Finding Meanings in Low Dimensional Structures: Stochastic Neighbor Embedding Applied to the Analysis of Indri indri Vocal Repertoire

Isochrony as ancestral condition to call and song in a primate

Animal songs differ from calls in function and structure, and have comparative and translational value, showing similarities to human music. Rhythm in music is often distributed in quantized classes of intervals known as rhythmic categories. These classes have been found in the songs of a few nonhuman species but never in their calls. Are rhythmic categories song-specific, as in human music, or can they transcend the song-call boundary? We analyze the vocal displays of one of the few mammals producing both songs and call sequences: Indri indri. We test whether rhythmic categories (a) are conserved across songs produced in different contexts, (b) exist in call sequences, and (c) differ between songs and call sequences. We show that rhythmic categories occur across vocal displays. Vocalization type and function modulate deployment of categories. We find isochrony (1:1 ratio, like the rhythm of a ticking clock) in all song types, but only advertisement songs show three rhythmic categories (1:1, 1:2, 2:1 ratios). Like songs, some call types are also isochronous. Isochrony is the backbone of most indri vocalizations, unlike human speech, where it is rare. In indri, isochrony underlies both songs and hierarchy-less call sequences and might be ancestral to both.

"The song remains the same": not really! Vocal flexibility in the song of the indris

In studying communicative signals, we can think of flexibility as a necessary correlate of creativity. Flexibility enables animals to find practical solutions and appropriate behaviors in mutable situations. In this study, we aimed to quantify the degree of flexibility in the songs of indris (Indri indri), the only singing lemur, using three different metrics: Jaro Distance, normalized diversity, and entropy. We hypothesized that the degree and the co-variation of the flexibility of indris singing together would vary according to their status and sex. We found that dominant females were more flexible than dominant males when concatenating elements into strings (element concatenation). The number of different elements in a song contribution normalized by the contribution length (contribution diversity) of dominant individuals positively co-varied for seven duetting pairs. Non-dominant individuals were more variable in element concatenation than dominant individuals, and they were more diverse in phrase type than dominant females. Independently from sex and status, individual contributions did not differ in entropy (a measure of the predictability of contributions). These results corroborate previous findings regarding the dimorphism by sex and by status of individual contributions to songs. Thus, they shed light on the presence and expression of flexibility in the behavior of a non-human primate species. Indeed, they potentially show an effect of social features in shaping vocal flexibility, which underlies many communication systems, including human language. We speculate that this degree of flexibility may account for creativity.

Bioacoustic characterization of the black-and-white ruffed lemur (Varecia variegata) vocal repertoire

Ruffed lemurs (Varecia spp.) exhibit a unique suite of behavioral traits compared to other lemur species, which includes their fluid fission-fusion social dynamics, communal rearing of parked litters, and pronounced frugivory in their humid rainforest habitats. Given these traits, and the dense rainforests they inhabit, vocal communication may be key to maintaining social cohesion, coordinating infant care, and/or defending their high-quality food resources. Indeed, they are known for their raucous 'roar-shriek' calls. However, there has been surprisingly little research on vocal communication in Varecia species and only two previously published repertoires, both of which were qualitative descriptions of their calls. In this study, we quantitatively examined the vocal repertoire of wild black-and-white ruffed lemurs (Varecia variegata) at Mangevo, Ranomafana National Park, Madagascar. We characterized 11 call types using 33 bioacoustic parameters related to frequency, duration, tonality, and composition. We also used discriminant function analysis and hierarchical clustering to quantitatively and objectively classify call types within the black-and-white ruffed lemur vocal repertoire. The repertoire consists of both monosyllabic and multisyllabic calls that are individually given or emitted in contagious choruses. Eight of the 11 calls were also used in combination or in larger multi-call sequences. The discriminant function analysis correctly assigned call types with 87% success, though this varied greatly by call type (1-65%). Hierarchical clustering identified 3-4 robust clusters, indicating low clustering structure in the data and suggesting that V. variegata exhibits a graded vocal repertoire. Future work should consider the environmental and behavioral contexts in which calls are used to better understand the function of these call types and combinations.

