Automated classification of mouse pup isolation syllables: from cluster analysis to an Excel-based "mouse pup syllable classification calculator"

Acoustic complexity of pup isolation calls in Mongolian hamsters: 3-frequency phenomena and chaos

Studying pup isolation calls of wild rodents provides background for developing new early-life animal models for biomedical research and drug testing. This study discovered a highly complex acoustic phenotype of pup isolation calls in 4-5-day-old Mongolian hamsters Allocricetulus curtatus. We analyzed the acoustic structure of 5,010 isolation calls emitted in the broad range of frequencies (sonic, below 20 kHz, and ultrasonic, from 20 to 128 kHz) by 23 pups during 2-min isolation test trials, 1 trial per pup. In addition, we measured 5 body size parameters and the body weight of each pup. The calls could contain up to 3 independent fundamental frequencies in their spectra, the low (f0), the medium (g0), and the high (h0), or purely consisted of chaos in which the fundamental frequency could not be tracked. By presence/absence of the 3 fundamental frequencies or their combinations and chaos, we classified calls into 6 distinctive categories (low-frequency [LF]-f0, LF-chaos, high-frequency [HF]-g0, HF-h0, HF-g0 + h0, and HF-chaos) and estimated the relative abundance of calls in each category. Between categories, we compared acoustic parameters and estimated their relationship with pup body size index. We discuss the results of this study with data on the acoustics of pup isolation calls reported for other species of rodents. We conclude that such high complexity of Mongolian hamster pup isolation calls is unusual for rodents. Decreased acoustic complexity serves as a good indicator of autism spectrum disorders in knockout mouse models, which makes knockout hamster models prospective new wild animal model of neurodevelopmental disorders.

Ultrasonic vocalization of pup and adult fat-tailed gerbils (Pachyuromys duprasi)

Ultrasonic vocalizations (USVs) of laboratory rodents indicate animal emotional arousal and may serve as models of human disorders. We analysed spectrographically USV calls of pup and adult fat-tailed gerbils Pachyuromys duprasi during 420-s tests, including isolation, touch and handling. Based on combination of six different USV syllable contour shapes and six different note compositions, we classified 782 USV syllables of 24 pups aged 5-10 days to 18 types and 232 syllables of 7 adults to 24 types. Pups and adults shared 16 of these 26 USV types. Percentages of USV syllables with certain contour shapes differed between pups and adults. The contour shape and note composition significantly affected most acoustic variables of USV syllables in either pups or adults. The 1-note USV syllables were most common in either pups or adults. Pup USV syllables were overall longer and higher-frequency than adult ones, reminiscent of the USV ontogenetic pathway of bats and distinctive to rats and mice. We discuss that the USV syllable types of fat-tailed gerbils were generally similar in contour shapes and note compositions with USV syllable types of mice and rats, what means that software developed for automated classifying of mice ultrasound might be easily adapted or re-tuned to gerbil USV calls. However, using fat-tailed gerbils as model for biomedical research including control of USV vocalization is only possible since 6th day of pup life, because of the delayed emergence of USV calls in ontogeny of this species.

MUPET-Mouse Ultrasonic Profile ExTraction: A Signal Processing Tool for Rapid and Unsupervised Analysis of Ultrasonic Vocalizations

Vocalizations play a significant role in social communication across species. Analyses in rodents have used a limited number of spectro-temporal measures to compare ultrasonic vocalizations (USVs), which limits the ability to address repertoire complexity in the context of behavioral states. Using an automated and unsupervised signal processing approach, we report the development of MUPET (Mouse Ultrasonic Profile ExTraction) software, an open-access MATLAB tool that provides data-driven, high-throughput analyses of USVs. MUPET measures, learns, and compares syllable types and provides an automated time stamp of syllable events. Using USV data from a large mouse genetic reference panel and open-source datasets produced in different social contexts, MUPET analyzes the fine details of syllable production and repertoire use. MUPET thus serves as a new tool for USV repertoire analyses, with the capability to be adapted for use with other species.

