Automatic detection for bioacoustic research: a practical guide from and for biologists and computer scientists

Recent years have seen a dramatic rise in the use of passive acoustic monitoring (PAM) for biological and ecological applications, and a corresponding increase in the volume of data generated. However, data sets are often becoming so sizable that analysing them manually is increasingly burdensome and unrealistic. Fortunately, we have also seen a corresponding rise in computing power and the capability of machine learning algorithms, which offer the possibility of performing some of the analysis required for PAM automatically. Nonetheless, the field of automatic detection of acoustic events is still in its infancy in biology and ecology. In this review, we examine the trends in bioacoustic PAM applications, and their implications for the burgeoning amount of data that needs to be analysed. We explore the different methods of machine learning and other tools for scanning, analysing, and extracting acoustic events automatically from large volumes of recordings. We then provide a step-by-step practical guide for using automatic detection in bioacoustics. One of the biggest challenges for the greater use of automatic detection in bioacoustics is that there is often a gulf in expertise between the biological sciences and the field of machine learning and computer science. Therefore, this review first presents an overview of the requirements for automatic detection in bioacoustics, intended to familiarise those from a computer science background with the needs of the bioacoustics community, followed by an introduction to the key elements of machine learning and artificial intelligence that a biologist needs to understand to incorporate automatic detection into their research. We then provide a practical guide to building an automatic detection pipeline for bioacoustic data, and conclude with a discussion of possible future directions in this field.

Call combination production is linked to the social environment in Western Australian magpies (Gymnorhina tibicen dorsalis)

It has recently become clear that some language-specific traits previously thought to be unique to humans (such as the capacity to combine sounds) are widespread in the animal kingdom. Despite the increase in studies documenting the presence of call combinations in non-human animals, factors promoting this vocal trait are unclear. One leading hypothesis proposes that communicative complexity co-evolved with social complexity owing to the need to transmit a diversity of information to a wider range of social partners. The Western Australian magpie (Gymnorhina tibicen dorsalis) provides a unique model to investigate this proposed link because it is a group-living, vocal learning species that is capable of multi-level combinatoriality (independently produced calls contain vocal segments and comprise combinations). Here, we compare variations in the production of call combinations across magpie groups ranging in size from 2 to 11 birds. We found that callers in larger groups give call combinations: (i) in greater diversity and (ii) more frequently than callers in smaller groups. Significantly, these observations support the hypothesis that combinatorial complexity may be related to social complexity in an open-ended vocal learner, providing an important step in understanding the role that sociality may have played in the development of vocal combinatorial complexity. This article is part of the theme issue 'The power of sound: unravelling how acoustic communication shapes group dynamics'.

Calls of the little auk (Alle alle) chicks reflect their behavioural contexts

Animal vocalisations can often inform conspecifics about the behavioural context of production and the underlying affective states, hence revealing whether a situation should be approached or avoided. While this is particularly important for socially complex species, little is known about affective expression in wild colonial animals, and even less to about their young. We studied vocalisations of the little auk (Alle alle) chicks in the Hornsund breeding colony, Svalbard. Little auks are highly colonial seabirds, and adults convey complex behavioural contexts through their calls. We recorded chick calls during two contexts of opposite affective valence: handing by a human, and while they interact with their parents inside the nest. Using permuted discriminant function analysis and a series of linear mixed models, we examined the effect of the production context/associated affective valence on the acoustic parameters of those calls. Calls were reliably classified to their context, with over 97% accuracy. Calls uttered during handling had higher mean entropy, fundamental frequency, as well as lower spectral centre of gravity and a less steep spectral slope compared to calls produced during interactions with a parent inside the nest. The individuality of handling calls, assessed by information content, was lower than the individuality of calls uttered in the nest. These findings suggest that seabird chicks can effectively communicate behavioural/affective contexts through calls, conveying socially important messages early in development. Our results are mostly in line with emotional expression patterns observed across taxa, supporting their evolutionary continuity.

