Biology subjects

Jacob, G.

Publications and source records attributed to Jacob, G..

12 recordsLinked to original sources

bioRxiv2026

Reactivation of neural signatures of food during REM-like sleep in the high-level visual cortex of monkeys

Can we tell what animals are dreaming about from their brain activity? This fascinating question has been explored extensively using the rodent hippocampus, where place cells are sequentially reactivated during sleep, consistent with replay of paths explored while awake. However, dreams involve vivid visual experiences, and whether analogous replays occur in the visual cortex has not been explored, that too in primates. To address this gap, we performed wireless neural recordings from the high-level visual (IT) and motor regions (PMv, PFC) in two monkeys while they viewed food images on a screen while awake, and afterwards while they slept in their natural setting. Decoders trained on sleep/wake neural activity in each region were able to accurately predict the ongoing sleep/wake state, as well as upcoming transitions between states. Interestingly, decoders trained to categorize neural responses to food (but not faces/objects) showed increased probability during REM-like sleep compared to NREM or awake states. Thus, behaviorally relevant visual stimuli seen while awake are reactivated during REM-like sleep. In other words, these monkeys saw food, faces and objects while awake, and dreamt selectively about food while sleeping.

neuroscience↗

bioRxiv2026

High-level visual and motor regions are doubly dissociated in controlled tasks but only at specific times during natural behaviors

Our knowledge of the neural basis of sensory and motor information processing comes largely from recording brain activity in controlled settings. This approach, while insightful, blinds us from understanding natural behaviors, which involve far richer visual inputs and far larger range of movements. The prevailing belief is that, during natural behaviors, movement information would modulate visual cortex, and visual inputs would modulate motor cortex. Alternatively, this mixing might only reflect correlations between sensory inputs and movements present during natural behavior. To resolve this issue, we performed wireless recordings from high-level visual (IT) and motor regions (PMv/PFC) in freely moving monkeys while they performed a natural task and a fixation task. In each task, we extracted visual and movement features and asked to what degree these features explained neural activity. In the fixation task, we found a striking double dissociation whereby visual (but not movement) features predicted neural activity in IT, whereas motor (but not visual) features predicted neural activity in PMv & PFC. This dissociation was far weaker in the natural task but present particularly at key events when the visual and motor features were less correlated. Thus, high-level sensory and motor regions in the brain are doubly dissociated under controlled conditions, and remain so at specific times during natural behavior.

neuroscience↗

bioRxiv2026

Natural behavior elicits reliable neural signatures in high-level sensory and motor regions of freely moving monkeys

Natural behaviors are challenging to study because they involve large variations in sensory inputs and motor outputs across trials. Even the simple act of eating can involve seeing food from many angles and reaching for it differently each time. The prevailing view is that natural behaviors are more noisy compared to controlled tasks, and involve mixing of sensorimotor information. Alternatively, natural behaviors might elicit reliable neural signatures in high-level visual and motor regions which contain invariant representations, and involve correlated sensory and motor information that leads to apparent mixing. Here, we provide evidence for the latter possibility through wireless recordings in freely moving monkeys performing natural tasks as well as controlled screen tasks. During natural interactions with food, neural activity was decodable with striking fidelity, equivalent to that of food images. Key events during these interactions elicited distinct and reliable neural signatures that reflected the encoding priorities of each region. Visual and motor regions were clearly dissociated in screen tasks, but were dissociated only at specific events in the natural task. Neurons active while seeing food were reactivated during sleep. Taken together, our results reveal that reliable neural signatures in high-level sensory and motor regions form the neural substrates for natural behaviors.

neuroscience↗

bioRxiv2025

Do monkeys see the way we do? Qualitative similarities and differences between monkey and human perception

Monkeys are widely used as model organisms for human vision and cognition. While their anatomy and physiology strongly correspond to humans, it is unclear to what extent their perception matches with ours. Previous studies have evaluated specific aspects of perception, after extensive training on customized tasks that could have altered their perception. To resolve these issues, we trained monkeys to perform an oddball visual search task on natural images, tested them on carefully controlled images to detect a variety of perceptual phenomena, and compared them with humans. This revealed a number of qualitative similarities and differences. Like humans, monkeys showed similar object relations, Webers law and amodal completion. However, unlike humans, monkeys did not show mirror confusion or a global advantage. These findings represent a first comprehensive evaluation of visual perception in monkeys and humans, revealing the limitations of monkeys as a model organism for human vision. SIGNIFICANCE STATEMENTMonkeys are widely used to study for vision and cognition, but is their perception like ours? Most previous studies have tested only single aspects of perception in monkeys, often after extensive training which could have altered their perception. Here, we overcame these limitations by training monkeys on a highly general oddball visual search task, testing them on many perceptual phenomena and comparing them with humans on the same tasks. Our results show that monkeys do indeed see the way we do, but with important differences that highlight their limitations as a model for human vision.

animal behavior and cognition↗

bioRxiv2025

Non-invasive eDNA reveals the ecological and genetic status of the Western Capercaillie (Tetrao urogallus aquitanicus) in the Eastern Pyrenees

