Estimating vocal repertoire size is like collecting coupons: A theoretical framework with heterogeneity in signal abundance

A machine learning approach for classifying and quantifying acoustic diversity

1. Assessing diversity of discretely varying behavior is a classical ethological problem. In particular, the challenge of calculating an individuals' or species' vocal repertoire size is often an important step in ecological and behavioral studies, but a reproducible and broadly applicable method for accomplishing this task is not currently available. 2. We offer a generalizable method to automate the calculation and quantification of acoustic diversity using an unsupervised random forest framework. We tested our method using natural and synthetic datasets of known repertoire sizes that exhibit standardized variation in common acoustic features as well as in recording quality. We tested two approaches to estimate acoustic diversity using the output from unsupervised random forest analyses: (i) cluster analysis to estimate the number of discrete acoustic signals (e.g., repertoire size) and (ii) an estimation of acoustic area in acoustic feature space, as a proxy for repertoire size. 3. We find that our unsupervised analyses classify acoustic structure with high accuracy. Specifically, both approaches accurately estimate element diversity when repertoire size is small to intermediate (5-20 unique elements). However, for larger datasets (20-100 unique elements), we find that calculating the size of the area occupied in acoustic space is a more reliable proxy for estimating repertoire size. 4. We conclude that our implementation of unsupervised random forest analysis offers a generalizable tool that researchers can apply to classify acoustic structure of diverse datasets. Additionally, output from these analyses can be used to compare the distribution and diversity of signals in acoustic space, creating opportunities to quantify and compare the amount of acoustic variation among individuals, populations, or species in a standardized way. We provide R code and examples to aid researchers interested in using these techniques.

Social pressure drives "conversational rules" in great apes

In the last decade, two hypotheses, one on the evolution of animal vocal communication in general and the other on the origins of human language, have gained ground. The first hypothesis argues that the complexity of communication co-evolved with the complexity of sociality. Species forming larger groups with complex social networks have more elaborate vocal repertoires. The second hypothesis posits that the core of communication is represented not only by what can be expressed by an isolated caller, but also by the way that vocal interactions are structured, language being above all a social act. Primitive forms of conversational rules based on a vocal turn-taking principle are thought to exist in primates. To support and bring together these hypotheses, more comparative studies of socially diverse species at different levels of the primate phylogeny are needed. However, the majority of available studies focus on monkeys, primates that are distant from the human lineage. Great apes represent excellent candidates for such comparative studies because of their phylogenetic proximity to humans and their varied social lives. We propose that studying vocal turn-taking in apes could address several major gaps regarding the social relevance of vocal turn-taking and the evolutionary trajectory of this behaviour among anthropoids. Indeed, how the social structure of a species may influence the vocal interaction patterns observed among group members remains an open question. We gathered data from the literature as well as original unpublished data (where absent in the literature) on four great ape species: chimpanzees Pan troglodytes, bonobos Pan paniscus, western lowland gorillas Gorilla gorilla gorilla and Bornean orang-utans Pongo pygmaeus. We found no clear-cut relationship between classical social complexity metrics (e.g. number of group members, interaction rates) and vocal complexity parameters (e.g. repertoire size, call rates). Nevertheless, the nature of the society (i.e. group composition, diversity and valence of social bonds) and the type of vocal interaction patterns (isolated calling, call overlap, turn-taking-based vocal exchanges) do appear to be related. Isolated calling is the main vocal pattern found in the species with the smallest social networks (orang-utan), while the other species show vocal interactions that are structured according to temporal rules. A high proportion of overlapping vocalisations is found in the most competitive species (chimpanzee), while vocal turn-taking predominates in more tolerant bonobos and gorillas. Also, preferentially interacting individuals and call types used to interact are not randomly distributed. Vocal overlap ('chorusing') and vocal exchange ('conversing') appear as possible social strategies used to advertise/strengthen social bonds. Our analyses highlight that: (i) vocal turn-taking is also observed in non-human great apes, revealing universal rules for conversing that may be deeply rooted in the primate lineage; (ii) vocal interaction patterns match the species' social lifestyle; (iii) although limited to four species here, adopting a targeted comparative approach could help to identify the multiple and subtle factors underlying social and vocal complexity. We believe that vocal interaction patterns form the basis of a promising field of investigation that may ultimately improve our understanding of the socially driven evolution of communication.

The many functions of vocal learning

The capacity to learn novel vocalizations has evolved convergently in a wide range of species. Courtship songs of male birds or whales are often treated as prototypical examples, implying a sexually selected context for the evolution of this ability. However, functions of learned vocalizations in different species are far more diverse than courtship, spanning a range of socio-positive contexts from individual identification, social cohesion, or advertising pair bonds, as well as agonistic contexts such as territorial defence, deceptive alarm calling or luring prey. Here, we survey the diverse usages and proposed functions of learned novel signals, to build a framework for considering the evolution of vocal learning capacities that extends beyond sexual selection. For each function that can be identified for learned signals, we provide examples of species using unlearned signals to accomplish the same goals. We use such comparisons to generate hypotheses concerning when vocal learning is adaptive, given a particular suite of socio-ecological traits. Finally, we identify areas of uncertainty where improved understanding would allow us to better test these hypotheses. Considering the broad range of potential functions of vocal learning will yield a richer appreciation of its evolution than a narrow focus on a few prototypical species. This article is part of the theme issue 'Vocal learning in animals and humans'.

