Biology subjects

de Polavieja, G. G.

Publications and source records attributed to de Polavieja, G. G..

6 recordsLinked to original sources

bioRxiv2025

New idtracker.ai: rethinking multi-animal tracking as a representation learning problem to increase accuracy and reduce tracking times

idTracker and idtracker.ai approach multi-animal tracking from video as an image classification problem. For this classification, both rely on segments of video where all animals are visible to extract images and their identity labels. When these segments are too short, tracking can become slow and inaccurate and, if they are absent, tracking is impossible. Here, we introduce a new idtracker.ai that reframes multi-animal tracking as a representation learning problem rather than a classification task. Specifically, we apply contrastive learning to image pairs that, based on video structure, are known to belong to the same or different identities. This approach maps animal images into a representation space where they cluster by animal identity. As a result, the new idtracker.ai eliminates the need for video segments with all animals visible, is more accurate, and tracks up to 700 times faster.

animal behavior and cognition↗

bioRxiv2024

Whistle variability and social acoustic interactions in bottlenose dolphins

Bottlenose dolphins exhibit a sophisticated social structure, known as a fission-fusion society. To sustain this complex system, dolphins rely on a rich vocal repertoire: clicks exclusively used for echolocation, burst-pulse sounds associated with emotions during social interactions, and whistles, including signature whistles that serve as individual-specific identifiers ( names). How dolphins maintain their complex social structure based only on a limited repertoire of sounds remains elusive. Previous studies suggest that contextual information can be transferred by the modulation of the whistles. Here, we investigated the whistle variability using a comprehensive computational approach, and studied the structure of the interactions between the whistle variants. Using a unique large dataset, acquired in a natural environment, we observed that signature whistles exhibit variations in their frequency contours. Unsupervised clustering revealed that signature whistles could be classified into sub-categories (signature whistle variants). The existence of these categories, and their independence on the emitter dolphin, indicate that these variations are not random. Analysis of pairwise interactions between sub-categories revealed a clustered structure similar to that of their social hierarchy. Network analysis of this structure showed that whistle sub-categories had different functional roles: some acted as hubs, others as bridges, and certain were used for turn-taking between the main whistle categories. We also found that the dolphins emit signature whistles of their deceased mothers, a phenomenon only observed in human language. Overall, these findings suggest that dolphins modulate signature whistles to transmit additional information beyond individual identity, and that they engage in "dialogue-like" acoustic interactions.

animal behavior and cognition↗

bioRxiv2020

Early-life social experience shapes social avoidance reactions in larval zebrafish

Social experiences greatly define successive social behavior. Lack of such experiences, especially during critical phases of development, can severely impede the ability to behave adequately in social contexts. To date it is not well characterized how early-life social isolation leads to social deficits and impacts development. In many model species, it is challenging to fully control social experiences, because they depend on parental care. Moreover, complex social behaviors involve multiple sensory modalities, contexts, and actions. Hence, when studying social isolation effects, it is particularly important to parse apart social deficits from general developmental effects, such as abnormal motor learning. Here, we characterized how social experiences during early development of zebrafish larvae modulate their social behavior, at one week of age, when social avoidance reactions can be measured as discrete swim events. We show that raising larvae in social isolation leads to enhanced social avoidance, in terms of reaction distance and reaction strength. Specifically, larvae raised in isolation use a high-acceleration escape swim bout, the short latency C-start, more frequently during social interactions. These behavioral differences are absent in non-social contexts. By ablating the lateral line and presenting the fish with local water vibrations, we show that lateral line inputs are both necessary and sufficient to drive enhanced social avoidance reactions. Taken together, our results show that social experience during development is a critical factor in shaping mechanosensory avoidance reactions in larval zebrafish. HighlightsO_LILarval zebrafish raised in isolation show enhanced social avoidance reactions C_LIO_LIEnhanced avoidance is composed of increased avoidance distances and usage of high acceleration escape swims C_LIO_LIThe lateral line sensory organ is necessary and sufficient for the increased usage of high acceleration escape swims C_LI

neuroscience↗

bioRxiv2018

Aggregation rule in animal collectives dynamically changes between majority and minority influence

