trade-offs between growth, reproduction, and maintenance. however, existing immunological methods are invasive and therefore not suitable for investigating health status in wild populations. thus, there is an urgent need for non-invasive methods to assess the immune status of animals. neopterin is involved in the cell-mediated pathway of the immune response (th1-type), secreted during the activ ...201728220080
discovery of african bat polyomaviruses and infrequent recombination in the large t antigen in the polyomaviridae.bat species represent natural reservoirs for a number of high-consequence human pathogens. the present study investigated the diversity of polyomaviruses (pyvs) in zambian insectivorous and fruit bat species. we describe the complete genomes from four newly proposed african bat pyv species employing the recently recommended criteria provided by the polyomaviridae study group of the international committee on taxonomy of viruses. a comprehensive phylogenetic and recombination analysis was perform ...201728430100
'unwilling' versus 'unable': tonkean macaques' understanding of human goal-directed actions.the present study investigated the understanding of goal-directed actions in tonkean macaques (macaca tonkeana) using the unwilling versus unable paradigm, previously used in several species. subjects were tested in three experimental conditions that varied according to the goal-directed actions of a human actor. in the "unwilling" condition, the actor was capable of giving the subject food but unwilling to do it; in the "unable" condition, she was willing to give food but was unable to do it be ...201728480137
african non-human primates host diverse enteroviruses.enteroviruses (evs) belong to the family picornaviridae and are responsible for mild to severe diseases in mammals including humans and non-human primates (nhp). simian evs were first discovered in the 1950s in the old world monkeys and recently in wild chimpanzee, gorilla and mandrill in cameroon. in the present study, we screened by pcr evs in 600 fecal samples of wild apes and monkeys that were collected at four sites in gabon. a total of 32 samples were positive for evs (25 from mandrills, 7 ...201728081564
genetic variations in the human g protein-coupled receptor class c, group 6, member a (gprc6a) control cell surface expression and function.gprc6a is a g protein-coupled receptor activated by l-amino acids, which, based on analyses of knock-out mice, has been suggested to have physiological functions in metabolism and testicular function. the human ortholog is, however, mostly retained intracellularly in contrast to the cell surface-expressed murine and goldfish orthologs. the latter orthologs are gq-coupled and lead to intracellular accumulation of inositol phosphates and calcium release. in the present study we cloned the bonobo c ...201727986810
primate empathy: three factors and their combinations for empathy-related phenomena.empathy as a research topic is receiving increasing attention, although there seems some confusion on the definition of empathy across different fields. frans de waal (de waal fbm. putting the altruism back into altruism: the evolution of empathy. annu rev psychol 2008, 59:279-300. doi:10.1146/annurev.psych.59.103006.093625) used empathy as an umbrella term and proposed a comprehensive model for the evolution of empathy with some of its basic elements in nonhuman animals. in de waal's model, emp ...201727977913
apes submentalise.making subtle and extensive use of eye-tracking technology, krupenye and colleagues showed that, like human infants, great apes - chimpanzees, bonobos and orangutans - can accurately anticipate the goal-directed behaviour of an agent that holds a false belief. how do they do it, by mentalising or by submentalising?201727919697
nut-cracking behaviour in wild-born, rehabilitated bonobos (pan paniscus): a comprehensive study of hand-preference, hand grips and efficiency.there has been an enduring interest in primate tool-use and manipulative abilities, most often with the goal of providing insight into the evolution of human manual dexterity, right-hand preference, and what behaviours make humans unique. chimpanzees (pan troglodytes) are arguably the most well-studied tool-users amongst non-human primates, and are particularly well-known for their complex nut-cracking behaviour, which has been documented in several west african populations. however, their siste ...201727564429
the gestural repertoire of the wild bonobo (pan paniscus): a mutually understood communication system.in animal communication, signallers and recipients are typically different: each signal is given by one subset of individuals (members of the same age, sex, or social rank) and directed towards another. however, there is scope for signaller-recipient interchangeability in systems where most signals are potentially relevant to all age-sex groups, such as great ape gestural communication. in this study of wild bonobos (pan paniscus), we aimed to discover whether their gestural communication is ind ...201727632158
