Expanding whole exome resequencing into non-human primates

Background  

Complete exome resequencing has the power to greatly expand our understanding of non-human primate genomes. This includes both a better appreciation of the variation that exists in non-human primate model species, but also an improved annotation of their genomes. By developing an understanding of the variation between individuals, non-human primate models of human disease can be better developed. This effort is hindered largely by the lack of comprehensive information on specific non-human primate genetic variation and the costs of generating these data. If the tools that have been developed in humans for complete exome resequencing can be applied to closely related non-human primate species, then these difficulties can be circumvented.     

The many faces of research on face perception

Face perception is fundamental to human social interaction. Many different types of important information are visible in faces and the processes and mechanisms involved in extracting this information are complex and can be highly specialized. The importance of faces has long been recognized by a wide range of scientists. Importantly, the range of perspectives and techniques that this breadth has brought to face perception research has, in recent years, led to many important advances in our understanding of face processing. The articles in this issue on face perception each review a particular arena of interest in face perception, variously focusing on (i) the social aspects of face perception (attraction, recognition and emotion), (ii) the neural mechanisms underlying face perception (using brain scanning, patient data, direct stimulation of the brain, visual adaptation and single-cell recording), and (iii) comparative aspects of face perception (comparing adult human abilities with those of chimpanzees and children). Here, we introduce the central themes of the issue and present an overview of the articles.     

Second-order relational manipulations affect both humans and monkeys

Recognition and individuation of conspecifics by their face is essential for primate social cognition. This ability is driven by a mechanism that integrates the appearance of facial features with subtle variations in their configuration (i.e., second-order relational properties) into a holistic representation. So far, there is little evidence of whether our evolutionary ancestors show sensitivity to featural spatial relations and hence holistic processing of faces as shown in humans. Here, we directly compared macaques with humans in their sensitivity to configurally altered faces in upright and inverted orientations using a habituation paradigm and eye tracking technologies. In addition, we tested for differences in processing of conspecific faces (human faces for humans, macaque faces for macaques) and non-conspecific faces, addressing aspects of perceptual expertise. In both species, we found sensitivity to second-order relational properties for conspecific (expert) faces, when presented in upright, not in inverted, orientation. This shows that macaques possess the requirements for holistic processing, and thus show similar face processing to that of humans.     

Voice cells in the primate temporal lobe

Communication signals are important for social interactions and survival and are thought to receive specialized processing in the visual and auditory systems. Whereas the neural processing of faces by face clusters and face cells has been repeatedly studied [1-5], less is known about the neural representation of voice content. Recent functional magnetic resonance imaging (fMRI) studies have localized voice-preferring regions in the primate temporal lobe [6, 7], but the hemodynamic response cannot directly assess neurophysiological properties. We investigated the responses of neurons in an fMRI-identified voice cluster in awake monkeys, and here we provide the first systematic evidence for voice cells. "Voice cells" were identified, in analogy to "face cells," as neurons responding at least 2-fold stronger to conspecific voices than to "nonvoice" sounds or heterospecific voices. Importantly, whereas face clusters are thought to contain high proportions of face cells [4] responding broadly to many faces [1, 2, 4, 5, 8-10], we found that voice clusters contain moderate proportions of voice cells. Furthermore, individual voice cells exhibit high stimulus selectivity. The results reveal the neurophysiological bases for fMRI-defined voice clusters in the primate brain and highlight potential differences in how the auditory and?visual systems generate selective representations of communication signals.     

The neuroscience of primate intellectual evolution: natural selection and passive and intentional niche construction

We trained Japanese macaque monkeys to use tools, an advanced cognitive function monkeys do not exhibit in the wild, and then examined their brains for signs of modification. Following tool-use training, we observed neurophysiological, molecular genetic and morphological changes within the monkey brain. Despite being 'artificially' induced, these novel behaviours and neural connectivity patterns reveal overlap with those of humans. Thus, they may provide us with a novel experimental platform for studying the mechanisms of human intelligence, for revealing the evolutionary path that created these mechanisms from the 'raw material' of the non-human primate brain, and for deepening our understanding of what cognitive abilities are and of those that are not uniquely human. On these bases, we propose a theory of 'intentional niche construction' as an extension of natural selection in order to reveal the evolutionary mechanisms that forged the uniquely intelligent human brain.     