Eliciting and Analyzing Male Mouse Ultrasonic Vocalization (USV) Songs

Mice produce ultrasonic vocalizations (USVs) in a variety of social contexts throughout development and adulthood. These USVs are used for mother-pup retrieval1, juvenile interactions2, opposite and same sex interactions345, and territorial interactions6. For decades, the USVs have been used by investigators as proxies to study neuropsychiatric and developmental or behavioral disorders789, and more recently to understand mechanisms and evolution of vocal communication among vertebrates10. Within the sexual interactions, adult male mice produce USV songs, which have some features similar to courtship songs of songbirds11. The use of such multisyllabic repertoires can increase potential flexibility and information they carry, as they can be varied in how elements are organized and recombined, namely syntax. In this protocol a reliable method to elicit USV songs from male mice in various social contexts, such as exposure to fresh female urine, anesthetized animals, and estrus females is described. This includes conditions to induce a large amount of syllables from the mice. We reduce recording of ambient noises with inexpensive sound chambers, and present a quantification method to automatically detect, classify and analyze the USVs. The latter includes evaluation of call-rate, vocal repertoire, acoustic parameters, and syntax. Various approaches and insight on using playbacks to study an animal's preference for specific song types are described. These methods were used to describe acoustic and syntax changes across different contexts in male mice, and song preferences in female mice.

Prenatal stress changes courtship vocalizations and bone mineral density in mice

Stress during the prenatal period has various effects on social and sexual behavior in both human and animal offspring. The present study examines the effects of chronic restraint stress in the second vs third trimester in pregnancy and glucocorticoid receptor (GR) heterozygous mutation on C57BL/6N male offspring's vocal courtship behavior in adulthood by applying a novel analyzing method. Finally, corticosterone and testosterone levels as well as bone mineral density were measured. Prenatal stress in the third, but not in the second trimester caused a significant qualitative change in males' courtship vocalizations, independent of their GR genotype. Bone mineral density was decreased also by prenatal stress exclusively in the third trimester in GR mutant and wildtype mice and - in contrast to corticosterone and testosterone - highly correlated with courtship vocalizations. In Gr^+/- males corticosterone serum levels were significantly increased in animals that had experienced prenatal stress in the third trimester. Testosterone serum levels were overall increased in Gr^+/- males in comparison to wildtypes as a tendency - whereas prenatal stress had no influence. Prenatal stress alters adult males' courtship vocalizations exclusively when applied in the third trimester, with closely related changes in bone mineral density. Bone mineral density seems to reflect best the complex neuroendocrine mechanisms underlying the production of courtship vocalizations. Besides, we demonstrated for the first time elevated basal corticosterone levels in Gr^+/- males after prenatal stress which suggests that the Gr^+/- mouse model of depression might also serve as a model of prenatal stress in male offspring.

Discrimination of frequency modulated sweeps by mice

Mice often produce ultrasonic vocalizations (USVs) that sweep upwards in frequency from around 60 to around 80 kHz and downwards in frequency from 80 to 60 kHz. Whether or not these USVs are used for communication purposes is still unknown. Here, mice were trained and tested using operant conditioning procedures and positive reinforcement to discriminate between synthetic upsweeps and downsweeps. The stimuli varied in bandwidth, duration, and direction of sweep. The mice performed significantly worse when discriminating between background and test stimuli when the stimuli all occupied the same bandwidths. Further, the mice's discrimination performance became much worse for stimuli that had durations similar to those natural vocalizations of the mice. Sweeps composed of different frequency ranges and longer durations had improved discrimination. These results collected using artificial stimuli created to mimic natural USVs indicate that the bandwidth of the vocalizations may be much more important for communication than the frequency contours of the vocalizations.

