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causal capture effects in chimpanzees (pan troglodytes).extracting a cause-and-effect structure from the physical world is an important demand for animals living in dynamically changing environments. human perceptual and cognitive mechanisms are known to be sensitive and tuned to detect and interpret such causal structures. in contrast to rigorous investigations of human causal perception, the phylogenetic roots of this perception are not well understood. in the present study, we aimed to investigate the susceptibility of nonhuman animals to mechanic ...201727835786
motor skill for tool-use is associated with asymmetries in broca's area and the motor hand area of the precentral gyrus in chimpanzees (pan troglodytes).among nonhuman primates, chimpanzees are well known for their sophistication and diversity of tool use in both captivity and the wild. the evolution of tool manufacture and use has been proposed as a driving mechanism for the development of increasing brain size, complex cognition and motor skills, as well as the population-level handedness observed in modern humans. notwithstanding, our understanding of the neurological correlates of tool use in chimpanzees and other primates remains poorly und ...201727816558
chimpanzee personality and the arginine vasopressin receptor 1a genotype.polymorphisms of the arginine vasopressin receptor 1a (avpr1a) gene have been linked to various measures related to human social behavior, including sibling conflict and agreeableness. in chimpanzees, avpr1a polymorphisms have been associated with traits important for social interactions, including sociability, joint attention, dominance, conscientiousness, and hierarchical personality dimensions named low alpha/stability, disinhibition, and negative emotionality/low dominance. we examined assoc ...201727804047
a neuroanatomical predictor of mirror self-recognition in chimpanzees.the ability to recognize one's own reflection is shared by humans and only a few other species, including chimpanzees. however, this ability is highly variable across individual chimpanzees. in humans, self-recognition involves a distributed, right-lateralized network including frontal and parietal regions involved in the production and perception of action. the superior longitudinal fasciculus (slf) is a system of white matter tracts linking these frontal and parietal regions. the current study ...201727803287
genenames.org: the hgnc and vgnc resources in 2017.the hugo gene nomenclature committee (hgnc) based at the european bioinformatics institute (embl-ebi) assigns unique symbols and names to human genes. currently the hgnc database contains almost 40 000 approved gene symbols, over 19 000 of which represent protein-coding genes. in addition to naming genomic loci we manually curate genes into family sets based on shared characteristics such as homology, function or phenotype. we have recently updated our gene family resources and introduced new im ...201727799471
commonly preserved and species-specific gyral folding patterns across primate brains.cortical folding pattern analysis is very important to understand brain organization and development. since previous studies mostly focus on human brain cortex, the regularity and variability of cortical folding patterns across primate brains (macaques, chimpanzees and human) remain largely unknown. this paper presents a novel computational framework to identify common or unique gyral folding patterns in macaque, chimpanzee and human brains using magnetic resonance imaging (mri) data. we quantit ...201727796591
chimpanzee seed dispersal in a montane forest fragment in rwanda.primate seed dispersal plays an important role in forest regeneration. it may be particularly important to anthropogenically disturbed habitats such as forest fragments. however, few studies have examined primate seed dispersal in these types of environments. chimpanzees (pan troglodytes) are frugivorous and large-bodied, and are therefore able to disperse both large and small seeds, making them an important seed dispersal species. we examined chimpanzee seed dispersal in gishwati forest, a 14 k ...201727900783
locomotor hand postures, carpal kinematics during wrist extension, and associated morphology in anthropoid primates.the biomechanics of wrist extension (or dorsiflexion) are important for understanding functional adaptation of the primate hand because extension mobility varies with habitual locomotor hand posture and facilitates certain manipulative tasks. here, intercarpal kinematics are employed to investigate mechanisms underlying wrist extension in a sample of anthropoids representing various arboreal and terrestrial locomotor modes. carpal kinematics are studied using computed-tomography of cadaveric for ...201727788281
sustained myrmecophagy in nigerian chimpanzees: preferred or fallback food?at some sites across africa, chimpanzees consume army ants, often aided by plant tools, although consumption frequencies vary greatly. other populations do not eat these insects at all, despite apparent abundance. the relative importance of this type of myrmecophagy for chimpanzee diet therefore remains unclear. we investigate if army ants constitute a preferred food or a fallback resource for chimpanzees at gashaka, nigeria, where army ants are consumed much more frequently than elsewhere.201727779749
a novel fecal stable isotope approach to determine the timing of age-related feeding transitions in wild infant chimpanzees.determining nutritional development in wild primates is difficult through observations because confirming dietary intake is challenging. physiological measures are needed to determine the relative contributions of maternal milk and other foods at different ages, and time of weaning. we used fecal stable carbon and nitrogen isotopes (δ(13) c, δ(15) n) and fecal nitrogen concentrations (%n) from wild chimpanzees at ngogo, uganda, to derive physiological dietary indicators during the transition fro ...201727768227
cloning, localization and focus formation at dna damage sites of canine xlf.understanding the molecular mechanisms of dna double-strand break (dsb) repair processes, especially nonhomologous dna-end joining (nhej), is critical for developing next-generation radiotherapies and chemotherapeutics for human and animal cancers. the localization, protein-protein interactions and post-translational modifications of core nhej factors, such as human ku70 and ku80, might play critical roles in controlling nhej activity. xrcc4-like factor (xlf) is a core nhej factor and plays a ke ...201727746407
paternal and grandpaternal ages at conception and descendant telomere lengths in chimpanzees and humans.telomeres are repeating dna at chromosome ends. telomere length (tl) declines with age in most human tissues, and shorter tl is thought to accelerate senescence. in contrast, older men have sperm with longer tl; correspondingly, older paternal age at conception (pac) predicts longer tl in offspring. this pac-effect could be a unique form of transgenerational genetic plasticity that modifies somatic maintenance in response to cues of recent ancestral experience. the pac-effect has not been examin ...201727731903
