Biology subjects

Zuberbühler, K.

Publications and source records attributed to Zuberbühler, K..

7 recordsLinked to original sources

bioRxiv2026

Supra-regular recursion in primate vocal sequences

Complex syntax is the widely accepted demarcation between animal and human communication. Although animal vocal systems occasionally contain pockets of syntax-like structures, their grammars are thought to be at best regular, whereas human language is supra-regular, i.e., including at least context-free computational complexity. Leveraging a new likelihood method for probabilistic formal grammars, we show that the call sequences of three phylogenetically diverse nonhuman primates (bonobos, olive colobus monkeys, common marmosets) include parts that are most likely generated by supra-regular recursive grammars, similar to human language. These findings challenge syntax as the major transition in hominid evolution and opens up prospects for alternative evolutionary scenarios.

animal behavior and cognition↗

bioRxiv2023

ASBAR: an Animal Skeleton-Based Action Recognition framework. Recognizing great ape behaviors in the wild using pose estimation with domain adaptation.

The study and classification of animal behaviors have traditionally relied on direct human observation or video analysis, processes that are labor-intensive, time-consuming, and prone to human bias. Advances in machine learning for computer vision, particularly in pose estimation and action recognition, offer transformative potential to enhance the understanding of animal behaviors. However, the integration of these technologies for behavior recognition remains underexplored, particularly in natural settings. We introduce ASBAR (Animal Skeleton-Based Action Recognition), a novel framework that integrates pose estimation and behavior recognition into a cohesive pipeline. To demonstrate its utility, we tackled the challenging task of classifying natural behaviors of great apes in the wild. Our approach leverages the OpenMonkeyChallenge dataset, one of the largest open-source primate pose datasets, to train a robust pose estimation model using DeepLabCut. Subsequently, we extracted skeletal motion data from the PanAf500 dataset, a collection of in-the-wild videos of gorillas and chimpanzees annotated with nine behavior categories. Using PoseConv3D from MMAction2, we trained a skeleton-based action recognition model, achieving a Top-1 accuracy of 75.3%. This performance is comparable to previous video-based methods while reducing input data size by approximately 20-fold, offering significant advantages in computational efficiency and storage. To support further research, we provide an open-source, terminal-based GUI for training and evaluation, along with a dataset of 5,440 annotated keypoints for replication and extension to other species and behaviors. All models, code, and data are publicly available at: https://github.com/MitchFuchs/asbar

animal behavior and cognition↗

bioRxiv2023

Many morphs: parsing gesture signals from the noise

Parsing signals from noise is a general problem for signallers and recipients, as well as for researchers studying communicative systems. Substantial research efforts have been invested in comparing how other species encode information and meaning in their signals, and how signalling is structured. However, our ability to do so depends on identifying and discriminating signals that represent meaningful units of analysis. Early approaches to defining signal repertoires applied top- down approaches, classifying cases into predefined signal types. Recently, more labour-intensive methods have taken a bottom-up approach describing the features of each signal in detail and clustering cases into types based on patterns of similarity between them in multi-dimensional feature-space that were previously undetectable. Nevertheless, it remains essential to assess whether the resulting repertoires are composed of relevant units from the perspective of the species using them, and redefining repertoires when additional data makes more detailed analyses feasible. In this paper we provide a framework that takes data from the largest set of wild chimpanzee (Pan troglodytes) gestures currently available, splitting gesture types at a fine scale based on modifying features of gesture expression and then determining whether this splitting process increases the information content of the communication system. Our method allows different features of interest to be incorporated into the splitting process, providing substantial future flexibility across - for example - species, populations, and levels of signal granularity. In doing so we provide a powerful tool allowing researchers interested in gestural communication to establish repertoires of relevant units for subsequent analyses within and between systems of communication.