the role of defensins in hiv pathogenesis.profound loss of cd4(+) t cells, progressive impairment of the immune system, inflammation, and sustained immune activation are the characteristics of human immunodeficiency virus-1 (hiv-1) infection. innate immune responses respond immediately from the day of hiv infection, and a thorough understanding of the interaction between several innate immune cells and hiv-1 is essential to determine to what extent those cells play a crucial role in controlling hiv-1 in vivo. defensins, divided into the ...201728839349
social disappointment explains chimpanzees' behaviour in the inequity aversion task.chimpanzees' refusal of less-preferred food when an experimenter has previously provided preferred food to a conspecific has been taken as evidence for a sense of fairness. here, we present a novel hypothesis-the social disappointment hypothesis-according to which food refusals express chimpanzees' disappointment in the human experimenter for not rewarding them as well as they could have. we tested this hypothesis using a two-by-two design in which food was either distributed by an experimenter ...201728835562
perception of the average size of multiple objects in chimpanzees (pan troglodytes).humans can extract statistical information, such as the average size of a group of objects or the general emotion of faces in a crowd without paying attention to any individual object or face. to determine whether summary perception is unique to humans, we investigated the evolutional origins of this ability by assessing whether chimpanzees, which are closely related to humans, can also determine the average size of multiple visual objects. five chimpanzees and 18 humans were able to choose the ...201728835550
the effects of captive versus wild rearing environments on long bone articular surfaces in common chimpanzees (pan troglodytes).the physical environments of captive and wild animals frequently differ in substrate types and compliance. as a result, there is an assumption that differences in rearing environments between captive and wild individuals produce differences in skeletal morphology. here, this hypothesis is tested using a sample of 42 captive and wild common chimpanzees (pan troglodytes). articular surface areas of the humerus, radius, ulna, femur, and tibia were calculated from linear breadth measurements, adjust ...201728828263
long-term consistency in chimpanzee consolation behaviour reflects empathetic personalities.in contrast to a wealth of human studies, little is known about the ontogeny and consistency of empathy-related capacities in other species. consolation-post-conflict affiliation from uninvolved bystanders to distressed others-is a suggested marker of empathetic concern in non-human animals. using longitudinal data comprising nearly a decade of observations on over 3000 conflict interactions in 44 chimpanzees (pan troglodytes), we provide evidence for relatively stable individual differences in ...201728819207
sex-biased dispersal of human ancestors.some anthropologists and primatologists have argued that, judging by extant chimpanzees and humans, which are female-biased dispersers, the common ancestors of humans and chimpanzees were also female-biased dispersers. it has been thought that sex-biased dispersal patterns have been genetically transmitted for millions of years. however, this character has changed many times with changes in environment and life-form during human evolution and historical times. i examined life-form and social org ...201728815964
spontaneous cross-species imitation in interactions between chimpanzees and zoo visitors.imitation is a cornerstone of human development, serving both a cognitive function (e.g. in the acquisition and transmission of skills and knowledge) and a social-communicative function, whereby the imitation of familiar actions serves to maintain social interaction and promote prosociality. in nonhuman primates, this latter function is poorly understood, or even claimed to be absent. in this observational study, we documented interactions between chimpanzees and zoo visitors and found that the ...201728815382
tooth wear inclination in great ape molars.primate dietary diversity is reflected in their dental morphology, with differences in size and shape of teeth. in particular, the tooth wear angle can provide insight into a species' ability to break down certain foods. to examine dietary and masticatory information, digitized polygon models of dental casts provide a basis for quantitative analysis of wear associated with tooth attrition. in this study, we analyze and compare the wear patterns of pongo pygmaeus, gorilla gorillagorilla and pan t ...201728810237