The effects of aging and sex on detection of ultrasonic vocalizations by adult CBA/CaJ mice (Mus musculus)

Mice are frequently used as animal models for human hearing research, yet their auditory capabilities have not been fully explored. Previous studies have established auditory threshold sensitivities for pure tone stimuli in CBA/CaJ mice using ABR and behavioral methodologies. Little is known about how they perceive their own ultrasonic vocalizations (USVs), and nothing is known about how aging influences this perception. The aim of the present study was to establish auditory threshold sensitivity for several USV types, as well as to track these thresholds across the mouse's lifespan. In order to determine how well mice detect these complex communication stimuli, several CBA/CaJ mice were trained and tested at various ages on a detection task using operant conditioning procedures. Results showed that mice were able to detect USVs into old age. Not surprisingly, thresholds differed for the different USV types. Male mice suffered greater hearing loss than females for all calls but not for 42 kHz tones. In conclusion, the results highlight the importance of studying complex signals across the lifespan.

A Mutation Associated with Stuttering Alters Mouse Pup Ultrasonic Vocalizations

A promising approach to understanding the mechanistic basis of speech is to study disorders that affect speech without compromising other cognitive or motor functions. Stuttering, also known as stammering, has been linked to mutations in the lysosomal enzyme-targeting pathway, but how this remarkably specific speech deficit arises from mutations in a family of general "cellular housekeeping" genes is unknown. To address this question, we asked whether a missense mutation associated with human stuttering causes vocal or other abnormalities in mice. We compared vocalizations from mice engineered to carry a mutation in the Gnptab (N-acetylglucosamine-1-phosphotransferase subunits alpha/beta) gene with wild-type littermates. We found significant differences in the vocalizations of pups with the human Gnptab stuttering mutation compared to littermate controls. Specifically, we found that mice with the mutation emitted fewer vocalizations per unit time and had longer pauses between vocalizations and that the entropy of the temporal sequence was significantly reduced. Furthermore, Gnptab missense mice were similar to wild-type mice on an extensive battery of non-vocal behaviors. We then used the same language-agnostic metrics for auditory signal analysis of human speech. We analyzed speech from people who stutter with mutations in this pathway and compared it to control speech and found abnormalities similar to those found in the mouse vocalizations. These data show that mutations in the lysosomal enzyme-targeting pathway produce highly specific effects in mouse pup vocalizations and establish the mouse as an attractive model for studying this disorder.

Knockout of Foxp2 disrupts vocal development in mice

The FOXP2 gene is important for the development of proper speech motor control in humans. However, the role of the gene in general vocal behavior in other mammals, including mice, is unclear. Here, we track the vocal development of Foxp2 heterozygous knockout (Foxp2+/−) mice and their wildtype (WT) littermates from juvenile to adult ages, and observe severe abnormalities in the courtship song of Foxp2+/− mice. In comparison to their WT littermates, Foxp2+/− mice vocalized less, produced shorter syllable sequences, and possessed an abnormal syllable inventory. In addition, Foxp2+/− song also exhibited irregular rhythmic structure, and its development did not follow the consistent trajectories observed in WT vocalizations. These results demonstrate that the Foxp2 gene is critical for normal vocal behavior in juvenile and adult mice, and that Foxp2 mutant mice may provide a tractable model system for the study of the gene’s role in general vocal motor control.

VoICE: A semi-automated pipeline for standardizing vocal analysis across models

The study of vocal communication in animal models provides key insight to the neurogenetic basis for speech and communication disorders. Current methods for vocal analysis suffer from a lack of standardization, creating ambiguity in cross-laboratory and cross-species comparisons. Here, we present VoICE (Vocal Inventory Clustering Engine), an approach to grouping vocal elements by creating a high dimensionality dataset through scoring spectral similarity between all vocalizations within a recording session. This dataset is then subjected to hierarchical clustering, generating a dendrogram that is pruned into meaningful vocalization “types” by an automated algorithm. When applied to birdsong, a key model for vocal learning, VoICE captures the known deterioration in acoustic properties that follows deafening, including altered sequencing. In a mammalian neurodevelopmental model, we uncover a reduced vocal repertoire of mice lacking the autism susceptibility gene, Cntnap2. VoICE will be useful to the scientific community as it can standardize vocalization analyses across species and laboratories.