Evidence that emotion mediates social attention in rhesus macaques

Background

Recent work on non-human primates indicates that the allocation of social attention is mediated by characteristics of the attending animal, such as social status and genotype, as well as by the value of the target to which attention is directed. Studies of humans indicate that an individual’s emotion state also plays a crucial role in mediating their social attention; for example, individuals look for longer towards aggressive faces when they are feeling more anxious, and this bias leads to increased negative arousal and distraction from other ongoing tasks. To our knowledge, no studies have tested for an effect of emotion state on allocation of social attention in any non-human species.

Methodology

We presented captive adult male rhesus macaques with pairs of adult male conspecific face images - one with an aggressive expression, one with a neutral expression - and recorded gaze towards these images. Each animal was tested twice, once during a putatively stressful condition (i.e. following a veterinary health check), and once during a neutral (or potentially positive) condition (i.e. a period of environmental enrichment). Initial analyses revealed that behavioural indicators of anxiety and stress were significantly higher after the health check than during enrichment, indicating that the former caused a negative shift in emotional state.

Principle Findings

The macaques showed initial vigilance for aggressive faces across both conditions, but subsequent responses differed between conditions. Following the health check, initial vigilance was followed by rapid and sustained avoidance of aggressive faces. By contrast, during the period of enrichment, the macaques showed sustained attention towards the same aggressive faces.

Conclusions/Significance

These data provide, to our knowledge, the first evidence that shifts in emotion state mediate social attention towards and away from facial cues of emotion in a non-human animal. This work provides novel insights into the evolution of emotion-attention interactions in humans, and mechanisms of social behaviour in non-human primates, and may have important implications for understanding animal psychological wellbeing.     

非人灵长类声音通讯的研究进展

声音通讯是非人灵长类研究一个重要的研究领域,有助于了解非人灵长类的社会行为、个体关系、行为进化和社会演化等,甚至对探究人类语言起源和进化等方面也具有十分重要的意义.本文通过对非人灵长类声音通讯的研究内容、影响因素和研究方法等进行了梳理,探讨非人灵长类声音通讯研究的前景和展望,旨在进一步推动国内非人灵长类声音通讯研究的深...     

Infants' knowledge of their own species

Recognition of individuals at first sight is important for social species and can be achieved by attending to facial or body information. Previous research suggests that infants possess a perceptual template for evolutionarily relevant stimuli, which may include humans, dangerous animals (e.g. snakes), but not non-dangerous animals. To be effective, such a mechanism should result in a systematic preference for attending to humans over non-dangerous animals. Using a preferential looking paradigm, the present studies investigated the nature of infants' early representation of humans. We show that 3.5- and six-month-old infants attend more to human beings than non-human primates (a gorilla or monkey) which are examplars of non-dangerous animals. This occurred when infants were presented with head or body information in isolation, as well as when both are presented simultaneously. This early preference for humans by 3.5 months of age suggests that there is a basic representation for humans, which includes both head and/or body information. However, neonates demonstrated a preference only for human faces over non-human primate faces, not for humans over non-human primates when the stimuli were presented with both head and body simultaneously. The results show that although neonates display a preference for human faces over others, preference for the human body only develops later, in the first few months of life. This suggests that infants have acquired some knowledge about the human body at 3.5 months of age that may have developed from their privileged experience with other humans in the first few months of life, rather than an innate ability to detect humans in their entirety.     

Are faces of different species perceived categorically by human observers?

What are the species boundaries of face processing? Using a face-feature morphing algorithm, image series intermediate between human, monkey (macaque), and bovine faces were constructed. Forced-choice judgement of these images showed sharply bounded categories for upright face images of each species. These predicted the perceptual discrimination boundaries for upright monkey-cow and cow-human images, but not human-monkey images. Species categories were also well-judged for inverted face images, but these did not give sharpened discrimination (categorical perception) at the category boundaries. While categorical species judgements are made reliably, only the distinction between primate faces and cow faces appears to be categorically perceived, and only in upright faces. One inference is that humans may judge monkey faces in terms of human characteristics, albeit distinctive ones.     