enamel biorhythms of humans and great apes: the havers-halberg oscillation hypothesis reconsidered.the havers-halberg oscillation (hho) hypothesis links evidence for the timing of a biorhythm retained in permanent tooth enamel (retzius periodicity) to adult body mass and life history traits across mammals. potentially, these links provide a way to access life history of fossil species from teeth. recently we assessed intra-specific predictions of the hho on human children. we reported retzius periodicity (rp) corresponded with enamel thickness, and cusp formation time, when calculated from is ...201727726135
the global synanthrome project: a call for an exhaustive study of human associates.here we coin the term synanthrome to describe all of the species we interact with. we propose that the time is now here for the global synanthrome project to describe all of our interacting species and how they have changed through time and across space. this effort must involve natural history, ecology, and evolutionary biology in addition to genomics studies that are already underway.201727717597
carbon and nitrogen stable isotopic offsets between diet and hair/feces in captive chimpanzees.estimation of the stable isotopic offsets between tissue and diet is important for dietary reconstructions. although stable isotopic studies of chimpanzees (pan troglodytes) are increasing, the isotopic offsets in chimpanzees have never been studied. in this study, the carbon and nitrogen stable isotopic offset values in hair and feces were measured for 13 captive chimpanzees for the first time.201727717069
reflections in the rainforest: full-length mirrors facilitate behavioral observations of unhabituated, wild chimpanzees.we describe behaviors of unhabituated wild chimpanzees in gabon during repeated encounters with large mirrors installed permanently in their home range. movement in proximity to the mirrors triggered video cameras that recorded the scene. data are presented for 51 mirror encounters spanning a 3-year period. after initial wariness, mirror-directed aggressive behaviors were common, especially in adult males, but aggression gradually diminished and eventually almost completely ceased. focusing on t ...201727629110
vertex- and atlas-based comparisons in measures of cortical thickness, gyrification and white matter volume between humans and chimpanzees.what changes in cortical organisation characterise global and localised variation between humans and chimpanzees remains a topic of considerable interest in evolutionary neuroscience. here, we examined regional variation in cortical thickness, gyrification and white matter in samples of human and chimpanzee brains. both species were mri scanned on the same platform using identical procedures. the images were processed and segmented by fsl and freesurfer and the relative changes in cortical thick ...201727100220
adolescent male chimpanzees do not form a dominance hierarchy with their peers.dominance hierarchies are a prominent feature of the lives of many primate species. these hierarchies have important fitness consequences, as high rank is often positively correlated with reproduction. although adult male chimpanzees strive for status to gain fitness benefits, the development of dominance relationships is not well understood. while two prior studies found that adolescent males do not display dominance relationships with peers, additional research at ngogo in kibale national park ...201727379650
laughter as an approach to vocal evolution: the bipedal theory.laughter is a simple, stereotyped, innate, human play vocalization that is ideal for the study of vocal evolution. the basic approach of describing the act of laughter and when we do it has revealed a variety of phenomena of social, linguistic, and neurological significance. findings include the acoustic structure of laughter, the minimal voluntary control of laughter, the punctuation effect (which describes the placement of laughter in conversation and indicates the dominance of speech over lau ...201727368630
what volume of seeds can a chimpanzee carry in its body?great apes are important seed dispersers with large bodies, able to swallow large seeds and travel long distances. although there have been several studies investigating seed dispersal quality [sensu schupp (vegetatio 107/108:15-29, 1993)] by chimpanzees, there is little information on the volume of seeds they can carry in their bodies. when a relatively fresh corpse of a mature female chimpanzee was found at mahale, tanzania, we took advantage of the rare opportunity to investigate the total we ...201727664100
cloning, localization and focus formation at dna damage sites of canine xrcc4.various chemotherapies and radiation therapies are useful for killing cancer cells mainly by inducing dna double-strand breaks (dsbs). uncovering the molecular mechanisms of dsb repair processes is crucial for developing next-generation radiotherapies and chemotherapeutics for human and animal cancers. xrcc4 plays a critical role in ku-dependent nonhomologous dna-end joining (nhej) in human cells, and is one of the core nhej factors. the localization of core nhej factors, such as human ku70 and ...201727644316
saliviruses-the first knowledge about a newly discovered human picornavirus.the salivirus, first discovered in the year 2009, is a member of the large and growing family picornaviridae. at present, the genus salivirus contains 1 species salivirus a and 2 genotypes, salivirus a1 and salivirus a2. salivirus has been identified in humans and chimpanzees and may cause acute gastroenteritis in humans, having been detected in 0% to 8.7% of fecal samples collected from gastroenteritis in different human populations. salivirus is ubiquitous in wastewater of human origin and riv ...201727641729
field studies of pan troglodytes reviewed and comprehensively mapped, focussing on japan's contribution to cultural primatology.field studies done over decades of wild chimpanzees in east, central and west africa have yielded impressive, cumulative findings in cultural primatology. japanese primatologists have been involved in this advance from the outset, over a wide variety of topics. here i review the origins and development of field studies of pan troglodytes, then assess their progress based on analogy between cultural primatology and cultural anthropology, through four stages: natural history, ethnography, ethnolog ...201727461577
feeding habitat quality and behavioral trade-offs in chimpanzees: a case for species distribution models.the distribution and abundance of food resources are among the most important factors that influence animal behavioral strategies. yet, spatial variation in feeding habitat quality is often difficult to assess with traditional methods that rely on extrapolation from plot survey data or remote sensing. here, we show that maximum entropy species distribution modeling can be used to successfully predict small-scale variation in the distribution of 24 important plant food species for chimpanzees at ...201727418751
