Acoustic sequences in non‐human animals: a tutorial review and prospectus

Animal acoustic communication often takes the form of complex sequences, made up of multiple distinct acoustic units. Apart from the well‐known example of birdsong, other animals such as insects, amphibians, and mammals (including bats, rodents, primates, and cetaceans) also generate complex acoustic sequences. Occasionally, such as with birdsong, the adaptive role of these sequences seems clear (e.g. mate attraction and territorial defence). More often however, researchers have only begun to characterise – let alone understand – the significance and meaning of acoustic sequences. Hypotheses abound, but there is little agreement as to how sequences should be defined and analysed. Our review aims to outline suitable methods for testing these hypotheses, and to describe the major limitations to our current and near‐future knowledge on questions of acoustic sequences. This review and prospectus is the result of a collaborative effort between 43 scientists from the fields of animal behaviour, ecology and evolution, signal processing, machine learning, quantitative linguistics, and information theory, who gathered for a 2013 workshop entitled, ‘Analysing vocal sequences in animals’. Our goal is to present not just a review of the state of the art, but to propose a methodological framework that summarises what we suggest are the best practices for research in this field, across taxa and across disciplines. We also provide a tutorial‐style introduction to some of the most promising algorithmic approaches for analysing sequences. We divide our review into three sections: identifying the distinct units of an acoustic sequence, describing the different ways that information can be contained within a sequence, and analysing the structure of that sequence. Each of these sections is further subdivided to address the key questions and approaches in that area. We propose a uniform, systematic, and comprehensive approach to studying sequences, with the goal of clarifying research terms used in different fields, and facilitating collaboration and comparative studies. Allowing greater interdisciplinary collaboration will facilitate the investigation of many important questions in the evolution of communication and sociality.     

Invariant chain modulates HLA class II protein recycling and peptide presentation in nonprofessional antigen presenting cells

The expression of MHC class II molecules and the invariant chain (Ii) chaperone, is coordinately regulated in professional antigen presenting cells (APC). Ii facilitates class II subunit folding as well as transit and retention in mature endosomal compartments rich in antigenic peptides in these APC. Yet, in nonprofessional APC such as tumors, fibroblasts and endocrine tissues, the expression of class II subunits and Ii may be uncoupled. Studies of nonprofessional APC indicate class II molecules access antigenic peptides by distinct, but poorly defined pathways in the absence of Ii. Here, investigations demonstrate that nonprofessional APC such as human fibroblasts lacking Ii internalize antigenic peptides prior to the binding of these ligands to recycling class II molecules. By contrast, fibroblast lines expressing Ii favor exogenous peptides binding directly to cell surface class II molecules without a need for ligand internalization. Endocytosis of class II molecules was enhanced in cells lacking Ii compared with Ii-expressing APC. These results suggest enhanced reliance on the endocytic recycling pathway for functional class II presentation in nonprofessional APC.     

GEOGRAPHIC VARIATION IN RATES OF VOCAL PRODUCTION OF FREE-RANGING BOTTLENOSE DOLPHINS

Echolocation and whistle production, group sizes, and activities of free-ranging bottlenose dolphins were compared across four regions (Wilmington, NC Intracoastal Waterway [ICW]; Wilmington coastline; Southport, NC coastline; and Sarasota, FL inshore waters). Number of whistles and echolo-cation bouts differed significantly across sites. Dolphins whistled significantly more in Southport than in the other sites, independent of group size. Unlike at the other sites, dolphin vocalizations in Southport did not vary significantly across activities; this difference may be due to the fact that Southport animals were often found behind shrimp-trawling vessels, which may affect their behavior. Resident Sarasota dolphins vocalized significantly less than dolphins at the NC sites. At most sites, echolocation production per dolphin decreased as group size increased, supporting the idea that echolocation information is shared. In the ICW and Sarasota, echolocation production per dolphin was highest while feeding, indicating that echolocation is used in foraging. At all sites but Southport, whistle production per dolphin was highest while socializing, indicating that whistles are used in communication. Overall, these data show that dolphins have different vocal and activity patterns at different sites; thus, caution should be used when extrapolating results from one study site to another.     