animal behavior and cognition↗

bioRxiv2023

Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids

Fine-scale knowledge of the changes in composition and function of the human gut microbiome compared that of our closest relatives is critical for understanding the evolutionary processes underlying its developmental trajectory. To infer taxonomic and functional changes in the gut microbiome across hominids at different timescales, we performed high-resolution metagenomic-based analyses of the fecal microbiome from over two hundred samples including diverse human populations, as well as wild-living chimpanzees, bonobos, and gorillas. We find human-associated taxa depleted within non-human apes and patterns of host-specific gut microbiota, suggesting the widespread acquisition of novel microbial clades along the evolutionary divergence of hosts. In contrast, we reveal multiple lines of evidence for a pervasive loss of diversity in humans populations in correlation with a high Human Development Index, including evolutionarily conserved clades. Similarly, patterns of co-phylogeny are found to be disrupted in humans. Together with identifying individual microbial taxa and functional adaptations that correlate to host phylogeny, these findings offer new and exciting insights into specific candidates playing a role in the diverging trajectories of the gut microbiome of hominids, demonstrating that repeated horizontal gene transfer and gene loss, as well as the adaptation to transient microaerobic conditions appear to have played a role in the evolution of the human gut microbiome.

evolutionary biology↗

bioRxiv2020

Primate phageomes are structured by superhost phylogeny and environment

The evolutionary origins of human-associated bacteriophage communities are poorly understood. To address this question, we examined fecal phageomes of 23 wild non-human primate taxa, including multiple representatives of all the major primate radiations, and find relatives of the majority of human-associated phages. Primate taxa have distinct phageome compositions that exhibit a clear phylosymbiotic signal, and phage-superhost co-divergence is detected for 44 individual phages. Within species, neighboring social groups harbor evolutionarily and compositionally distinct phageomes, structured by superhost social behavior. However, captive non-human primate phageomes are more similar to humans than their wild counterparts, revealing replacement of wild-associated phages with human-associated ones. Together, our results suggest that potentially labile primate-phage associations persisted across millions of years of evolution, potentially facilitated by transmission between groupmates. One Sentence SummaryRelatives of human-associated phages in wild primates reveal ancient but dynamic superhost-phage associations shaped by social transmission.

microbiology↗

bioRxiv2019

Early vocal production and functional flexibility in wild infant chimpanzees

How did human language evolve from earlier forms of communication? One way to address this question is to compare prelinguistic human vocal behavior with nonhuman primate calls. Here, an important finding has been that, prior to speech, human infant vocal behavior exhibits functional flexibility, the capacity of producing protophones that are not tied to one specific function. Nonhuman primate vocal behavior, by contrast, is comparably inflexible, with different call types tied to specific functions. Our research challenges the generality of this claim, with new findings of flexible vocal behavior in infant chimpanzees. We used artificial intelligence consisting of automated feature extraction and supervised learning algorithms to analyze grunt and whimper vocalizations from free-ranging infants during their first year of life. We found that grunt production was highly flexible occurring in positive, neutral and negative circumstances, as already shown in human infants. We also found acoustic variants of grunts produced in different affective contexts, suggesting gradation within this vocal category. By contrast, the second most common call type of infant chimpanzees, the whimpers, was produced in only one affective context in line with standard models of nonhuman primate vocal behavior. We concluded that the most common chimpanzee vocalization, the grunt, qualifies as functionally flexible, suggesting that evolution of vocal functional flexibility occurred before the split between the Homo and Pan lineages.

animal behavior and cognition↗

bioRxiv2019

Machine learning reveals adaptive maternal responses to infant distress calls in wild chimpanzees

Distress calls are an acoustically variable group of vocalizations ubiquitous in mammals and other animals. Their presumed function is to recruit help, but it is uncertain whether this is mediated by listeners extracting the nature of the disturbance from calls. To address this, we used machine learning to analyse distress calls produced by wild infant chimpanzees. It enabled us to classify calls and examine them in relation to the external event triggering them and the distance to the intended receiver, the mother. In further steps, we tested whether the acoustic variants produced by infants predicted maternal responses. Our results demonstrated that, although infant chimpanzee distress calls were highly graded, they conveyed information about discrete events, which in turn guided maternal parenting decisions. We discuss these findings in light of one the most vexing problems in communication theory, the evolution of vocal flexibility in the human lineage.

animal behavior and cognition↗