learning the rules of the rock-paper-scissors game: chimpanzees versus children.the present study aimed to investigate whether chimpanzees (pan troglodytes) could learn a transverse pattern by being trained in the rules of the rock-paper-scissors game in which "paper" beats "rock," "rock" beats "scissors," and "scissors" beats "paper." additionally, this study compared the learning processes between chimpanzees and children. seven chimpanzees were tested using a computer-controlled task. they were trained to choose the stronger of two options according to the game rules. th ...201728795255
hiv-1-neutralizing antibody induced by simian adenovirus- and poxvirus mva-vectored bg505 native-like envelope trimers.rabbits and monkeys immunized with hiv type 1 (hiv-1) native-like bg505 sosip.664 (bg505s) glycoprotein trimers are known to induce antibodies that can neutralize the autologous tier-2 virus. here, we assessed the induction of hiv-1 trimer binding and neutralizing antibody (nab) titres when bg505s trimers were also delivered by non-replicating simian (chimpanzee) adenovirus and non-replicating poxvirus modified vaccinia virus ankara (mva) vaccine vectors. first, we showed that approximately two- ...201728792942
studying primate cognition in a social setting to improve validity and welfare: a literature review highlighting successful approaches.studying animal cognition in a social setting is associated with practical and statistical challenges. however, conducting cognitive research without disturbing species-typical social groups can increase ecological validity, minimize distress, and improve animal welfare. here, we review the existing literature on cognitive research run with primates in a social setting in order to determine how widespread such testing is and highlight approaches that may guide future research planning.201728791199
predation by female chimpanzees: toward an understanding of sex differences in meat acquisition in the last common ancestor of pan and homo.among modern foraging societies, men hunt more than women, who mostly target relatively low-quality, reliable resources (i.e., plants). this difference has long been assumed to reflect human female reproductive constraints, particularly caring for and provisioning mates and offspring. long-term studies of chimpanzees (pan troglodytes) enable tests of hypotheses about the possible origins of human sex differences in hunting, prior to pair-bonding and regular provisioning. we studied two eastern c ...201728778463
animal models of hbv infection.the mechanisms determining hepatitis b virus (hbv) persistence and pathogenesis are not fully elucidated, but appear to be multi-factorial. current medication to repress viral replication is available; however, the unique replication strategies employed by hbv enable the virus to persist within the infected hepatocytes. consequently, cure is rarely achieved. progresses in hbv research and preclinical testing of antiviral agents have been limited by the narrow species- and tissue-tropism of the v ...201728774409
persistent anthrax as a major driver of wildlife mortality in a tropical rainforest.anthrax is a globally important animal disease and zoonosis. despite this, our current knowledge of anthrax ecology is largely limited to arid ecosystems, where outbreaks are most commonly reported. here we show that the dynamics of an anthrax-causing agent, bacillus cereus biovar anthracis, in a tropical rainforest have severe consequences for local wildlife communities. using data and samples collected over three decades, we show that rainforest anthrax is a persistent and widespread cause of ...201728770842
triarchic psychopathy dimensions in chimpanzees (pan troglodytes): investigating associations with genetic variation in the vasopressin receptor 1a gene.vasopressin is a neuropeptide known to be associated with the development and evolution of complex socio-emotional behaviors including those relevant to psychopathic personality. in both humans and chimpanzees, recent research suggests a strong genetic contribution to individual variation in psychopathic traits. to date, however, little is known concerning specific genes that might explain the observed heritability of psychopathy. in a relatively large sample of captive chimpanzees (n = 164), th ...201728769746