Voice processing in human and non-human primates

Humans share with non-human primates a number of voice perception abilities of crucial importance in social interactions, such as the ability to identify a conspecific individual from its vocalizations. Speech perception is likely to have evolved in our ancestors on the basis of pre-existing neural mechanisms involved in extracting behaviourally relevant information from conspecific vocalizations (CVs). Studying the neural bases of voice perception in primates thus not only has the potential to shed light on cerebral mechanisms that may be--unlike those involved in speech perception--directly homologous between species, but also has direct implications for our understanding of how speech appeared in humans. In this comparative review, we focus on behavioural and neurobiological evidence relative to two issues central to voice perception in human and non-human primates: (i) are CVs 'special', i.e. are they analysed using dedicated cerebral mechanisms not used for other sound categories, and (ii) to what extent and using what neural mechanisms do primates identify conspecific individuals from their vocalizations?     

Our Faces in the Dog's Brain: Functional Imaging Reveals Temporal Cortex Activation during Perception of Human Faces

Dogs have a rich social relationship with humans. One fundamental aspect of it is how dogs pay close attention to human faces in order to guide their behavior, for example, by recognizing their owner and his/her emotional state using visual cues. It is well known that humans have specific brain regions for the processing of other human faces, yet it is unclear how dogs’ brains process human faces. For this reason, our study focuses on describing the brain correlates of perception of human faces in dogs using functional magnetic resonance imaging (fMRI). We trained seven domestic dogs to remain awake, still and unrestrained inside an MRI scanner. We used a visual stimulation paradigm with block design to compare activity elicited by human faces against everyday objects. Brain activity related to the perception of faces changed significantly in several brain regions, but mainly in the bilateral temporal cortex. The opposite contrast (i.e., everyday objects against human faces) showed no significant brain activity change. The temporal cortex is part of the ventral visual pathway, and our results are consistent with reports in other species like primates and sheep, that suggest a high degree of evolutionary conservation of this pathway for face processing. This study introduces the temporal cortex as candidate to process human faces, a pillar of social cognition in dogs.     

Behavioural and neurophysiological evidence for face identity and face emotion processing in animals

Visual cues from faces provide important social information relating to individual identity, sexual attraction and emotional state. Behavioural and neurophysiological studies on both monkeys and sheep have shown that specialized skills and neural systems for processing these complex cues to guide behaviour have evolved in a number of mammals and are not present exclusively in humans. Indeed, there are remarkable similarities in the ways that faces are processed by the brain in humans and other mammalian species. While human studies with brain imaging and gross neurophysiological recording approaches have revealed global aspects of the face-processing network, they cannot investigate how information is encoded by specific neural networks. Single neuron electrophysiological recording approaches in both monkeys and sheep have, however, provided some insights into the neural encoding principles involved and, particularly, the presence of a remarkable degree of high-level encoding even at the level of a specific face. Recent developments that allow simultaneous recordings to be made from many hundreds of individual neurons are also beginning to reveal evidence for global aspects of a population-based code. This review will summarize what we have learned so far from these animal-based studies about the way the mammalian brain processes the faces and the emotions they can communicate, as well as associated capacities such as how identity and emotion cues are dissociated and how face imagery might be generated. It will also try to highlight what questions and advances in knowledge still challenge us in order to provide a complete understanding of just how brain networks perform this complex and important social recognition task.     

The fusiform face area: a cortical region specialized for the perception of faces

Faces are among the most important visual stimuli we perceive, informing us not only about a person's identity, but also about their mood, sex, age and direction of gaze. The ability to extract this information within a fraction of a second of viewing a face is important for normal social interactions and has probably played a critical role in the survival of our primate ancestors. Considerable evidence from behavioural, neuropsychological and neurophysiological investigations supports the hypothesis that humans have specialized cognitive and neural mechanisms dedicated to the perception of faces (the face-specificity hypothesis). Here, we review the literature on a region of the human brain that appears to play a key role in face perception, known as the fusiform face area (FFA). Section 1 outlines the theoretical background for much of this work. The face-specificity hypothesis falls squarely on one side of a longstanding debate in the fields of cognitive science and cognitive neuroscience concerning the extent to which the mind/brain is composed of: (i) special-purpose ('domain-specific') mechanisms, each dedicated to processing a specific kind of information (e.g. faces, according to the face-specificity hypothesis), versus (ii) general-purpose ('domain-general') mechanisms, each capable of operating on any kind of information. Face perception has long served both as one of the prime candidates of a domain-specific process and as a key target for attack by proponents of domain-general theories of brain and mind. Section 2 briefly reviews the prior literature on face perception from behaviour and neurophysiology. This work supports the face-specificity hypothesis and argues against its domain-general alternatives (the individuation hypothesis, the expertise hypothesis and others). Section 3 outlines the more recent evidence on this debate from brain imaging, focusing particularly on the FFA. We review the evidence that the FFA is selectively engaged in face perception, by addressing (and rebutting) five of the most widely discussed alternatives to this hypothesis. In section 4, we consider recent findings that are beginning to provide clues into the computations conducted in the FFA and the nature of the representations the FFA extracts from faces. We argue that the FFA is engaged both in detecting faces and in extracting the necessary perceptual information to recognize them, and that the properties of the FFA mirror previously identified behavioural signatures of face-specific processing (e.g. the face-inversion effect). Section 5 asks how the computations and representations in the FFA differ from those occurring in other nearby regions of cortex that respond strongly to faces and objects. The evidence indicates clear functional dissociations between these regions, demonstrating that the FFA shows not only functional specificity but also area specificity. We end by speculating in section 6 on some of the broader questions raised by current research on the FFA, including the developmental origins of this region and the question of whether faces are unique versus whether similarly specialized mechanisms also exist for other domains of high-level perception and cognition.     