the spread of a novel behavior in wild chimpanzees: new insights into the ape cultural mind.for years, the animal culture debate has been dominated by the puzzling absence of direct evidence for social transmission of behavioral innovations in the flagship species of animal culture, the common chimpanzee. although social learning of novel behaviors has been documented in captivity, critics argue that these findings lack ecological validity and therefore may not be relevant for understanding the evolution of culture. for the wild, it is possible that group-specific behavioral difference ...201726479151
endogenous retrovirus-mediated genomic variations in chimpanzees.transposable elements (tes) have played a significant role in the evolution of host genome by triggering genomic rearrangements. tes have been studied in various research fields, ranging from population genomics to personalized medicines. human-specific tes and tes existing in the human genome have been well studied. unlike them, non-human primate-specific tes remain shrouded in mystery. however, the study of te-mediated genomic or genetic variations through comparative genomics is essential to ...201726442175
distal communication by chimpanzees (pan troglodytes): evidence for common ground?van der goot et al. (2014) proposed that distal, deictic communication indexed the appreciation of the psychological state of a common ground between a signaler and a receiver. in their study, great apes did not signal distally, which they construed as evidence for the human uniqueness of a sense of common ground. this study exposed 166 chimpanzees to food and an experimenter, at an angular displacement, to ask, "do chimpanzees display distal communication?" apes were categorized as (a) proximal ...201726292996
the more g-loaded, the more heritable, evolvable, and phenotypically variable: homology with humans in chimpanzee cognitive abilities.expanding on a recent study that identified a heritable general intelligence factor (g) among individual chimpanzees from a battery of cognitive tasks, we hypothesized that the cognitive abilities that are more g-loaded would be more heritable and would present more additive genetic variance, in addition to showing more phenotypic variability. this pattern was confirmed, and is comparable to that found in humans, indicating fundamental homology. finally, tool use presented the highest heritabili ...201726005227
meaning and ostension in great ape gestural communication.it is sometimes argued that while human gestures are produced ostensively and intentionally, great ape gestures are produced only intentionally. if true, this would make the psychological mechanisms underlying the different species' communication fundamentally different, and ascriptions of meaning to chimpanzee gestures would be inappropriate. while the existence of different underlying mechanisms cannot be ruled out, in fact claims about difference are driven less by empirical data than by cont ...201626223212
the complete mitochondrial genome of the central chimpanzee, pan troglodytes troglodytes.this study first report the complete mitochondrial genome sequence of the central chimpanzee, pan troglodytes troglodytes. the genome was a total of 16 556 bp in length and had a base composition of a (31.05%), g (12.95%), c (30.84%), and t (25.16%), indicating that the percentage of a + t (56.21%) is higher than g + c (43.79%). similar to other primates, it possessed a typically conserved structure, including 13 protein-coding genes, 22 transfer rna genes, 2 ribosomal rna genes and 1 control re ...201626190079
towards a computational comparative neuroprimatology: framing the language-ready brain.we make the case for developing a computational comparative neuroprimatology to inform the analysis of the function and evolution of the human brain. first, we update the mirror system hypothesis on the evolution of the language-ready brain by (i) modeling action and action recognition and opportunistic scheduling of macaque brains to hypothesize the nature of the last common ancestor of macaque and human (lca-m); and then we (ii) introduce dynamic brain modeling to show how apes could acquire g ...201626482863
comprehension of iconic gestures by chimpanzees and human children.iconic gestures-communicative acts using hand or body movements that resemble their referent-figure prominently in theories of language evolution and development. this study contrasted the abilities of chimpanzees (n=11) and 4-year-old human children (n=24) to comprehend novel iconic gestures. participants learned to retrieve rewards from apparatuses in two distinct locations, each requiring a different action. in the test, a human adult informed the participant where to go by miming the action ...201626448391
production of grooming-associated sounds by chimpanzees (pan troglodytes) at ngogo: variation, social learning, and possible functions.chimpanzees (pan troglodytes) use some communicative signals flexibly and voluntarily, with use influenced by learning. these signals include some vocalizations and also sounds made using the lips, oral cavity, and/or teeth, but not the vocal tract, such as "attention-getting" sounds directed at humans by captive chimpanzees and lip smacking during social grooming. chimpanzees at ngogo, in kibale national park, uganda, make four distinct sounds while grooming others. here, i present data on two ...201626546459
social grooming network in captive chimpanzees: does the wild or captive origin of group members affect sociality?many chimpanzees throughout the world are housed in captivity, and there is an increasing effort to recreate social groups by mixing individuals with captive origins with those with wild origins. captive origins may entail restricted rearing conditions during early infant life, including, for example, no maternal rearing and a limited social life. early rearing conditions have been linked with differences in tool-use behavior between captive- and wild-born chimpanzees. if physical cognition can ...201626403665
the effects of being watched on resource acquisition in chimpanzees and human children.animals react in many different ways to being watched by others. in the context of cooperation, many theories emphasize reputational effects: individuals should cooperate more if other potential cooperators are watching. in the context of competition, individuals might want to show off their strength and prowess if other potential competitors are watching. in the current study, we observed chimpanzees and human children in three experimental conditions involving resource acquisition: participant ...201626376987
trading up: chimpanzees (pan troglodytes) show self-control through their exchange behavior.self-control is defined as the ability or capacity to obtain an objectively more valuable outcome rather than an objectively less valuable outcome though tolerating a longer delay or a greater effort requirement (or both) in obtaining that more valuable outcome. a number of tests have been devised to assess self-control in non-human animals, including exchange tasks. in this study, three chimpanzees (pan troglodytes) participated in a delay of gratification task that required food exchange as th ...201626325355