estimation of fst and the impact of de novo mutation.wright defined fst as a measure of genetic differentiation. cockerham developed an estimator of fst based on binary indicators in an anova framework. here, we address 2 issues regarding the estimation of fst. first, we derive a new estimator of fst based on the anova framework using the doubly truncated normal distribution as an approximation of the binomial distribution to estimate variances. second, we consider the impact of de novo mutation on fst estimation.201728768256
correction: the malagarasi river does not form an absolute barrier to chimpanzee movement in western tanzania.[this corrects the article doi: 10.1371/journal.pone.0058965.].201728763511
evolution of male strategies with sex-ratio-dependent pay-offs: connecting pair bonds with grandmothering.men's provisioning of mates and offspring has been central to ideas about human evolution because paternal provisioning is absent in our closest evolutionary cousins, the great apes, and is widely assumed to result in pair bonding, which distinguishes us from them. yet mathematical modelling has shown that paternal care does not readily spread in populations where competition for multiple mates is the common male strategy. here we add to models that point to the mating sex ratio as an explanatio ...201728760768
isolation and identification of bifidobacterium species from feces of captive chimpanzees.recently, gut-dwelling bifidobacteria from chimpanzees, which are phylogenetically close to humans and have feeding habits similar to humans, have been frequently investigated. given this, we speculated that like humans, chimpanzees would have a unique diversity of bifidobacteria. we herein describe a taxonomically novel member of bifidobacteria isolated from fecal samples of captive chimpanzees. bifidobacteria were detected in all fecal samples by quantitative polymerase chain reaction. a bifid ...201728748130
functionality of intrinsic disorder in tumor necrosis factor-α and its receptors.tumor necrosis factor-α (tnf-α) is a pleiotropic inflammatory cytokine that exerts potent cytotoxic effects on solid tumor cells, while not affecting their normal counterparts. it is also known that tnf-α exerts many of its biological functions via interaction with specific receptors. to understand the potential roles of intrinsic disorder in the functioning of this important cytokine, we explored the peculiarities of intrinsic disorder distribution in human tnf-α and its homologs from various s ...201728746777
development of a new structural class of broadly acting hcv non-nucleoside inhibitors leading to the discovery of mk-8876.studies directed at developing a broadly acting non-nucleoside inhibitor of hcv ns5b led to the discovery of a novel structural class of 5-aryl benzofurans that simultaneously interact with both the palm i and palm ii binding regions. an initial candidate was potent in vitro against hcv gt1a and gt1b replicons, and induced multi-log reductions in hcv viral load when orally dosed to chronic gt1 infected chimpanzees. however, in vitro potency losses against clinically relevant gt1a variants prompt ...201728741898
culture extends the scope of evolutionary biology in the great apes.discoveries about the cultures and cultural capacities of the great apes have played a leading role in the recognition emerging in recent decades that cultural inheritance can be a significant factor in the lives not only of humans but also of nonhuman animals. this prominence derives in part from these primates being those with whom we share the most recent common ancestry, thus offering clues to the origins of our own thoroughgoing reliance on cumulative cultural achievements. in addition, the ...201728739927
a heterologous prime-boost ebola virus vaccine regimen induces durable neutralizing antibody response and prevents ebola virus-like particle entry in mice.ebola virus (ebov) is one of the most virulent pathogens known to humans. neutralizing antibodies play a major role in the protection against ebov infections. thus, an ebov vaccine capable of inducing a long-lasting neutralizing antibody response is highly desirable. we report here that a heterologous prime-boost vaccine regimen can elicit durable ebov-neutralizing antibody response in mice. a chimpanzee serotype 7 adenovirus expressing ebov gp (denoted adc7-gp) was generated and used for primin ...201728733113
evolutionary scenarios and primate natural history.scenarios summarize evolutionary patterns and processes by interpreting organismal traits and their natural history correlates in a phylogenetic context. they are constructed by (1) describing phenotypes (including physiology and behavior), ideally with attention to formative roles of development, experience, and culture; (2) inferring homologies, homoplasies, ancestral character states, and their transformations with phylogenetic analyses; and (3) integrating those components with ecological an ...201728731824