The evolution of face processing in primates

The ability to recognize faces is an important socio-cognitive skill that is associated with a number of cognitive specializations in humans. While numerous studies have examined the presence of these specializations in non-human primates, species where face recognition would confer distinct advantages in social situations, results have been mixed. The majority of studies in chimpanzees support homologous face-processing mechanisms with humans, but results from monkey studies appear largely dependent on the type of testing methods used. Studies that employ passive viewing paradigms, like the visual paired comparison task, report evidence of similarities between monkeys and humans, but tasks that use more stringent, operant response tasks, like the matching-to-sample task, often report species differences. Moreover, the data suggest that monkeys may be less sensitive than chimpanzees and humans to the precise spacing of facial features, in addition to the surface-based cues reflected in those features, information that is critical for the representation of individual identity. The aim of this paper is to provide a comprehensive review of the available data from face-processing tasks in non-human primates with the goal of understanding the evolution of this complex cognitive skill.     

The baboon as a non-human primate model of human schistosome infection

Over the past three decades, intensive studies of murine schistosomiasis have provided important clues to the understanding of the human disease, but growing evidence suggests that these results derived from highly inbred strains of mice might not have direct applicability to the human infection. Recent data based on the baboon indicate that infection in this non-human primate might mirror the human situation. In this review, Mramba Nyindo and Idle Farah demonstrate that baboons provide an excellent non-human primate model that produces pathology and disease closely resembling that observed in humans, and address how studies in baboons can provide insights into mechanisms regulating schistosomiasis mansoni pathology and immunity. They also address, in a general way, issues related to the use of non-human primates in biomedical research.     

Brain systems for assessing the affective value of faces

Cognitive neuroscience research on facial expression recognition and face evaluation has proliferated over the past 15 years. Nevertheless, large questions remain unanswered. In this overview, we discuss the current understanding in the field, and describe what is known and what remains unknown. In §2, we describe three types of behavioural evidence that the perception of traits in neutral faces is related to the perception of facial expressions, and may rely on the same mechanisms. In §3, we discuss cortical systems for the perception of facial expressions, and argue for a partial segregation of function in the superior temporal sulcus and the fusiform gyrus. In §4, we describe the current understanding of how the brain responds to emotionally neutral faces. To resolve some of the inconsistencies in the literature, we perform a large group analysis across three different studies, and argue that one parsimonious explanation of prior findings is that faces are coded in terms of their typicality. In §5, we discuss how these two lines of research--perception of emotional expressions and face evaluation--could be integrated into a common, cognitive neuroscience framework.     

Face processing limitation to own species in primates: a comparative study in brown capuchins, Tonkean macaques and humans

Most primates live in social groups which survival and stability depend on individuals' abilities to create strong social relationships with other group members. The existence of those groups requires to identify individuals and to assign to each of them a social status. Individual recognition can be achieved through vocalizations but also through faces. In humans, an efficient system for the processing of own species faces exists. This specialization is achieved through experience with faces of conspecifics during development and leads to the loss of ability to process faces from other primate species. We hypothesize that a similar mechanism exists in social primates. We investigated face processing in one Old World species (genus Macaca) and in one New World species (genus Cebus). Our results show the same advantage for own species face recognition for all tested subjects. This work suggests in all species tested the existence of a common trait inherited from the primate ancestor: an efficient system to identify individual faces of own species only.     