Encoding of Arousal and Physical Characteristics in Audible and Ultrasonic Vocalizations of Mongolian Gerbil Pups Testing Common Rules for Mammals

In mammals, common rules for the encoding of arousal and physical characteristics of the sender are suggested based on a similar vocal production apparatus. In this study, we want to investigate to what extent vocalizations of developing Mongolian gerbil pups fulfill these rules. We recorded vocalizations of 28 Mongolian gerbil pups in four developmental stages using a separation paradigm, suggested to induce different arousal levels. For low arousal, a pup was placed in an arena isolated from its siblings and parents; for high arousal, the pup was additionally stressed through the simulation of a predator. An unsupervised cluster analysis revealed three call types: ultrasonic (USV), audible vocalizations (ADV), and transitions between both (USV-ADV). The USV and USV-ADV rate showed an age-dependent decrease, contrasting an age-dependent increase for ADVs. Vocal correlates for the encoding of arousal were found for USVs and of physical characteristics for USVs and ADVs. However, the pattern of encoding these cues differed between call types and only partly confirmed the common rules suggested for mammals. Our results show that divergent encoding patterns do not only differ between species but also between call types within a species, indicating that coding rules can be shaped by socio-ecological factors or call type specific production mechanisms.

Improving the workflow to crack Small, Unbalanced, Noisy, but Genuine (SUNG) datasets in bioacoustics: The case of bonobo calls

Despite the accumulation of data and studies, deciphering animal vocal communication remains challenging. In most cases, researchers must deal with the sparse recordings composing Small, Unbalanced, Noisy, but Genuine (SUNG) datasets. SUNG datasets are characterized by a limited number of recordings, most often noisy, and unbalanced in number between the individuals or categories of vocalizations. SUNG datasets therefore offer a valuable but inevitably distorted vision of communication systems. Adopting the best practices in their analysis is essential to effectively extract the available information and draw reliable conclusions. Here we show that the most recent advances in machine learning applied to a SUNG dataset succeed in unraveling the complex vocal repertoire of the bonobo, and we propose a workflow that can be effective with other animal species. We implement acoustic parameterization in three feature spaces and run a Supervised Uniform Manifold Approximation and Projection (S-UMAP) to evaluate how call types and individual signatures cluster in the bonobo acoustic space. We then implement three classification algorithms (Support Vector Machine, xgboost, neural networks) and their combination to explore the structure and variability of bonobo calls, as well as the robustness of the individual signature they encode. We underscore how classification performance is affected by the feature set and identify the most informative features. In addition, we highlight the need to address data leakage in the evaluation of classification performance to avoid misleading interpretations. Our results lead to identifying several practical approaches that are generalizable to any other animal communication system. To improve the reliability and replicability of vocal communication studies with SUNG datasets, we thus recommend: i) comparing several acoustic parameterizations; ii) visualizing the dataset with supervised UMAP to examine the species acoustic space; iii) adopting Support Vector Machines as the baseline classification approach; iv) explicitly evaluating data leakage and possibly implementing a mitigation strategy.

There You Are! Automated Detection of Indris' Songs on Features Extracted from Passive Acoustic Recordings

The growing concern for the ongoing biodiversity loss drives researchers towards practical and large-scale automated systems to monitor wild animal populations. Primates, with most species threatened by extinction, face substantial risks. We focused on the vocal activity of the indri (Indri indri) recorded in Maromizaha Forest (Madagascar) from 2019 to 2021 via passive acoustics, a method increasingly used for monitoring activities in different environments. We first used indris’ songs, loud distinctive vocal sequences, to detect the species’ presence. We processed the raw data (66,443 10-min recordings) and extracted acoustic features based on the third-octave band system. We then analysed the features extracted from three datasets, divided according to sampling year, site, and recorder type, with a convolutional neural network that was able to generalise to recording sites and previously unsampled periods via data augmentation and transfer learning. For the three datasets, our network detected the song presence with high accuracy (>90%) and recall (>80%) values. Once provided the model with the time and day of recording, the high-performance values ensured that the classification process could accurately depict both daily and annual habits of indris‘ singing pattern, critical information to optimise field data collection. Overall, using this easy-to-implement species-specific detection workflow as a preprocessing method allows researchers to reduce the time dedicated to manual classification.

Parent-offspring turn-taking dynamics influence parents’ song structure and elaboration in a singing primate

Parent-offspring interactions are essential to interpret animal social evolution and behavior, but their role in mediating acoustic communication in animals that interact vocally is still unclear. Increasing evidence shows that primate vocal communication is way more flexible than previously assumed, and research on this topic can provide further information on how the social environment shaped vocal plasticity during the evolution of the Primate order. Indris communicate through elaborated vocal emissions, usually termed songs. Songs are interactive vocal displays in which all members of the family group alternate their emissions, taking turns during chorusing events. We aimed to understand whether specific rules regulate the turn-taking of different group members and investigate the flexibility of indris’ vocal behavior when co-singing with their offspring. We found that social factors can influence the turn-taking organization in a chorus, as offspring were more likely to drop out from the parents’ duet than join in, and we speculate that overlap might signal competition by members of the same-sex. The duet between the reproductive pair was the most common type of singing organization, followed by a duet between mothers and sons and the triadic interaction between mother, father, and son. Interestingly, parents’ solo singing seems to stimulate offspring to vocalize, and we also found that mothers and fathers simplify, at least in part, song elaboration when chorusing with offspring. Our results indicate that indris can perform short-time adjustments to the number of co-emitters and their identity: our approach is advantageous in highlighting the multilevel influences on primate vocal flexibility. Moreover, it provides evidence that some aspects of our vocal plasticity were already present in the lemur lineage.