age- and sex-associated differences in phenotypic and functional characteristics of peripheral blood lymphocytes in chimpanzees (pan troglodytes).chimpanzees are the closest phylogenetic relatives to humans, sharing more than 98% genetic sequence identity. thesegenetic similarities prompted the belief that chimpanzees can serve as an ideal model for human disease conditions andvaccine development. however, in light of the recent nih decision to phase out biomedical research in chimpanzees and retire nih-supported chimpanzees, data from the present study will continue to provide value for the care of aged and sick chimpanzees located in zo ...201728726600
expression of myhc isoforms mrna transcripts in different regions of the masseter and medial pterygoid muscles in chimpanzees.the aim of this study is to examine the expression pattern of the different myosin heavy chain (myhc) isoforms in the masseter and medial pterygoid muscles by real time quantitative polymerase chain reaction (rt-qpcr) to obtain information at molecular level which can be related to the functional characteristics of these two muscles.201728719832
rna editing independently occurs at three mir-376a-1 sites and may compromise the stability of the microrna hairpin.rna editing is being recognized as an important post-transcriptional mechanism that may have crucial roles in introducing genetic variation and phenotypic diversity. despite microrna editing recurrence, defining its biological relevance is still under extended debate. to better understand microrna editing function and regulation we performed an exhaustive characterization of the a-to-i site-specific patterns in mir-376a-1, a mammalian microrna which rna editing is involved in the regulation of d ...201728710037
the social organization of homo ergaster: inferences from anti-predator responses in extant primates.patterns of primate socioecology have been used to suggest that the first truly savanna-dwelling hominin, homo ergaster, lived in sizeable groups. here, we revisit these estimates and infer additional features of the social organization of these early hominins based on anti-predator responses observed across the primate taxon. we first show that the effect of habitat on primate group size, composition, and sexual dimorphism is negligible after controlling for substrate use and phylogeny: terrest ...201728688456
foot use during vertical climbing in chimpanzees (pan troglodytes).upright bipedalism is a hallmark of hominin locomotion, however debates continue regarding the extent of arboreal locomotion and the nature of bipedalism practiced by early hominins. pedal form and function play a prominent role in these debates, as the foot is the element that directly interacts with the locomotor substrate. recent finds have substantially increased the availability of associated foot remains of early hominins and emphasized the enigmatic nature of the early evolution of human ...201728688455
modeling social dominance: elo-ratings, prior history, and the intensity of aggression.among studies of social species, it is common practice to rank individuals using dyadic social dominance relationships. the elo-rating method for achieving this is powerful and increasingly popular, particularly among studies of nonhuman primates, but suffers from two deficiencies that hamper its usefulness: an initial burn-in period during which the model is unreliable and an assumption that all win-loss interactions are equivalent in their influence on rank trajectories. here, i present r code ...201728680188
whole mitochondrial genome capture from faecal samples and museum-preserved specimens.population-scale molecular studies of endangered and cryptic species are often limited by access to high-quality samples. the use of noninvasively collected samples or museum-preserved specimens reduces the pressure on modern populations by removing the need to capture and handle live animals. however, endogenous dna content in such samples is low, making shotgun sequencing a financially prohibitive approach. here, we apply a target enrichment method to retrieve mitochondrial genomes from 65 mus ...201728675688
t cell activation and differentiation is modulated by a cd6 domain 1 antibody itolizumab.cd6 is associated with t-cell modulation and is implicated in several autoimmune diseases. we previously demonstrated that itolizumab, a cd6 domain 1 (cd6d1) specific humanized monoclonal antibody, inhibited the proliferation and cytokine production by t lymphocytes stimulated with anti-cd3 antibody or when co-stimulated with alcam. aberrant il-17 producing cd4+ helper t-cells (th17) have been identified as pivotal for the pathogenesis of certain inflammatory autoimmune disorders, including psor ...201728672038