Mockingbird Morphing Music: Structured Transitions in a Complex Bird Song

The song of the northern mockingbird, Mimus polyglottos, is notable for its extensive length and inclusion of numerous imitations of several common North American bird species. Because of its complexity, it is not widely studied by birdsong scientists. When they do study it, the specific imitations are often noted, and the total number of varying phrases. What is rarely noted is the systematic way the bird changes from one syllable to the next, often with a subtle transition where one sound is gradually transformed into a related sound, revealing an audible and specific compositional mode. It resembles a common strategy in human composing, which can be described as variation of a theme. In this paper, we present our initial attempts to describe the specific compositional rules behind the mockingbird song, focusing on the way the bird transitions from one syllable type to the next. We find that more often than chance, syllables before and after the transition are spectrally related, i.e., transitions are gradual, which we describe as morphing. In our paper, we categorize four common modes of morphing: timbre change, pitch change, squeeze (shortening in time), and stretch (lengthening in time). This is the first time such transition rules in any complex birdsong have been specifically articulated.

Comparative bioacoustics: a roadmap for quantifying and comparing animal sounds across diverse taxa

Animals produce a wide array of sounds with highly variable acoustic structures. It is possible to understand the causes and consequences of this variation across taxa with phylogenetic comparative analyses. Acoustic and evolutionary analyses are rapidly increasing in sophistication such that choosing appropriate acoustic and evolutionary approaches is increasingly difficult. However, the correct choice of analysis can have profound effects on output and evolutionary inferences. Here, we identify and address some of the challenges for this growing field by providing a roadmap for quantifying and comparing sound in a phylogenetic context for researchers with a broad range of scientific backgrounds. Sound, as a continuous, multidimensional trait can be particularly challenging to measure because it can be hard to identify variables that can be compared across taxa and it is also no small feat to process and analyse the resulting high-dimensional acoustic data using approaches that are appropriate for subsequent evolutionary analysis. Additionally, terminological inconsistencies and the role of learning in the development of acoustic traits need to be considered. Phylogenetic comparative analyses also have their own sets of caveats to consider. We provide a set of recommendations for delimiting acoustic signals into discrete, comparable acoustic units. We also present a three-stage workflow for extracting relevant acoustic data, including options for multivariate analyses and dimensionality reduction that is compatible with phylogenetic comparative analysis. We then summarize available phylogenetic comparative approaches and how they have been used in comparative bioacoustics, and address the limitations of comparative analyses with behavioural data. Lastly, we recommend how to apply these methods to acoustic data across a range of study systems. In this way, we provide an integrated framework to aid in quantitative analysis of cross-taxa variation in animal sounds for comparative phylogenetic analysis. In addition, we advocate the standardization of acoustic terminology across disciplines and taxa, adoption of automated methods for acoustic feature extraction, and establishment of strong data archival practices for acoustic recordings and data analyses. Combining such practices with our proposed workflow will greatly advance the reproducibility, biological interpretation, and longevity of comparative bioacoustic studies.

The coupon collector urn model with unequal probabilities in ecology and evolution

The sequential sampling of populations with unequal probabilities and with replacement in a closed population is a recurrent problem in ecology and evolution. Examples range from biodiversity sampling, epidemiology to the estimation of signal repertoire in animal communication. Many of these questions can be reformulated as urn problems, often as special cases of the coupon collector problem, most simply expressed as the number of coupons that must be collected to have a complete set. We aimed to apply the coupon collector model in a comprehensive manner to one example-hosts (balls) being searched (draws) and parasitized (ball colour change) by parasitic wasps-to evaluate the influence of differences in sampling probabilities between items on collection speed. Based on the model of a complete multinomial process over time, we define the distribution, distribution function, expectation and variance of the number of hosts parasitized after a given time, as well as the inverse problem, estimating the sampling effort. We develop the relationship between the risk distribution on the set of hosts and the speed of parasitization and propose a more elegant proof of the weak stochastic dominance among speeds of parasitization, using the concept of Schur convexity and the 'Robin Hood transfer' numerical operation. Numerical examples are provided and a conjecture about strong dominance-an ordering characteristic of random variables-is proposed. The speed at which new items are discovered is a function of the entire shape of the sampling probability distribution. The sole comparison of values of variances is not sufficient to compare speeds associated with different distributions, as generally assumed in ecological studies.

Multiple estimation methods suggest similar repertoire sizes for Gulf Coast and eastern marsh wrens with no correlation between repertoire size and migratory distance

There are many ways for signalling systems to be complex, one of which is a large signal repertoire. However, it is frequently challenging to estimate larger repertoires accurately. We present the first description of repertoire size for a subspecies of marsh wren on the Gulf Coast of North America,Cistothorus palustris thryophilus, using four repertoire estimation techniques (simple enumeration, Wildenthal curve-fitting, Davidson & Wilkinson curve-fitting, and the Coupon Collector model). We demonstrate that the repertoire estimation methods in question perform with varying degrees of accuracy under natural conditions, and propose that rather than establishing an absolute repertoire size for a given individual it may instead be necessary to use multiple techniques to establish a repertoire range. We find thatC. p. thryophilushas a song repertoire size falling well within the range of repertoires produced by other marsh wren subspecies in eastern North America, although it may be on the larger end of this range. We find no evidence supporting a correlation between migratory distance and increased repertoire size in this species, as might be predicted under a sexual selection hypothesis.