the end of chimpanzee research.in june 2010, rosie, a descendant of the chimpanzees sent into space, and thirteen others were shipped from new mexico to a laboratory in texas for possible use in hepatitis research. they were to be the first group of approximately two hundred chimpanzees to be reintroduced to invasive research. these chimpanzees had been in semiretirement for a decade after being removed from an enormous laboratory that was in egregious violation of the animal welfare act. i, along with many bioethicists, scie ...201627417870
nonhuman primates, human need, and ethical constraints."the ethics of infection challenges in primates," by anne barnhill, steven joffe, and franklin miller, is an exceptionally timely contribution to the literature on animal research ethics. animal research has long been both a source of high hopes and a cause for moral concern. when it comes to infection challenge studies with nonhuman primates, neither the hope-to save thousands of human lives from such diseases as ebola and marburg-nor the concern-the conviction that primates deserve especially ...201627417866
animal intuitions.as described by lori gruen in the perspective column at the back of this issue, federally supported biomedical research conducted on chimpanzees has now come to an end in the united states, although the wind-down has taken longer than expected. the process began with a 2011 institute of medicine report that set up several stringent criteria that sharply limited biomedical research. the national institutes of health accepted the recommendations and formed a committee to determine how best to impl ...201627417859
translating chimpanzee personality to humans: investigating the transportability of chimpanzee-derived personality scales to humans.there is a growing interest in the study of personality in chimpanzees with repeated findings of a similar structure of personality in apes to that found in humans. to date, however, the direct translational value of instruments used to assess chimpanzee personality to humans has yet to be explicitly tested. as such, in the current study we sought to determine the transportability of factor analytically-derived chimpanzee personality scales to humans in a large human sample (n = 301). human info ...201626716761
human-specific increase of dopaminergic innervation in a striatal region associated with speech and language: a comparative analysis of the primate basal ganglia.the dopaminergic innervation of the striatum has been implicated in learning processes and in the development of human speech and language. several lines of evidence suggest that evolutionary changes in dopaminergic afferents of the striatum may be associated with uniquely human cognitive and behavioral abilities, including the association of the human-specific sequence of the foxp2 gene with decreased dopamine in the dorsomedial striatum of mice. to examine this possibility, we quantified the d ...201626715195
testicular receptor 2, nr2c1, is associated with stem cells in the developing olfactory epithelium and other cranial sensory and skeletal structures.comparative genomic analysis of the nuclear receptor family suggests that the testicular receptor 2, nr2c1, undergoes positive selection in the human-chimpanzee clade based upon a significant increase in nonsynonymous compared to synonymous substitutions. previous in situ analyses of nr2c1 lacked the temporal range and spatial resolution necessary to characterize cellular expression of this gene from early to mid gestation, when many nuclear receptors are key regulators of tissue specific stem o ...201626712358
integrative genomic analysis of interleukin-36rn and its prognostic value in cancer.interleukin (il)-36rn, previously known as il1-f5 and il-1δ, shares a 360-kb region of chromosome 2q13 with members of il-1 systems. il-36rn encodes an anti-inflammatory cytokine, il-36 receptor antagonist (il-36ra). in spite of il-36ra showing the highest homology to il-1 receptor (il-1r) antagonist, it differs from the latter in aspects including its binding to il-lrrp2 but not to il-1r1. il-36rn is mainly expressed in epithelial cells and has important roles in inflammatory diseases. in the p ...201626676204
chimpanzee food preferences, associative learning, and the origins of cooking.a recent report suggested that chimpanzees demonstrate the cognitive capacities necessary to understand cooking (warneken & rosati, 2015). we offer alternate explanations and mechanisms that could account for the behavioral responses of those chimpanzees, without invoking the understanding of cooking as a process. we discuss broader issues surrounding the use of chimpanzees in modeling hominid behavior and understanding aspects of human evolution.201626659967
nasal temperature drop in response to a playback of conspecific fights in chimpanzees: a thermo-imaging study.emotion is one of the central topics in animal studies and is likely to attract attention substantially in the coming years. recent studies have developed a thermo-imaging technique to measure the facial skin temperature in the studies of emotion in humans and macaques. here we established the procedures and techniques needed to apply the same technique to great apes. we conducted two experiments respectively in the two established research facilities in germany and japan. total twelve chimpanze ...201626657470
human-specific derived alleles of cd33 and other genes protect against postreproductive cognitive decline.the individuals of most vertebrate species die when they can no longer reproduce. humans are a rare exception, having evolved a prolonged postreproductive lifespan. elders contribute to cooperative offspring care, assist in foraging, and communicate important ecological and cultural knowledge, increasing the survival of younger individuals. age-related deterioration of cognitive capacity in humans compromises these benefits and also burdens the group with socially costly members. we investigated ...201626621708
genetic and phylogenetic characterization of novel bocaparvovirus infecting chimpanzee.primate bocaparvoviruses were first described in 2005, since then further human and gorilla bocaparvoviruses have been identified. to uncover diversity of non-human primates' bocaparvoviruses, their phylogenetic relationship and potential to cross the host species barrier, we tested 153 fecal samples from 17 captive primate species. the only one captive female of central chimpanzee (coded cpzh2) has been identified as bocaparvovirus positive. based on the full genome phylogenetic analyses, cpzh2 ...201626616676
how chimpanzees (pan troglodytes) perform in a modified emotional stroop task.the emotional stroop task is an experimental paradigm developed to study the relationship between emotion and cognition. human participants required to identify the color of words typically respond more slowly to negative than to neutral words (emotional stroop effect). here we investigated whether chimpanzees (pan troglodytes) would show a comparable effect. using a touch screen, eight chimpanzees were trained to choose between two simultaneously presented stimuli based on color (two identical ...201626613593