the critically endangered western chimpanzee declines by 80.african large mammals are under extreme pressure from unsustainable hunting and habitat loss. certain traits make large mammals particularly vulnerable. these include late age at first reproduction, long inter-birth intervals, and low population density. great apes are a prime example of such vulnerability, exhibiting all of these traits. here we assess the rate of population change for the western chimpanzee, pan troglodytes verus, over a 24-year period. as a proxy for change in abundance, we u ...201728671715
developmental trajectory of the corpus callosum from infancy to the juvenile stage: comparative mri between chimpanzees and humans.how brains develop during early life is one of the most important topics in neuroscience because it underpins the neuronal functions that mature during this period. a comparison of the neurodevelopmental patterns among humans and nonhuman primates is essential to infer evolutional changes in neuroanatomy that account for higher-order brain functions, especially those specific to humans. the corpus callosum (cc) is the major white matter bundle that connects the cerebral hemispheres, and therefor ...201728654656
chimpanzee super strength and human skeletal muscle evolution.since at least the 1920s, it has been reported that common chimpanzees (pan troglodytes) differ from humans in being capable of exceptional feats of "super strength," both in the wild and in captive environments. a mix of anecdotal and more controlled studies provides some support for this view; however, a critical review of available data suggests that chimpanzee mass-specific muscular performance is a more modest 1.5 times greater than humans on average. hypotheses for the muscular basis of th ...201728652350
evolution of the sperm methylome of primates is associated with retrotransposon insertions and genome instability.changes in gene expression resulting from epigenetic and/or genetic changes play an important role in the evolutionary divergence of phenotypes. to explore how epigenetic and genetic changes are linked during primate evolution, we have compared the genome-wide dna methylation profiles (methylomes) of humans and chimpanzees, which have a 1.2% dna sequence divergence, of sperm, the frontal cortices, b cells, and neutrophils. we revealed that species-specific differentially methylated regions (s-dm ...201728637190
silencing effect of hominoid highly conserved noncoding sequences on embryonic brain development.superfamily hominoidea, which consists of hominidae (humans and great apes) and hylobatidae (gibbons), is well-known for sharing human-like characteristics, however, the genomic origins of these shared unique phenotypes have mainly remained elusive. to decipher the underlying genomic basis of hominoidea-restricted phenotypes, we identified and characterized hominoidea-restricted highly conserved noncoding sequences (hcnss) that are a class of potential regulatory elements which may be involved i ...201728633494
response to: chimpanzee culture extends beyond matrilineal family units.we thank van leeuwen et al.[1] for their response to our finding that matrilineal relationships strongly influence the style of high-arm grooming in wild chimpanzees of the kanyawara community. we agree with them that grooming styles could be transmitted by different mechanisms in different contexts, and we appreciate their effort to assess whether the transmission of grooming styles within two captive groups in chimfunshi accords with our result.201728633026
chimpanzee culture extends beyond matrilineal family units.the 'grooming handclasp' is one of the most well-established cultural traditions in chimpanzees. a recent study by wrangham et al.[1] reduced the cultural scope of grooming-handclasp behavior by showing that grooming-handclasp style convergence is "explained by matrilineal relationship rather than conformity" [1]. given that we previously reported cultural differences in grooming-handclasp style preferences in captive chimpanzees [2], we tested the alternative view posed by wrangham et al.[1] in ...201728633025
reconstruction and evolutionary history of eutherian chromosomes.whole-genome assemblies of 19 placental mammals and two outgroup species were used to reconstruct the order and orientation of syntenic fragments in chromosomes of the eutherian ancestor and six other descendant ancestors leading to human. for ancestral chromosome reconstructions, we developed an algorithm (deschrambler) that probabilistically determines the adjacencies of syntenic fragments using chromosome-scale and fragmented genome assemblies. the reconstructed chromosomes of the eutherian, ...201728630326