Individual recognition in wild bottlenose dolphins: a field test using playback experiments

We conducted playback experiments with wild bottlenose dolphins, Tursiops truncatus, to determine whether there is sufficient information in their individually distinctive signature whistles for individual recognition. We conducted experiments with members of a resident community of dolphins in waters near Sarasota, Florida, during temporary capture-release projects. We used a paired playback design, wherein the same two whistle sequences were predicted to evoke opposite responses from two different target animals. This design controlled for any unknown cues that may have been present in the playback stimuli. We predicted that mothers would respond more strongly to the whistles of their own independent offspring than to the whistles of a familiar, similar-aged nonoffspring. Similarly, we predicted that independent offspring would respond more strongly to the whistles of their own mother than to the whistles of a familiar, similar-aged female. Target animals were significantly (P<0.02) more likely to respond to the predicted stimuli, with responses measured by the number of head turns towards the playback speaker. In bottlenose dolphin societies, stable, individual-specific relationships are intermixed with fluid patterns of association between individuals. In primate species that live in similar 'fission-fusion' type societies, individual recognition is commonplace. Thus, when taken in the context of what is known about the social structure and behaviour of bottlenose dolphins, these playback experiments suggest that signature whistles are used for individual recognition. Copyright 1999 The Association for the Study of Animal Behaviour.     

Communication in bottlenose dolphins: 50 years of signature whistle research

Bottlenose dolphins (Tursiops truncatus) produce individually distinctive signature whistles that broadcast the identity of the caller. Unlike voice cues that affect all calls of an animal, signature whistles are distinct whistle types carrying identity information in their frequency modulation pattern. Signature whistle development is influenced by vocal production learning. Animals use a whistle from their environment as a model, but modify it, and thus invent a novel signal. Dolphins also copy signature whistles of others, effectively addressing the whistle owner. This copying occurs at low rates and the resulting copies are recognizable as such by parameter variations in the copy. Captive dolphins can learn to associate novel whistles with objects and use these whistles to report on the presence or absence of the object. If applied to signature whistles, this ability would make the signature whistle a rare example of a learned referential signal in animals. Here, we review the history of signature whistle research, covering definitions, acoustic features, information content, contextual use, developmental aspects, and species comparisons with mammals and birds. We show how these signals stand out amongst recognition calls in animals and how they contribute to our understanding of complexity in animal communication.     

Identifying signature whistles from recordings of groups of unrestrained bottlenose dolphins (Tursiops truncatus)

Bottlenose dolphins (Tursiops truncatus) have individually distinctive signature whistles. Each individual dolphin develops its own unique frequency modulation pattern and uses it to broadcast its identity. However, underwater sound localization is challenging, and researchers have had difficulties identifying signature whistles. The traditional method to identify them involved isolating individuals. In this context, the signature whistle is the most commonly produced whistle type of an animal. However, most studies on wild dolphins cannot isolate animals. We present a novel method, SIGnature IDentification (SIGID), that can identify signature whistles in recordings of groups of dolphins recorded via a single hydrophone. We found that signature whistles tend to be delivered in bouts with whistles of the same type occurring within 1–10 s of each other. Nonsignature whistles occur with longer or shorter interwhistle intervals, and this distinction can be used to identify signature whistles in a recording. We tested this method on recordings from wild and captive bottlenose dolphins and show thresholds needed to identify signature whistles reliably. SIGID will facilitate the study of signature whistle use in the wild, signature whistle diversity between different populations, and potentially allow signature whistles to be used in mark‐recapture studies.     

The Encoding of Individual Identity in Dolphin Signature Whistles: How Much Information Is Needed?

Bottlenose dolphins (Tursiops truncatus) produce many vocalisations, including whistles that are unique to the individual producing them. Such “signature whistles” play a role in individual recognition and maintaining group integrity. Previous work has shown that humans can successfully group the spectrographic representations of signature whistles according to the individual dolphins that produced them. However, attempts at using mathematical algorithms to perform a similar task have been less successful. A greater understanding of the encoding of identity information in signature whistles is important for assessing similarity of whistles and thus social influences on the development of these learned calls. We re-examined 400 signature whistles from 20 individual dolphins used in a previous study, and tested the performance of new mathematical algorithms. We compared the measure used in the original study (correlation matrix of evenly sampled frequency measurements) to one used in several previous studies (similarity matrix of time-warped whistles), and to a new algorithm based on the Parsons code, used in music retrieval databases. The Parsons code records the direction of frequency change at each time step, and is effective at capturing human perception of music. We analysed similarity matrices from each of these three techniques, as well as a random control, by unsupervised clustering using three separate techniques: k-means clustering, hierarchical clustering, and an adaptive resonance theory neural network. For each of the three clustering techniques, a seven-level Parsons algorithm provided better clustering than the correlation and dynamic time warping algorithms, and was closer to the near-perfect visual categorisations of human judges. Thus, the Parsons code captures much of the individual identity information present in signature whistles, and may prove useful in studies requiring quantification of whistle similarity.