Comparative Analysis of the Vocal Repertoires of the Indri (Indri indri) and the Diademed Sifaka (Propithecus diadema)

Strepsirrhine vocalisations are extraordinarily diverse and cross-species comparisons are needed to explore how this variability evolved. We contributed to the investigation of primate acoustic diversity by comparing the vocal repertoire of two sympatric lemur species, Propithecus diadema and Indri indri. These diurnal species belong to the same taxonomic family and have similar activity patterns but different social structures. These features make them excellent candidates for an investigation of the phylogenetic, environmental, and social influence on primate vocal behavior. We recorded 3 P. diadema groups in 2014 and 2016. From 1,872 recordings we selected and assigned 3814 calls to 9 a priori call types, on the basis of their acoustic structure. We implemented a reproducible technique performing an acoustic feature extraction relying on frequency bins, t-SNE data reduction, and a hard-clustering analysis. We first quantified the vocal repertoire of P. diadema, finding consistent results for the 9 putatively identified call types. When comparing this repertoire with a previously published repertoire of I. indri, we found highly species-specific repertoires, with only 2% of the calls misclassified by species identity. The loud calls of the two species were very distinct, while the low-frequency calls were more similar. Our results pinpoint the role of phylogenetic history, social and environmental features on the evolution of communicative systems and contribute to a deeper understanding of the evolutionary roots of primate vocal differentiation. We conclude by arguing that standardized and reproducible techniques, like the one we employed, allow robust comparisons and should be prioritized in the future.

Rhythm in dyadic interactions

This review paper discusses rhythmic interactions and distinguishes them from non-rhythmic interactions. We report on communicative behaviours in social and sexual contexts, as found in dyads of humans, non-human primates, non-primate mammals, birds, anurans and insects. We discuss observed instances of rhythm in dyadic interactions, identify knowledge gaps and propose suggestions for future research. We find that most studies on rhythmicity in interactive signals mainly focus on one modality (acoustic or visual) and we suggest more work should be performed on multimodal signals. Although the social functions of interactive rhythms have been fairly well described, developmental research on rhythms used to regulate social interactions is still lacking. Future work should also focus on identifying the exact timing mechanisms involved. Rhythmic signalling behaviours are widespread and critical in regulating social interactions across taxa, but many questions remain unexplored. A multidisciplinary, comparative cross-species approach may help provide answers. This article is part of the theme issue 'Synchrony and rhythm interaction: from the brain to behavioural ecology'.

Sexually dimorphic phrase organization in the song of the indris (Indri indri)

Animal acoustic communication often takes the form of complex sequences, composed of multiple distinct acoustic units, which can vary in their degree of stereotypy. Studies of sequence variation may contribute to our understanding of the structural flexibility of primates' songs, which can provide essential ecological and behavioral information about variability at the individual, population, and specific level and provide insights into the mechanisms and drivers responsible for the evolutionary change of communicative traits. Several methods have been used for investigating different levels of structural information and sequence similarity in acoustic displays. We studied intra and interindividual variation in the song structuring of a singing primate, the indri (Indri indri), which inhabits the montane rain forests of Madagascar. Indri groups emit duets and choruses in which they combine long notes, short single units, and phrases consisting of a variable number of units (from two to six) with slightly descending frequency. Males' and females' contributions to the song differ in the temporal and frequency structure of song units and repertoire size. We calculated the similarity of phrase organization across different individual contributions using the Levenshtein distance, a logic distance that expressed the minimum cost to convert a sequence into another and can measure differences between two sequences of data. We then analyzed the degree of similarity within and between individuals and found that: (a) the phrase structure of songs varied between reproductive males and females: female structuring of the song showed a higher number of phrases if compared to males; (b) male contributions to the song were overall more similar to those of other males than were female contributions to the song of other females; (c) male contributions were more stereotyped than female contributions, which showed greater individual flexibility. The picture emerging from phrase combinatorics in the indris is in agreement with previous findings of rhythmic features and song repertoire size of the indris, which also suggested that female songs are potentially less stereotyped than those of males.