The Anthropocene era is expected to bring about significant biodiversity and habitat loss for many species. These geographical changes, whether driven by climatic or anthropogenic factors, are likely to lead to considerable alterations in population size, structure, and genetic diversity. Monitoring natural populations is therefore essential to assess these impacts and enable informed conservation strategies for threatened species. The Western Capercaillie (Tetrao urogallus, L. 1758) has a widespread distribution in Boreal forests but fragmented in mountainous regions of the Palearctic, and is locally threatened by climate change, habitat destruction, and human disturbance. Our study focused on the eastern population of the subspecies T. u. aquitanicus, which is endemic to the Pyrenees mountains. The monitoring of this population has relied on direct methods and no genetic information had been generated so far. Here, we conducted a molecular study based on 229 non-invasive samples (faeces) to assess the ecological and genetic status of local population in the Catalan Nature Reserves of the Pyrenees-Orientales (Occitanie region, France). At the individual level, we assessed multi-locus genotypes, sexing, levels of inbreeding, stress level (Fecal Corticosterone Metabolites; FCMs) and diet. At the population level, we assessed sex ratio, genetic diversity and structure. We identified 62 individuals with a balanced sex ratio and estimated a census size of 79 individuals [95%CI = 68-92] in the study area. Genetic diversity was low and suggested significant inbreeding levels. FCM levels were lower in birds of areas considered as disturbed by humans and metabarcoding approach indicated a geographical structuring of diet composition at the reserve scale, with individuals exhibiting feeding behavior upon only one or few plant species. Our estimate of population census size was higher with figures assessed from lek counts, and the genetic approach provided additional insights on this population, establishing a baseline that will support conservation management plans.

ecology↗

bioRxiv2024

Distinct representational properties of cues and contexts shape fear learning and extinction

When we learn that something is dangerous, a fear memory is formed. However, this memory is not fixed and can be updated through new experiences, such as learning that the threat is no longer present. This process of updating, known as extinction or reversal learning, is highly dependent on the context in which it occurs. How the brain represents cues, contexts, and their changing threat value remains a major question. Here, we used functional magnetic resonance imaging and a novel fear learning paradigm to track the neural representations of stimuli across fear acquisition, reversal, and test phases. We found that initial fear learning creates generalized neural representations for all threatening cues in the brains fear network. During reversal learning, when threat contingencies switched for some of the cues, two distinct representational strategies were observed. On the one hand, we still identified generalized patterns for currently threatening cues, whereas on the other hand, we observed highly stable representations of individual cues (i.e., item-specific) that changed their valence, particularly in the precuneus and prefrontal cortex. Furthermore, we observed that the brain represents contexts more distinctly during reversal learning. Furthermore, additional exploratory analyses showed that the degree of this context specificity in the prefrontal cortex predicted the subsequent return of fear, providing a potential neural mechanism for fear renewal. Our findings reveal that the brain uses a flexible combination of generalized and specific representations to adapt to a changing world, shedding new light on the mechanisms that support cognitive flexibility and the treatment of anxiety disorders via exposure therapy.

neuroscience↗

bioRxiv2022

Visual homogeneity computations in the brain enable solving generic visual tasks

Most visual tasks involve looking for specific object features. But we also often perform property-based tasks where we look for specific property in an image, such as finding an odd item, deciding if two items are same, or if an object has symmetry. How do we solve such tasks? These tasks do not fit into standard models of decision making because their underlying feature space and decision process is unclear. Using well-known principles governing multiple object representations, we show that displays with repeating elements can be distinguished from heterogeneous displays using a property we define as visual homogeneity. In behavior, visual homogeneity predicted response times on visual search, same-different and symmetry tasks. Brain imaging during visual search and symmetry tasks revealed that visual homogeneity was localized to a region in the object-selective cortex. Thus, property-based visual tasks are solved in a localized region in the brain by computing visual homogeneity. SIGNIFICANCE STATEMENTMost visual tasks involve looking for specific features, like finding a face in a crowd. But we also often look for a particular image property - such as finding an odd item, deciding if two items are same, or judging if an object is symmetric. How does our brain solve these disparate tasks? Here, we show that these tasks can all be solved using a simple computation over object representations in higher visual cortex, which we define as visual homogeneity.

neuroscience↗

bioRxiv2020

Turning traditional neurophysiology on its head: A naturalistic environment to study natural behaviors and cognitive tasks in freely moving monkeys

Macaque monkeys are widely used to study the neural basis of cognition. In the traditional approach, the monkey is brought into a lab to perform tasks while it is restrained to obtain stable gaze tracking and neural recordings. This unnatural setting prevents studying brain activity during natural, social and complex behaviors. Here, we designed a naturalistic environment with an integrated behavioral workstation that enables complex task training with viable gaze tracking in freely moving monkeys. We used this facility to train monkeys on a challenging same-different task. Remarkably, this facility enabled a naive monkey to learn the task merely by observing trained monkeys. This social training was faster primarily because the naive monkey first learned the task structure and then the same-different rule. We propose that such hybrid environments can be used to study brain activity during natural behaviors as well as during controlled cognitive tasks.

animal behavior and cognition↗

bioRxiv2019

Do deep neural networks see the way we do?