chimpanzees return favors at a personal cost.humans regularly provide others with resources at a personal cost to themselves. chimpanzees engage in some cooperative behaviors in the wild as well, but their motivational underpinnings are unclear. in three experiments, chimpanzees (pan troglodytes) always chose between an option delivering food both to themselves and a partner and one delivering food only to themselves. in one condition, a conspecific partner had just previously taken a personal risk to make this choice available. in another ...201728630319
group augmentation, collective action, and territorial boundary patrols by male chimpanzees.how can collective action evolve when individuals benefit from cooperation regardless of whether they pay its participation costs? according to one influential perspective, collective action problems are common, especially when groups are large, but may be solved when individuals who have more to gain from the collective good or can produce it at low costs provide it to others as a byproduct. several results from a 20-y study of one of the most striking examples of collective action in nonhuman ...201728630310
raw material procurement for termite fishing tools by wild chimpanzees in the issa valley, western tanzania.chimpanzee termite fishing has been studied for decades, yet the selective processes preceding the manufacture of fishing tools remain largely unexplored. we investigate raw material selection and potential evidence of forward planning in the chimpanzees of issa valley, western tanzania.201728621823
preparatory responses to socially determined, mutually exclusive possibilities in chimpanzees and children.the capacity to imagine and prepare for alternative future possibilities is central to human cognition. recent research suggests that between age 2 and 4 children gradually begin to demonstrate a capacity to prepare for two simple, mutually exclusive alternatives of an immediate future event. when children were given the opportunity to catch a target an experimenter dropped into an inverted y-shaped tube, 2-year olds-as well as great apes-tended to cover only one of the exits, whereas 4-year-old ...201728615352
human vaccination against plasmodium vivax duffy-binding protein induces strain-transcending antibodies.plasmodium vivax is the most widespread human malaria geographically; however, no effective vaccine exists. red blood cell invasion by the p. vivax merozoite depends on an interaction between the duffy antigen receptor for chemokines (darc) and region ii of the parasite's duffy-binding protein (pvdbp_rii). naturally acquired binding-inhibitory antibodies against this interaction associate with clinical immunity, but it is unknown whether these responses can be induced by human vaccination.201728614791
wild chimpanzees' use of single and combined vocal and gestural signals.we describe the individual and combined use of vocalizations and gestures in wild chimpanzees. the rate of gesturing peaked in infancy and, with the exception of the alpha male, decreased again in older age groups, while vocal signals showed the opposite pattern. although gesture-vocal combinations were relatively rare, they were consistently found in all age groups, especially during affiliative and agonistic interactions. within behavioural contexts rank (excluding alpha-rank) had no effect on ...201728596637
chimpanzee ankle and foot joint kinematics: arboreal versus terrestrial locomotion.many aspects of chimpanzee ankle and midfoot joint morphology are believed to reflect adaptations for arboreal locomotion. however, terrestrial travel also constitutes a significant component of chimpanzee locomotion, complicating functional interpretations of chimpanzee and fossil hominin foot morphology. here we tested hypotheses of foot motion and, in keeping with general assumptions, we predicted that chimpanzees would use greater ankle and midfoot joint ranges of motion during travel on arb ...201728594068
gene expression and adaptive noncoding changes during human evolution.despite evidence for adaptive changes in both gene expression and non-protein-coding, putatively regulatory regions of the genome during human evolution, the relationship between gene expression and adaptive changes in cis-regulatory regions remains unclear.201728583075
effective treatment of sivcpz-induced immunodeficiency in a captive western chimpanzee.simian immunodeficiency virus of chimpanzees (sivcpz), the progenitor of human immunodeficiency virus type 1 (hiv-1), is associated with increased mortality and aids-like immunopathology in wild-living chimpanzees (pan troglodytes). surprisingly, however, similar findings have not been reported for chimpanzees experimentally infected with sivcpz in captivity, raising questions about the intrinsic pathogenicity of this lentivirus.201728576126