asymmetries in the production of self-directed behavior by chimpanzees and gorillas during a computerized cognitive test.self-directed behaviors (sdbs) are a commonly used behavioral indicator of arousal in nonhuman primates. experimental manipulations, designed to increase arousal and uncertainty, have been used to elicit sdb production in primates. beyond measuring rates of sdb production, researchers have also recorded their lateralized production by primates, thought to reflect laterality of hemispheric brain control and response to emotion. although a handful of such studies exist, all have been conducted wit ...201626577088
the degradome database: expanding roles of mammalian proteases in life and disease.since the definition of the degradome as the complete repertoire of proteases in a given organism, the combined effort of numerous laboratories has greatly expanded our knowledge of its roles in biology and pathology. once the genomic sequences of several important model organisms were made available, we presented the degradome database containing the curated sets of known protease genes in human, chimpanzee, mouse and rat. here, we describe the updated degradome database, featuring 81 new prote ...201626553809
an observation of a severely disabled infant chimpanzee in the wild and her interactions with her mother.we report the physical and behavioral development of one severely disabled female infant chimpanzee (pan troglodytes schweinfurthii) of the well-habituated m group in the mahale mountains national park. we documented interactions between the infant and its mother and with other group members. congenital disabilities occur in many primate species, including chimpanzees. however, there have been only a few case studies of congenitally disabled chimpanzee infants and no reports examining how a chim ...201626553203
environmental variables across pan troglodytes study sites correspond with the carbon, but not the nitrogen, stable isotope ratios of chimpanzee hair.diet influences the stable isotope ratios of carbon and nitrogen (δ(13) c and δ(15) n values) in animal tissue; but here we explore the influences of particular aspects of the local environment on those values in chimpanzees (pan troglodytes). in this article we present new δ(13) c and δ(15) n values in gombe chimpanzees using hairs collected from night nests in 1989. then, we explore the influence of environmental factors by comparing our gombe data to those from eight additional pan study site ...201626513527
strain-dependent and distinctive t-cell responses to hiv antigens following immunisation of mice with differing chimpanzee adenovirus vaccine vectors.in vivo vaccination studies are conventionally conducted in a single mouse strain with results, only reflecting responses to a single immunogenetic background. we decided to examine the immune response to an hiv transgene (gag, pol and nef fusion protein) in 3 strains of mice (cba, c57bl/6 and balb/c) to determine the spectrum of responses and in addition to determine whether the serotype of the adenoviral vector used (chad3 and chad63) impacted the outcome of response. our results demonstrated ...201627452864
in silico phylogenomics using complete genomes: a case study on the evolution of hominoids.the increasing availability of complete genome data is facilitating the acquisition of phylogenomic data sets, but the process of obtaining orthologous sequences from other genomes and assembling multiple sequence alignments remains piecemeal and arduous. we designed software that performs these tasks and outputs anonymous loci (al) or anchored enrichment/ultraconserved element loci (ae/uce) data sets in ready-to-analyze formats. we demonstrate our program by applying it to the hominoids. starti ...201627435933
travel fosters tool use in wild chimpanzees.ecological variation influences the appearance and maintenance of tool use in animals, either due to necessity or opportunity, but little is known about the relative importance of these two factors. here, we combined long-term behavioural data on feeding and travelling with six years of field experiments in a wild chimpanzee community. in the experiments, subjects engaged with natural logs, which contained energetically valuable honey that was only accessible through tool use. engagement with th ...201627431611
the potency of nef-mediated serinc5 antagonism correlates with the prevalence of primate lentiviruses in the wild.the cellular factor serine incorporator 5 (serinc5) impairs hiv-1 infectivity but is antagonized by the viral nef protein. we analyzed the anti-serinc5 activity of nef proteins across primate lentiviruses and examined whether serinc5 represents a barrier to cross-species transmissions and/or within-species viral spread. hiv-1, hiv-2, and siv nefs counteract human, ape, monkey, and murine serinc5 orthologs with similar potency. however, hiv-1 nefs are more active against serinc5 than hiv-2 nefs, ...201627631701
selective sweeps across twenty millions years of primate evolution.the contribution from selective sweeps to variation in genetic diversity has proven notoriously difficult to assess, in part because polymorphism data only allows detection of sweeps in the most recent few hundred thousand years. here, we show how linked selection in ancestral species can be quantified across evolutionary timescales by analyzing patterns of incomplete lineage sorting (ils) along the genomes of closely related species. we show that sweeps in the human-chimpanzee and human-orangut ...201627660295
wild chimpanzees modify modality of gestures according to the strength of social bonds and personal network size.primates form strong and enduring social bonds with others and these bonds have important fitness consequences. however, how different types of communication are associated with different types of social bonds is poorly understood. wild chimpanzees have a large repertoire of gestures, from visual gestures to tactile and auditory gestures. we used social network analysis to examine the association between proximity bonds (time spent in close proximity) and rates of gestural communication in pairs ...201627649626
molecular determinants of gs-9620-dependent tlr7 activation.gs-9620 is an orally administered agonist of toll-like receptor (tlr)7 currently being evaluated in clinical studies for the treatment of chronic hbv and hiv patients. gs-9620 has shown antiviral efficacy in preclinical models of chronic hepadnavirus infection in woodchuck as well as chimpanzee. however, the molecular determinants of gs-9620-dependent activation of tlr7 are not well defined. the studies presented here elucidate gs-9620 subcellular distribution and characterize its molecular inte ...201626784926
it all adds up …. or does it? numbers, mathematics and purpose.no chimpanzee knows what a square root is, let alone a complex number. yet not only our closest ape cousins but even some invertebrates, possess a capacity for numerosity, that is the ability to assess relative numerical magnitudes and distances. that numerosity should confer adaptive advantages, such as social species that choose shoal size, is obvious. moreover, it is widely assumed that numerosity and mathematics are seamlessly linked, as would be consistent with darwinian notions of descent ...201626783082