Deep neural networks have revolutionized computer vision, and their object representations match coarsely with the brain. As a result, it is widely believed that any fine scale differences between deep networks and brains can be fixed with increased training data or minor changes in architecture. But what if there are qualitative differences between brains and deep networks? Do deep networks even see the way we do? To answer this question, we chose a deep neural network optimized for object recognition and asked whether it exhibits well-known perceptual and neural phenomena despite not being explicitly trained to do so. To our surprise, many phenomena were present in the network, including the Thatcher effect, mirror confusion, Webers law, relative size, multiple object normalization and sparse coding along multiple dimensions. However, some perceptual phenomena were notably absent, including processing of 3D shape, patterns on surfaces, occlusion, natural parts and a global advantage. Our results elucidate the computational challenges of vision by showing that learning to recognize objects suffices to produce some perceptual phenomena but not others and reveal the perceptual properties that could be incorporated into deep networks to improve their performance.

neuroscience↗

bioRxiv2019

How the forest interacts with the trees: Multiscale shape integration explains global and local processing

Hierarchical stimuli (such as a circle made of diamonds) have been widely used to study global and local processing. Two classic phenomena have been observed using these stimuli: the global advantage effect (that we identify the circle faster than the diamonds) and the incongruence effect (that we identify the circle faster when both global and local shapes are circles). Understanding them has been difficult because they occur during shape detection, where an unknown categorical judgement is made on an unknown feature representation.\n\nHere we report two essential findings. First, these phenomena are present both in a general same-different task and a visual search task, suggesting that they may be intrinsic properties of the underlying representation. Second, in both tasks, responses were explained using linear models that combined multiscale shape differences and shape distinctiveness. Thus, global and local processing can be understood as properties of a systematic underlying feature representation.

neuroscience↗

bioRxiv2019

Demography, genetic, and extinction process in a spatially structured population of lekking bird

Understanding the mechanisms underlying biological extinctions is a critical challenge for conservation biologists. Both deterministic (e.g. habitat loss, fragmentation) and stochastic (i.e. demographic stochasticity, Allee effect) demographic processes are involved in population decline. Simultaneously, a decrease of population size has far-reaching consequences for genetics of populations by increasing the risk of inbreeding and the effects of genetic drift, which together inevitably results in a loss of genetic diversity and a reduced effective population size (Ne). These genetic factors may retroactively affect vital rates (a phenomenon coined inbreeding depression), and therefore reduce population growth and accelerate the extinction process of small populations. To date, few studies have simultaneously examined the demographic and genetic mechanisms driving the extinction of wild populations, and have most of the time neglected the spatial structure of populations. In this study, we examined demographic and genetic factors involved in the extinction process of a spatially structured population of a lekking bird, the western capercaillie (Tetrao urogallus). To address this issue, we collected capture-recapture and genetic data over a 6-years period in Vosges mountains, France. Our study showed that the population of T. urogallus experienced a severe decline between 2010 and 2015. We did not detect any Allee effect on survival and recruitment. By contrast, individuals of both sexes dispersed to avoid small leks, suggesting a behavioral response to a mate finding Allee effect. In parallel to this demographic decline, the population showed a low genetic diversity and high inbreeding. In addition, the effective population sizes at both lek and population levels was low. Despite this, we did not detected evidence of inbreeding depression: neither survival nor recruitment were affected by individual inbreeding level. Our study underlines the benefit from combining demographic and genetic approaches to investigate processes that are involved in biological extinctions.

ecology↗

bioRxiv2019

Kin-dependent dispersal influences relatedness and genetic structuring in a lek system

Kin selection and dispersal play a critical role in the evolution of cooperative breeding systems. Limited dispersal dramatically increases relatedness in spatially structured populations (population viscosity), with the result that neighbours tend to be genealogical relatives. Yet the increase in neighbours performance through altruistic interaction may also result in habitat saturation and thus exacerbate local competition between kin. Our goal was to detect the footprint of kin selection and competition by examining the spatial structure of relatedness and by comparing non-effective and effective dispersal in a population of a lekking bird, Tetrao urogallus. For this purpose, we analysed capture-recapture and genetic data collected over a 6-year period on a spatially structured population of T. urogallus in France. Our findings revealed a strong spatial structure of relatedness in males. They also indicated that the population viscosity allowed male cooperation through two non-exclusive mechanisms. First, at their first lek attendance, males aggregate in a lek composed of relatives. Second, the distance corresponding to non-effective dispersal dramatically outweighed effective dispersal distance, which suggests that dispersers incur high post-settlement costs. These two mechanisms result in strong population genetic structuring in males. In females, our findings revealed a lower level of spatial structure of relatedness and genetic structure in respect to males. Additionally, non-effective dispersal and effective dispersal distances in females were highly similar, which suggests limited post-settlement costs. These results indicate that kin-dependent dispersal decisions and costs are factors driving the evolution of cooperative courtship and have a genetic footprint in wild populations.

ecology↗