Allelic lineages of the ficolin genes (FCNs) are passed from ancestral to descendant primates

The ficolins recognize carbohydrates and acetylated compounds on microorganisms and dying host cells and are able to activate the lectin pathway of the complement system. In humans, three ficolin genes have been identified: FCN1, FCN2 and FCN3, which encode ficolin-1, ficolin-2 and ficolin-3, respectively. Rodents have only two ficolins designated ficolin-A and ficolin-B that are closely related to human ficolin-1, while the rodent FCN3 orthologue is a pseudogene. Ficolin-2 and ficolin-3 have so far only been observed in humans. Thus, we performed a systematic investigation of the FCN genes in non-human primates. The exons and intron-exon boundaries of the FCN1-3 genes were sequenced in the following primate species: chimpanzee, gorilla, orangutan, rhesus macaque, cynomolgus macaque, baboon and common marmoset. We found that the exon organisation of the FCN genes was very similar between all the non-human primates and the human FCN genes. Several variations in the FCN genes were found in more than one primate specie suggesting that they were carried from one species to another including humans. The amino acid diversity of the ficolins among human and non-human primate species was estimated by calculating the Shannon entropy revealing that all three proteins are generally highly conserved. Ficolin-1 and ficolin-2 showed the highest diversity, whereas ficolin-3 was more conserved. Ficolin-2 and ficolin-3 were present in non-human primate sera with the same characteristic oligomeric structures as seen in human serum. Taken together all the FCN genes show the same characteristics in lower and higher primates. The existence of trans-species polymorphisms suggests that different FCN allelic lineages may be passed from ancestral to descendant species.     

Electrophysiology and brain imaging of biological motion

The movements of the faces and bodies of other conspecifics provide stimuli of considerable interest to the social primate. Studies of single cells, field potential recordings and functional neuroimaging data indicate that specialized visual mechanisms exist in the superior temporal sulcus (STS) of both human and non-human primates that produce selective neural responses to moving natural images of faces and bodies. STS mechanisms also process simplified displays of biological motion involving point lights marking the limb articulations of animate bodies and geometrical shapes whose motion simulates purposeful behaviour. Facial movements such as deviations in eye gaze, important for gauging an individual's social attention, and mouth movements, indicative of potential utterances, generate particularly robust neural responses that differentiate between movement types. Collectively such visual processing can enable the decoding of complex social signals and through its outputs to limbic, frontal and parietal systems the STS may play a part in enabling appropriate affective responses and social behaviour.     

Heterochrony and Cross-Species Intersensory Matching by Infant Vervet Monkeys

Background

Understanding the evolutionary origins of a phenotype requires understanding the relationship between ontogenetic and phylogenetic processes. Human infants have been shown to undergo a process of perceptual narrowing during their first year of life, whereby their intersensory ability to match the faces and voices of another species declines as they get older. We investigated the evolutionary origins of this behavioral phenotype by examining whether or not this developmental process occurs in non-human primates as well.

Methodology/Principal Findings

We tested the ability of infant vervet monkeys (Cercopithecus aethiops), ranging in age from 23 to 65 weeks, to match the faces and voices of another non-human primate species (the rhesus monkey, Macaca mulatta). Even though the vervets had no prior exposure to rhesus monkey faces and vocalizations, our findings show that infant vervets can, in fact, recognize the correspondence between rhesus monkey faces and voices (but indicate that they do so by looking at the non-matching face for a greater proportion of overall looking time), and can do so well beyond the age of perceptual narrowing in human infants. Our results further suggest that the pattern of matching by vervet monkeys is influenced by the emotional saliency of the Face+Voice combination. That is, although they looked at the non-matching screen for Face+Voice combinations, they switched to looking at the matching screen when the Voice was replaced with a complex tone of equal duration. Furthermore, an analysis of pupillary responses revealed that their pupils showed greater dilation when looking at the matching natural face/voice combination versus the face/tone combination.

Conclusions/Significance

Because the infant vervets in the current study exhibited cross-species intersensory matching far later in development than do human infants, our findings suggest either that intersensory perceptual narrowing does not occur in Old World monkeys or that it occurs later in development. We argue that these findings reflect the faster rate of neural development in monkeys relative to humans and the resulting differential interaction of this factor with the effects of early experience.