long bone cross-sectional properties reflect changes in locomotor behavior in developing chimpanzees.recent studies indicate that the locomotor behavior of wild chimpanzees changes during development. before transitioning to quadrupedal knuckle-walking in adulthood, young chimpanzees engage in a significant amount of upper limb loading suspensory behavior. we investigated whether these dramatic changes in locomotion influence the strength and shape of chimpanzee long bones.201626780478
a chimpanzee (pan troglodytes) model of triarchic psychopathy constructs: development and initial validation.the current work sought to operationalize constructs of the triarchic model of psychopathy in chimpanzees (pan troglodytes), a species well-suited for investigations of basic biobehavioral dispositions relevant to psychopathology. across three studies, we generated validity evidence for scale measures of the triarchic model constructs in a large sample (n=238) of socially-housed chimpanzees. using a consensus-based rating approach, we first identified candidate items for the chimpanzee triarchic ...201626779396
chimpanzees trust their friends.the identification and recruitment of trustworthy partners represents an important adaptive challenge for any species that relies heavily on cooperation [1, 2]. from an evolutionary perspective, trust is difficult to account for as it involves, by definition, a risk of non-reciprocation and defection by cheaters [3, 4]. one solution for this problem is to form close emotional bonds, i.e., friendships, which enable trust even in contexts where cheating would be profitable [5]. little is known abo ...201626776735
placentophagy in wild chimpanzees (pan troglodytes verus) at bossou, guinea.despite intensive observation of nonhuman great apes during long-term field studies, observations of great ape births in the wild are rare. research on wild chimpanzees (pan troglodytes verus) at bossou in the republic of guinea has been ongoing for 35 years, yet chimpanzee parturitions have been observed on only two occasions. here we provide information regarding both chimpanzee births, with detailed information from the close observation of one. during this birth, the mother built a day nest ...201626769192
reproductive state and rank influence patterns of meat consumption in wild female chimpanzees (pan troglodytes schweinfurthii).an increase in faunivory is a consistent component of human evolutionary models. animal matter is energy- and nutrient-dense and can provide macronutrients, minerals, and vitamins that are limited or absent in plant foods. for female humans and other omnivorous primates, faunivory may be of particular importance during the costly periods of pregnancy and early lactation. yet, because animal prey is often monopolizable, access to fauna among group-living primates may be mediated by social factors ...201626767956
maternal effects on offspring stress physiology in wild chimpanzees.early life experiences are known to influence hypothalamic-pituitary-adrenal (hpa) axis development, which can impact health outcomes through the individual's ability to mount appropriate physiological reactions to stressors. in primates, these early experiences are most often mediated through the mother and can include the physiological environment experienced during gestation. here, we investigate stress physiology of dependent offspring in wild chimpanzees for the first time and examine wheth ...201626757681
cortical cell and neuron density estimates in one chimpanzee hemisphere.the density of cells and neurons in the neocortex of many mammals varies across cortical areas and regions. this variability is, perhaps, most pronounced in primates. nonuniformity in the composition of cortex suggests regions of the cortex have different specializations. specifically, regions with densely packed neurons contain smaller neurons that are activated by relatively few inputs, thereby preserving information, whereas regions that are less densely packed have larger neurons that have m ...201626729880
safety and immunogenicity of a chimpanzee adenovirus-vectored ebola vaccine in healthy adults: a randomised, double-blind, placebo-controlled, dose-finding, phase 1/2a study.the ongoing ebola outbreak led to accelerated efforts to test vaccine candidates. on the basis of a request by who, we aimed to assess the safety and immunogenicity of the monovalent, recombinant, chimpanzee adenovirus type-3 vector-based ebola zaire vaccine (chad3-ebo-z).201626725450
faster reproductive rates trade off against offspring growth in wild chimpanzees.life history theory predicts a trade-off between offspring quality and quantity. among large-bodied mammals, prolonged lactation and infant dependence suggest particularly strong potential for a quality-quantity trade-off to exist. humans are one of the only such species to have been examined, providing mixed evidence under a peculiar set of circumstances, including extensive nutritional provisioning by nonmothers and extrasomatic wealth transmission. here, we examine trade-offs between reproduc ...201627354523
children's and apes' preparatory responses to two mutually exclusive possibilities.animal brains have evolved to predict outcomes of events in the immediate environment [1-5]. adult humans are particularly adept at dealing with environmental uncertainty, being able to mentally represent multiple, even mutually exclusive versions of the future and prepare accordingly. this capacity is fundamental to many complex future-oriented behaviors [6, 7], yet little is known about when it develops in children [8] and whether it is shared with non-human animals [9]. here we show that chil ...201627345164
copy number variation in tas2r bitter taste receptor genes: structure, origin, and population genetics.bitter taste receptor genes (tas2rs) harbor extensive diversity, which is broadly distributed across human populations and strongly associated with taste response phenotypes. the majority of tas2r variation is composed of single-nucleotide polymorphisms. however, 2 closely positioned loci at 12p13, tas2r43 and -45, harbor high-frequency deletion (δ) alleles in which genomic segments are absent, resulting in copy number variation (cnv). to resolve their chromosomal structure and organization, we ...201627340135
cpg island evolution in the mammalian dhrs4 gene cluster and its role in the regulation of gene transcription.the dehydrogenase/reductase (sdr family) member 4 (dhrs4) gene is copied during mammalian evolution; therefore, while only one dhrs4 gene is expressed in the mouse genome, the gene cluster consists of two (dhrs4 and dhrs4l1) and three (dhrs4, dhrs4l2, and dhrs4l1) copies in chimpanzees and humans, respectively. in this study, we explored the possible regulatory mechanism of the dhrs4 gene cluster in mammalian evolution by analyzing the promoter sequence, methylation of cpg islands, and rna expre ...201627323117