chimpanzee intellect: personality, performance and motivation with touchscreen tasks.human intellect is characterized by intercorrelated psychological domains, including intelligence, academic performance and personality. higher openness is associated with higher intelligence and better academic performance, yet high performance among individuals is itself attributable to intelligence, not openness. high conscientiousness individuals, although not necessarily more intelligent, are better performers. work with other species is not as extensive, yet animals display similar relatio ...201728573025
consolation in the aftermath of robberies resembles post-aggression consolation in chimpanzees.post-aggression consolation is assumed to occur in humans as well as in chimpanzees. while consolation following peer aggression has been observed in children, systematic evidence of consolation in human adults is rare. we used surveillance camera footage of the immediate aftermath of nonfatal robberies to observe the behaviors and characteristics of victims and bystanders. consistent with empathy explanations, we found that consolation was linked to social closeness rather than physical closene ...201728562686
interferon-β response is impaired by hepatitis b virus infection in tupaia belangeri.to date, the chimpanzee has been used as the natural infection model for hepatitis b virus (hbv). however, as this model is very costly and difficult to use because of ethical and animal welfare issues, we aimed to establish the tupaia (tupaia belangeri) as a new model for hbv infection and characterized its intrahepatic innate immune response upon hbv infection. first, we compared the propagation of hbv genotypes a2 and c in vivo in tupaia hepatocytes. at 8-10days post infection (dpi), the leve ...201728551415
thrombotic thrombocytopenic purpura related to adamts13 deficiency, and successful treatment in a chimpanzee (pan troglodytes verus).a 27-year-old male chimpanzee (pan troglodytes verus) developed signs of thrombotic thrombocytopenic purpura (ttp). adamts13 deficiency appeared to be the cause of disease. after treatment with high-dose prednisone, haematological values and clinical signs recovered. this is the first description of spontaneous ttp associated with adamts13 deficiency in a non-human primate.201728547839
chimpanzees (pan troglodytes) flexibly use introduced species for nesting and bark feeding in a human-dominated habitat.as habitat loss and fragmentation place growing pressure on endangered nonhuman primate populations, researchers find increasing evidence for novel responses in behavior. in western uganda between the budongo and bugoma forests, chimpanzees (pan troglodytes schweinfurthii) inhabit a mosaic landscape comprising forest fragments, human settlements, and agricultural land. we recorded nests and feeding evidence of unhabituated chimpanzees in this region over a 12-mo period. we found extensive eviden ...201728546652
activity and habitat use of chimpanzees (pan troglodytes verus) in the anthropogenic landscape of bossou, guinea, west africa.many primate populations inhabit anthropogenic landscapes. understanding their long-term ability to persist in such environments and associated real and perceived risks for both primates and people is essential for effective conservation planning. primates in forest-agricultural mosaics often consume cultivars to supplement their diet, leading to potentially negative encounters with farmers. when crossing roads, primates also face the risk of encounters with people and collision with vehicles. c ...201728546651
the evolution of stories: from mimesis to language, from fact to fiction.why a species as successful as homo sapiens should spend so much time in fiction, in telling one another stories that neither side believes, at first seems an evolutionary riddle. because of the advantages of tracking and recombining true information, capacities for event comprehension, memory, imagination, and communication evolved in a range of animal species-yet even chimpanzees cannot communicate beyond the here and now. by homo erectus, our forebears had reached an increasing dependence on ...201728544658
natural pathology of the captive chimpanzee (pan troglodytes): a 35-year review.we present the spontaneous pathological lesions identified as a result of necropsy or biopsy for 245 chimpanzees (pan troglodytes) over a 35-year period. a review of the pathology database was performed for all diagnoses on chimpanzees from 1980 to 2014. all morphologic diagnoses, associated system, organ, etiology, and demographic information were reviewed and analyzed. cardiomyopathy was the most frequent lesion observed followed by hemosiderosis, hyperplasia, nematodiasis, edema, and hemorrha ...201728543059
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