A variety of simple models has been proposed to understand the collective motion of animals. These models can be insightful but lack important elements necessary to predict the motion of each individual in the collective. Adding more detail increases predictability but can make models too complex to be insightful. Here we report that deep attention networks can obtain in a data-driven way a model of collective behavior that is simultaneously predictive and insightful thanks to an organization in modules. The model obtains that interactions between two zebrafish, Danio rerio, in a large groups of 60-100, can be approximately be described as repulsive, attractive or as alignment, but only when moving slowly. At high velocities, interactions correspond only to alignment or alignment mixed with repulsion at close distances. The model also shows that each zebrafish decides where to move by aggregating information from the group as a weighted average over neighbours. Weights are higher for neighbours that are close, in a collision path or moving faster in frontal and lateral locations. These weights effectively select 5 relevant neighbours on average, but this number is dynamical, changing between a single neighbour to up to 12, often in less than a second. Our results suggest that each animal in a group decides by dynamically selecting information from the group.\n\nHighlightsO_LIAt 30 days postfertilization, zebrafish, Danio rerio, can move in very cohesive and predictable large groups\nC_LIO_LIDeep attention networks obtain a predictive and understadable model of collective motion\nC_LIO_LIWhen moving slowly, interations between pairs of zebrafish have clear components of repulsion, attraction and alignment\nC_LIO_LIWhen moving fast, interactions correspond to alignment and a mixture of alignment and repulsion at close distances\nC_LIO_LIZebrafish turn left or right depending on a weighted average of interaction information with other fish, with weights higher for close fish, those in a collision path or those moving fast in front or to the sides\nC_LIO_LIAggregation is dynamical, oscillating between 1 and 12 neighbouring fish, with 5 on average\nC_LI

animal behavior and cognition↗

bioRxiv2017

Histone 4 acetylation regulates behavioral individuality in zebrafish

Animals can show very different behaviors even in isogenic populations, but the underlying mechanisms to generate this variability remain elusive. We found that laboratory and isogenic zebrafish (Danio rerio) larvae showed consistent individual behaviors when swimming freely in identical wells or in reaction to stimuli. We also found that this behavioral inter-individual variability was reduced when we impaired the histone deacetylation pathway. Individuals with high levels of histone H4 acetylation, and specifically H4K12, behaved similar to the average of the population, but those with low levels deviated from it. More precisely, we found a set of genomic regions whose histone H4 acetylation is reduced with the distance between the individual and the average population behavior. We found evidence that this modulation depends on a complex of Yin-yang 1 (YY1) and histone deacetylase 1 (HDAC1) that binds to and deacetylates these regions. These changes were not only maintained at the transcriptional level but also amplified, as most target regions were located near genes encoding transcription factors. We suggest that stochasticity in the histone deacetylation pathway participates the generation of genetic-independent behavioral inter-individual variability.

animal behavior and cognition↗

bioRxiv2016

Microsaccadic information sampling provides Drosophila hyperacute vision

Small fly eyes should not see fine image details. Because flies exhibit saccadic visual behaviors and their compound eyes have relatively few ommatidia (sampling points), their photoreceptors would be expected to generate blurry and coarse retinal images of the world. Here we demonstrate that Drosophila see the world far better than predicted from the classic theories. By using electrophysiological, optical and behavioral assays, we found that R1-R6 photoreceptors encoding capacity in time is maximized to fast high-contrast bursts, which resemble their light input during saccadic behaviors. Whilst over space, R1-R6s resolve moving objects at saccadic speeds beyond the predicted motion-blur-limit. Our results show how refractory phototransduction and rapid photomechanical photoreceptor contractions jointly sharpen retinal images of moving objects in space-time, enabling hyperacute vision, and explain how such microsaccadic information sampling exceeds the compound eyes optical limits. These discoveries elucidate how acuity depends upon photoreceptor function and eye movements.

neuroscience↗