Discrimination of partial from whole ultrasonic vocalizations using a go/no-go task in mice

Mice are a commonly used model in hearing research, yet little is known about how they perceive conspecific ultrasonic vocalizations (USVs). Humans and birds can distinguish partial versions of a communication signal, and discrimination is superior when the beginning of the signal is present compared to the end of the signal. Since these effects occur in both humans and birds, it was hypothesized that mice would display similar facilitative effects with the initial portions of their USVs. Laboratory mice were tested on a discrimination task using operant conditioning procedures. The mice were required to discriminate incomplete versions of a USV target from a repeating background containing the whole USV. The results showed that the mice had difficulty discriminating incomplete USVs from whole USVs, especially when the beginning of the USVs were presented. This finding suggests that the mice perceive the initial portions of a USV as more similar to the whole USV than the latter parts of the USV, similar to results from humans and birds.

Automatic classification of a taxon-rich community recorded in the wild

There is a rich literature on automatic species identification of a specific target taxon as regards various vocalizing animals. Research usually is restricted to specific species--in most cases a single one. It is only very recently that the number of monitored species has started to increase for certain habitats involving birds. Automatic acoustic monitoring has not yet been proven to be generic enough to scale to other taxa and habitats than the ones described in the original research. Although attracting much attention, the acoustic monitoring procedure is neither well established yet nor universally adopted as a biodiversity monitoring tool. Recently, the multi-instance multi-label framework on bird vocalizations has been introduced to face the obstacle of simultaneously vocalizing birds of different species. We build on this framework to integrate novel, image-based heterogeneous features designed to capture different aspects of the spectrum. We applied our approach to a taxon-rich habitat that included 78 birds, 8 insect species and 1 amphibian. This dataset constituted the Multi-label Bird Species Classification Challenge-NIPS 2013 where the proposed approach achieved an average accuracy of 91.25% on unseen data.

Discrimination of ultrasonic vocalizations by CBA/CaJ mice (Mus musculus) is related to spectrotemporal dissimilarity of vocalizations

The function of ultrasonic vocalizations (USVs) produced by mice (Mus musculus) is a topic of broad interest to many researchers. These USVs differ widely in spectrotemporal characteristics, suggesting different categories of vocalizations, although this has never been behaviorally demonstrated. Although electrophysiological studies indicate that neurons can discriminate among vocalizations at the level of the auditory midbrain, perceptual acuity for vocalizations has yet to be determined. Here, we trained CBA/CaJ mice using operant conditioning to discriminate between different vocalizations and between a spectrotemporally modified vocalization and its original version. Mice were able to discriminate between vocalization types and between manipulated vocalizations, with performance negatively correlating with spectrotemporal similarity. That is, discrimination performance was higher for dissimilar vocalizations and much lower for similar vocalizations. The behavioral data match previous neurophysiological results in the inferior colliculus (IC), using the same stimuli. These findings suggest that the different vocalizations could carry different meanings for the mice. Furthermore, the finding that behavioral discrimination matched neural discrimination in the IC suggests that the IC plays an important role in the perceptual discrimination of vocalizations.

Encoding of situations in the vocal repertoire of piglets (Sus scrofa): a comparison of discrete and graded classifications

Two important questions in bioacoustics are whether vocal repertoires of animals are graded or discrete and how the vocal expressions are linked to the context of emission. Here we address these questions in an ungulate species. The vocal repertoire of young domestic pigs, Sus scrofa, was quantitatively described based on 1513 calls recorded in 11 situations. We described the acoustic quality of calls with 8 acoustic parameters. Based on these parameters, the k-means clustering method showed a possibility to distinguish either two or five clusters although the call types are rather blurred than strictly discrete. The division of the vocal repertoire of piglets into two call types has previously been used in many experimental studies into pig acoustic communication and the five call types correspond well to previously published partial repertoires in specific situations. Clear links exist between the type of situation, its putative valence, and the vocal expression in that situation. These links can be described adequately both with a set of quantitative acoustic variables and through categorisation into call types. The information about the situation of emission of the calls is encoded through five call types almost as accurately as through the full quantitative description.