Neuroendocrine mechanisms contributing to the coevolution of sociality and communication

Communication is inherently social, so signaling systems should evolve with social systems. The 'social complexity hypothesis' posits that social complexity necessitates communicative complexity and is generally supported in vocalizing mammals. This hypothesis, however, has seldom been tested outside the acoustic modality, and comparisons across studies are confounded by varying definitions of complexity. Moreover, proximate mechanisms underlying coevolution of sociality and communication remain largely unexamined. In this review, we argue that to uncover how sociality and communication coevolve, we need to examine variation in the neuroendocrine mechanisms that coregulate social behavior and signal production and perception. Specifically, we focus on steroid hormones, monoamines, and nonapeptides, which modulate both social behavior and sensorimotor circuits and are likely targets of selection during social evolution. Lastly, we highlight weakly electric fishes as an ideal system in which to comparatively address the proximate mechanisms underlying relationships between social and signal diversity in a novel modality.

Seabird's cry: repertoire and vocal expression of contextual valence in the little auk (Alle alle)

Many seabird species breed in colonies counting up to hundreds of thousands of individuals. Life in such crowded colonies might require special coding-decoding systems to reliably convey information through acoustic cues. This can include, for example, developing complex vocal repertoires and adjusting the properties of their vocal signals to communicate behavioural contexts, and thus regulate social interactions with their conspecifics. We studied vocalisations produced by the little auk (Alle alle)-a highly vocal, colonial seabird-over mating and incubation periods on the SW coast of Svalbard. Using passive acoustic recordings registered in a breeding colony, we extracted eight vocalisation types: single call, clucking, classic call, low trill, short call, short-trill, terror, and handling vocalisation. Calls were grouped by production context (based on the typically associated behaviour), to which a valence (positive vs negative) was later attributed, when possible, according to fitness threats, i.e. predator or human presence (negative) and promoters, i.e. interaction with a partner (positive). The effect of the putative valence on eight selected frequency and duration variables was then investigated. The putative contextual valence significantly affected the acoustic properties of the calls. Calls assigned positive valence had higher fundamental frequency and spectral centre of gravity as well as shorter sound duration than these assigned negative valence. These results indicate that the little auk's vocal communication system may facilitate expression of complex behavioural contexts, and seems to include vocal plasticity within vocalisation types-however, more data are necessary to better understand this effect and possible interplays of other factors.

Evolution of acoustic signals associated with cooperative parental behavior in a poison frog

The emergence of complex social interactions is predicted to be an important selective force in the diversification of communication systems. Parental care presents a key social context in which to study the evolution of novel signals, as care often requires communication and behavioral coordination between parents and is an evolutionary stepping-stone toward increasingly complex social systems. Anuran amphibians (frogs and toads) are a classic model of acoustic communication and the vocal repertoires of many species have been characterized in the contexts of advertisement, courtship, and aggression, yet quantitative descriptions of calls elicited in the context of parental care are lacking. The biparental poison frog, Ranitomeya imitator, exhibits a remarkable parenting behavior in which females, cued by the calls of their male partners, feed tadpoles unfertilized eggs. Here, we characterized and compared calls across three social contexts, for the first time including a parental care context. We found that egg-feeding calls share some properties with both advertisement and courtship calls but also had unique properties. Multivariate analysis revealed high classification success for advertisement and courtship calls but misclassified nearly half of egg feeding calls as either advertisement or courtship calls. Egg feeding and courtship calls both contained less identity information than advertisement calls, as expected for signals used in close-range communication where uncertainty about identity is low and additional signal modalities may be used. Taken together, egg-feeding calls likely borrowed and recombined elements of both ancestral call types to solicit a novel, context-dependent parenting response.

Syntax-like Structures in Maternal Contact Calls of Chestnut-Crowned Babblers (Pomatostomus ruficeps)

The combination of meaning-bearing units (e.g., words) into higher-order structures (e.g., compound words and phrases) is integral to human language. Despite this central role of syntax in language, little is known about its evolutionary progression. Comparative data using animal communication systems offer potential insights, but only a handful of species have been identified to combine meaningful calls together into larger signals. We investigated a candidate for syntax-like structure in the highly social chestnut-crowned babbler (Pomatostomus ruficeps). Using a combination of behavioral observations, acoustic analyses, and playback experiments, we test whether the form and function of maternal contact calls is modified by combining the core "piping" elements of such calls with at least one other call element or call. Results from the acoustic analyses (236 analysed calls from 10 individuals) suggested that piping call elements can be flexibly initiated with either "peow" elements from middle-distance contact calls or adult "begging" calls to form "peow-pipe" and "beg-pipe" calls. Behavioral responses to playbacks (20 trials to 7 groups) of natural peow-pipe and beg-pipe calls were comparable to those of artificially generated versions of each call using peow elements and begging calls from other contexts. Furthermore, responses to playbacks (34 trials to 7 groups) of the three forms of maternal contact calls (piping alone, peow-pipe, beg-pipe) differed. Together these data suggest that meaning encoded in piping calls is modified by combining such calls with begging calls or peow elements used in other contexts and so provide rare empirical evidence for syntactic-like structuring in a nonhuman animal.