aav natural infection induces broad cross-neutralizing antibody responses to multiple aav serotypes in chimpanzees.cross-sectional studies of primates have revealed that natural neutralizing antibody (nab) responses to adeno-associated viruses (aav) span multiple serotypes. this differs from the phenotype of the nab response to an aav vector delivered to seronegative nonhuman primates that is typically restricted to the administered aav serotype. to better understand the mechanism by which natural aav infections result in broad nab responses, we conducted a longitudinal study spanning 10 years in which we ev ...201627314914
constraints on the exploitation of the functional properties of objects in expert tool-using chimpanzees (pan troglodytes).many species exploit immediately apparent dimensions of objects during tool use and manufacture and operate over internal perceptual representations of objects (they move and reorient objects in space, have rules of operation to deform or modify objects, etc). humans, however, actively test for functionally relevant object properties before such operations begin, even when no previous percepts of a particular object's qualities in the domain have been established. we hypothesize that such prospe ...201627309530
phylogenetic analysis reveals that ervs "die young" but herv-h is unusually conserved.about 8% of the human genome is made up of endogenous retroviruses (ervs). though most human endogenous retroviruses (hervs) are thought to be irrelevant to our biology notable exceptions include members of the herv-h family that are necessary for the correct functioning of stem cells. ervs are commonly found in two forms, the full-length proviral form, and the more numerous solo-ltr form, thought to result from homologous recombination events. here we introduce a phylogenetic framework to study ...201627295277
euthanasia is not an option: 10 years' care of a chimpanzee with acute tetraparesis. 201627290696
letter to the editor: avoiding a lost opportunity for psychological medicine: importance of chimpanzee research to the national institutes of health portfolio. 201627283031
feature: chimpanzees, our cultured cousins. 201627280267
genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome.the human genome is 99% complete. this study contributes to filling the 1% gap by enriching previously unknown repeat regions called microsatellites (mst). we devised a global mst enrichment (gme) kit to enrich and nextgen sequence 2 colorectal cell lines and 16 normal human samples to illustrate its utility in identifying contigs from reads that do not map to the genome reference. the analysis of these samples yielded 790 novel extra-referential concordant contigs that are observed in more than ...201627278669
purifying selection shapes the coincident snp distribution of primate coding sequences.genome-wide analysis has observed an excess of coincident single nucleotide polymorphisms (cosnps) at human-chimpanzee orthologous positions, and suggested that this is due to cryptic variation in the mutation rate. while this phenomenon primarily corresponds with non-coding cosnps, the situation in coding sequences remains unclear. here we calculate the observed-to-expected ratio of cosnps (cosnpo/e) to estimate the prevalence of human-chimpanzee cosnps, and show that the excess of cosnps is al ...201627255481
aav natural infection induces broad cross-neutralizing antibody responses to multiple aav serotypes in chimpanzees.cross-sectional studies of primates have revealed that natural neutralizing antibody (nab) responses to adeno-associated viruses (aav) span multiple serotypes. this differs from the phenotype of the nab response to an aav vector delivered to sero-negative nonhuman primates which is typically restricted to the administered aav serotype. to better understand the mechanism by which natural aav infections result in broad nab responses, we conducted a longitudinal study spanning 10 years in which we ...201627247123
comus: simulating coalescent histories and polymorphic data from multiple species.the simultaneous analysis of intra- and interspecies variation is challenging mainly because our knowledge about patterns of polymorphisms where both intra- and interspecies samples coexist is limited. in this study, we present comus (coalescent of multiple species), a multispecies coalescent software that can simulate intra- and interspecies polymorphisms. comus supports a variety of speciation models and demographic scenarios related to the history of each species. in comus, speciation can be ...201627238297
behavioral research as physical enrichment for captive chimpanzees.in this study, we evaluated the potential for a behavioral research study, designed to evaluate chimpanzee decision-making behavior, to also encourage increased activity in a group of zoo-housed chimpanzees. for the behavioral study, the chimpanzees had to carry tokens to different locations such that they always had to travel farther to obtain a more-preferred reward. we recorded the distance travelled by each subject in each of the three phases of the 15-month study. by the final phase, the ch ...201627232752
genetic characterization and classification of human and animal sapoviruses.sapoviruses (savs) are enteric caliciviruses that have been detected in multiple mammalian species, including humans, pigs, mink, dogs, sea lions, chimpanzees, and rats. they show a high level of diversity. a sav genome commonly encodes seven nonstructural proteins (nss), including the rna polymerase protein ns7, and two structural proteins (vp1 and vp2). we classified human and animal savs into 15 genogroups (g) based on available vp1 sequences, including three newly characterized genomes from ...201627228126
one for you, one for me: humans' unique turn-taking skills.long-term collaborative relationships require that any jointly produced resources be shared in mutually satisfactory ways. prototypically, this sharing involves partners dividing up simultaneously available resources, but sometimes the collaboration makes a resource available to only one individual, and any sharing of resources must take place across repeated instances over time. here, we show that beginning at 5 years of age, human children stabilize cooperation in such cases by taking turns ac ...201627225221
the discovery of fire by humans: a long and convoluted process.numbers of animal species react to the natural phenomenon of fire, but only humans have learnt to control it and to make it at will. natural fires caused overwhelmingly by lightning are highly evident on many landscapes. birds such as hawks, and some other predators, are alert to opportunities to catch animals including invertebrates disturbed by such fires and similar benefits are likely to underlie the first human involvements with fires. early hominins would undoubtedly have been aware of suc ...201627216521
the progress of early growth response factor 1 and leukemia.early growth response gene-1 (egr1) widely exists in the cell nucleus of such as, zebrafish, mice, chimpanzees and humans, an it also can be observed in the cytoplasm of some tumors. egr1 was named just after its brief and rapid expression of different stimuli. accumulating studies have extensively demonstrated that the widespread dysregulation of egr1 is involved in hematological malignancies such as human acute myeloid leukemia (aml), chronic myelogenous leukemia, chronic lymphocytic leukemia, ...201627195189