Coevolution of social and communicative complexity in lemurs

The endemic lemurs of Madagascar (Lemuriformes: Primates) exhibit great social and communicative diversity. Given their independent evolutionary history, lemurs provide an excellent opportunity to identify fundamental principles in the coevolution of social and communicative traits. We conducted comparative phylogenetic analyses to examine patterns of interspecific variation among measures of social complexity and repertoire sizes in the vocal, olfactory and visual modality, while controlling for environmental factors such as habitat and number of sympatric species. We also examined potential trade-offs in signal evolution as well as coevolution between body mass or brain size and communicative complexity. Repertoire sizes in the vocal, olfactory and visual modality correlated positively with group size, but not with environmental factors. Evolutionary changes in social complexity presumably antedated corresponding changes in communicative complexity. There was no trade-off in the evolution of signals in different modalities and neither body mass nor brain size correlated with any repertoire size. Hence, communicative complexity coevolved with social complexity across different modalities, possibly to service social relationships flexibly and effectively in pair- and group-living species. Our analyses shed light on the requirements and adaptive possibilities in the coevolution of core elements of social organization and social structure in a basal primate lineage. This article is part of the theme issue 'Cognition, communication and social bonds in primates'.

Chimpanzees produce diverse vocal sequences with ordered and recombinatorial properties

The origins of human language remains a major question in evolutionary science. Unique to human language is the capacity to flexibly recombine a limited sound set into words and hierarchical sequences, generating endlessly new sentences. In contrast, sequence production of other animals appears limited, stunting meaning generation potential. However, studies have rarely quantified flexibility and structure of vocal sequence production across the whole repertoire. Here, we used such an approach to examine the structure of vocal sequences in chimpanzees, known to combine calls used singly into longer sequences. Focusing on the structure of vocal sequences, we analysed 4826 recordings of 46 wild adult chimpanzees from Taï National Park. Chimpanzees produced 390 unique vocal sequences. Most vocal units emitted singly were also emitted in two-unit sequences (bigrams), which in turn were embedded into three-unit sequences (trigrams). Bigrams showed positional and transitional regularities within trigrams with certain bigrams predictably occurring in either head or tail positions in trigrams, and predictably co-occurring with specific other units. From a purely structural perspective, the capacity to organize single units into structured sequences offers a versatile system potentially suitable for expansive meaning generation. Further research must show to what extent these structural sequences signal predictable meanings.

Body size and sexual selection shaped the evolution of parrot calls

Morphology, habitat and various selective pressures (e.g., social and sexual selection) can influence the evolution of acoustic signals, but the relative importance of their effects is not well understood. The order Psittaciformes (parrots, sensu lato) is a large clade of very vocal and often gregarious species for which large-scale comparative studies of vocalizations are lacking. We measured acoustic traits (duration, sound frequency, frequency bandwidth and sound entropy) of the predominant call type for >200 parrot species to test: (1) for associations with body size; (2) the acoustic adaptation hypothesis (predicting differences between forest and open-habitat species); (3) the social complexity hypothesis (predicting more complex calls in gregarious species); and (4) influences of sexual selection (predicting correlated evolution with colour ornamentation). Larger species had on average longer calls, lower sound frequency and wider frequency bandwidth. These associations with body size are all predicted by physical principles of sound production. We found no evidence for the acoustic adaptation and social complexity hypotheses, but perhaps social complexity is associated with vocal traits not studied here, such as call repertoire sizes. More sexually dichromatic species had on average simpler calls (shorter, with lower entropy and narrower frequency bandwidth) indicating an influence of sexual selection, namely an evolutionary negative correlation between colour ornamentation and elaborate acoustic signals, as predicted by the transference hypothesis. Our study is the first large-scale attempt at understanding acoustic diversity across the Psittaciformes, and indicates that body size and sexual selection influenced the evolution of species differences in vocal signals.