the relationship between testosterone and long-distance calling in wild male chimpanzees.long-distance calling is a common behaviour in animals that has various important social functions. at a physiological level, calling is often mediated by gonadal hormones such as testosterone (t), particularly when its function is linked to intra-sexual competition for mates or territory. t also plays an important role in the development of vocal characteristics associated with dominance in humans. however, the few available studies of t and vocal behaviour in non-human primates suggest that in ...201627182103
chimpanzees' responses to the dead body of a 9-year-old group member.the social behavior of chimpanzees has been extensively studied, yet not much is known about how they behave in response to the death of a group member. here, we provide a detailed report of the reactions of a group of chimpanzees to finding the dead body of a 9-year-old male group member. the behavior of the group was characterized by quiet attendance and close inspections punctuated by rare displays. moreover, the body was continuously attended and closely inspected by several adults and juven ...201627159804
a new method of walking rehabilitation using cognitive tasks in an adult chimpanzee (pan troglodytes) with a disability: a case study.there are few studies of long-term care and rehabilitation of animals which acquired physical disabilities in captivity, despite their importance for welfare. an adult male chimpanzee named reo at the primate research institute of kyoto university, developed acute myelitis, inflammation of the spinal cord, which resulted in impaired leg function. this report describes a walking rehabilitation system set up in a rehabilitation room where he lives. the rehabilitation apparatus consisted of a touch ...201627150249
non-invasive quantification of immunoglobulin a in chimpanzees (pan troglodytes schweinfurthii) at gombe national park, tanzania.immunoglobulin a (iga) is the primary antibody responsible for mucosal defense in mammals and has been used as a marker for chronic stress and immune status. therefore, this antibody may provide a more reliable indicator of an individual's immunocompetence than is currently available through other methods. immunoglobulin a has never before been quantified in a wild population of non-human primates using non-invasive sample collection techniques. in this study, we present methodology for non-inva ...201627149678
wild capuchin monkeys spontaneously adjust actions when using hammer stones of different mass to crack nuts of different resistance.expert tool users are known to adjust their actions skillfully depending on aspects of tool type and task. we examined if bearded capuchin monkeys cracking nuts with stones of different mass adjusted the downward velocity and the height of the stone when striking palm nuts.201627135182
corrigendum: early maternal loss affects social integration of chimpanzees throughout their lifetime. 201627128814
insights into the dn/ds ratio heterogeneity between brain specific genes and widely expressed genes in species of different complexity.in mammals, it has long been suggested that brain-specific genes (bsgs) and widely expressed genes (wegs) have seemingly lower dn/ds ratio than any other gene sets. however, to what extent these genes differ in their dn/ds ratio has still remained controversial. here, we have revealed lower dn/ds ratio of bsgs than wegs in human-mouse, human-orangutan, human-chimpanzee and mouse-rat orthologous pair. the significance level of dn/ds ratio difference indicates a trend of decreasing difference as c ...201627126306
nih to end all chimpanzee research. 201627120864
systematic reanalysis of partial trisomy 21 cases with or without down syndrome suggests a small region on 21q22.13 as critical to the phenotype.a 'down syndrome critical region' (dscr) sufficient to induce the most constant phenotypes of down syndrome (ds) had been identified by studying partial (segmental) trisomy 21 (pt21) as an interval of 0.6-8.3 mb within human chromosome 21 (hsa21), although its existence was later questioned. we propose an innovative, systematic reanalysis of all described pt21 cases (from 1973 to 2015). in particular, we built an integrated, comparative map from 125 cases with or without ds fulfilling stringent ...201627106104
functional divergence of the nuclear receptor nr2c1 as a modulator of pluripotentiality during hominid evolution.genes encoding nuclear receptors (nrs) are attractive as candidates for investigating the evolution of gene regulation because they (1) have a direct effect on gene expression and (2) modulate many cellular processes that underlie development. we employed a three-phase investigation linking nr molecular evolution among primates with direct experimental assessment of nr function. phase 1 was an analysis of nr domain evolution and the results were used to guide the design of phase 2, a codon-model ...201627075724
chimpanzees, cooking, and a more comparative psychology.a recent report suggested that chimpanzees demonstrate the cognitive capacities necessary to understand cooking (warneken & rosati, 2015). we offered alternative explanations and mechanisms that could account for the behavioral responses of those chimpanzees, and questioned the manner in which the data were used to examine human evolution (beran, hopper, de waal, sayers, & brosnan, 2015). two commentaries suggested either that we were overly critical of the original report's claims and methodolo ...201627068300
the influence of avpr1a genotype on individual differences in behaviors during a mirror self-recognition task in chimpanzees (pan troglodytes).the mark/rouge test has been used to assess mirror self-recognition (msr) in many species. despite consistent evidence of msr in great apes, genetic or non-genetic factors may account for the individual differences in behavioral responses that have been reported. we examined whether vasopressin receptor gene (avpr1a) polymorphisms are associated with msr-related behaviors in chimpanzees since vasopressin has been implicated in the development and evolution of complex social relations and cogniti ...201627058969
de novo genes arise at a slow but steady rate along the primate lineage and have been subject to incomplete lineage sorting.de novo protein-coding gene origination is increasingly recognized as an important evolutionary mechanism. however, there remains a large amount of uncertainty regarding the frequency of these events and the mechanisms and speed of gene establishment. here, we describe a rigorous search for cases of de novo gene origination in the great apes. we analyzed annotated proteomes as well as full genomic dna and transcriptional and translational evidence. it is notable that results vary between databas ...201627056411
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