Functional clustering of mouse ultrasonic vocalization data

Rodent ultrasonic vocal interaction resolved with millimeter precision using hybrid beamforming

Ultrasonic vocalizations (USVs) fulfill an important role in communication and navigation in many species. Because of their social and affective significance, rodent USVs are increasingly used as a behavioral measure in neurodevelopmental and neurolinguistic research. Reliably attributing USVs to their emitter during close interactions has emerged as a difficult, key challenge. If addressed, all subsequent analyses gain substantial confidence. We present a hybrid ultrasonic tracking system, Hybrid Vocalization Localizer (HyVL), that synergistically integrates a high-resolution acoustic camera with high-quality ultrasonic microphones. HyVL is the first to achieve millimeter precision (~3.4-4.8 mm, 91% assigned) in localizing USVs, ~3× better than other systems, approaching the physical limits (mouse snout ~10 mm). We analyze mouse courtship interactions and demonstrate that males and females vocalize in starkly different relative spatial positions, and that the fraction of female vocalizations has likely been overestimated previously due to imprecise localization. Further, we find that when two male mice interact with one female, one of the males takes a dominant role in the interaction both in terms of the vocalization rate and the location relative to the female. HyVL substantially improves the precision with which social communication between rodents can be studied. It is also affordable, open-source, easy to set up, can be integrated with existing setups, and reduces the required number of experiments and animals.

Capturing the songs of mice with an improved detection and classification method for ultrasonic vocalizations (BootSnap)

House mice communicate through ultrasonic vocalizations (USVs), which are above the range of human hearing (>20 kHz), and several automated methods have been developed for USV detection and classification. Here we evaluate their advantages and disadvantages in a full, systematic comparison, while also presenting a new approach. This study aims to 1) determine the most efficient USV detection tool among the existing methods, and 2) develop a classification model that is more generalizable than existing methods. In both cases, we aim to minimize the user intervention required for processing new data. We compared the performance of four detection methods in an out-of-the-box approach, pretrained DeepSqueak detector, MUPET, USVSEG, and the Automatic Mouse Ultrasound Detector (A-MUD). We also compared these methods to human visual or ‘manual’ classification (ground truth) after assessing its reliability. A-MUD and USVSEG outperformed the other methods in terms of true positive rates using default and adjusted settings, respectively, and A-MUD outperformed USVSEG when false detection rates were also considered. For automating the classification of USVs, we developed BootSnap for supervised classification, which combines bootstrapping on Gammatone Spectrograms and Convolutional Neural Networks algorithms with Snapshot ensemble learning. It successfully classified calls into 12 types, including a new class of false positives that is useful for detection refinement. BootSnap outperformed the pretrained and retrained state-of-the-art tool, and thus it is more generalizable. BootSnap is freely available for scientific use.

House mice and many other species use ultrasonic vocalizations to communicate in various contexts including social and sexual interactions. These vocalizations are increasingly investigated in research on animal communication and as a phenotype for studying the genetic basis of autism and speech disorders. Because manual methods for analyzing vocalizations are extremely time consuming, automatic tools for detection and classification are needed. We evaluated the performance of the available tools for analyzing ultrasonic vocalizations, and we compared detection tools for the first time to manual methods (“ground truth”) using recordings from wild-derived and laboratory mice. For the first time, class-wise inter-observer reliability of manual labels used for ground truth are analyzed and reported. Moreover, we developed a new classification method based on ensemble deep learning that provides more generalizability than the current state-of-the-art tool (both pretrained and retrained). Our new classification method is free for scientific use.

Vocal and physical phenotypes of calsyntenin2 knockout mouse pups model early-life symptoms of the autism spectrum disorder

This study discovered a novel acoustic phenotype in Calsyntenin2 deficient knockout (Clstn2-KO) pups in the neurodevelopment period of 5-9 postnatal days (PND 5-9). The narrowband ultrasonic calls (nUSVs) were less complex (mostly one-note, shorter in duration and higher in peak frequency) in Clsnt2-KO than in wild-type (WT) C57BL/6 J pups. The wideband ultrasonic calls (wUSVs) were produced substantially more often by Clstn2-KO than WT pups. The clicks were longer in duration and higher in peak frequency and power quartiles in Clstn2-KO pups. The elevated discomfort due to additional two-minute maternal separation coupled with experimenter's touch, resulted in significantly higher call rates of both nUSVs and clicks in pups of both genotypes and sexes compared to the previous two-minute maternal separation, whereas the call rate of wUSVs was not affected. In Clstn2-KO pups, the prevalence of emission of wUSVs retained at both sex and both degrees of discomfort, thus providing a reliable quantitative acoustic indicator for this genetic line. Besides the acoustic differences, we also detected the increased head-to-body ratio in Clstn2-KO pups. Altogether, this study demonstrated that lack of such synaptic adhesion protein as calsyntenin2 affects neurodevelopment of vocalization in a mouse as a model organism.

Daurian pika (Ochotona dauurica) alarm calls: individual acoustic variation in a lagomorph with audible through ultrasonic vocalizations

Colonial lagomorphs warn conspecifics of potential danger with alarm calls encoding information about attributes of presumptive predators as well as the caller. In this study, we show that alarm calls of Daurian pikas, Ochotona dauurica (Pallas, 1776), encode information about caller identity. We recorded the alarm calls produced toward a surrogate predator (researcher), slowly moving (0.5–1 km/h) between densely distributed colonies. The alarm calls of most (32 of the 35) callers started in the ultrasonic range at 22.41 kHz on average and rapidly decreased to 3.88 kHz on average at call end. Call duration was very short (0.057 s on average). The accuracy of classifying alarm calls to correct callers with discriminant function analysis (DFA) was 93.71% for the manually measured set of 12 acoustic variables and 95.43% for the semiautomatically measured set of 12 acoustic variables; in both cases exceeding the level of chance (17.28% or 17.33%, respectively). Nonlinear vocal phenomena (biphonations) only were detected in one individual. We discuss the relationship between vocal traits, individuality, vocal production mechanisms, and functions, of pika alarm calls. We propose a potential divergence of alarm calls in Asian pikas to high-frequency whistles (> 20 kHz in Daurian pikas) and in American pikas to low-frequency emissions (0.4–1.3 kHz in Ochotona princeps) during the evolutionary radiation of pikas at the center of the origin of lagomorphs in East Asia and their subsequent geographic dispersal.

Rapid development of mature vocal patterns of ultrasonic calls in a fast-growing rodent, the yellow steppe lemming (Eolagurus luteus)

Ultrasonic vocalizations (USV) of laboratory rodents may serve as age-dependent indicators of emotional arousal and anxiety. Fast-growing Arvicolinae rodent species might be advantageous wild-type animal models for behavioural and medical research related to USV ontogeny. For the yellow steppe lemming Eolagurus luteus, only audible calls of adults were previously described. This study provides categorization and spectrographic analyses of 1176 USV calls emitted by 120 individual yellow steppe lemmings at 12 age classes, from birth to breeding adults over 90 days (d) of age, 10 individuals per age class, up to 10 USV calls per individual. The USV calls emerged since 1st day of pup life and occurred at all 12 age classes and in both sexes. The unified 2-min isolation procedure on an unfamiliar territory was equally applicable for inducing USV calls at all age classes. Rapid physical growth (1 g body weight gain per day from birth to 40 d of age) and the early (9-12 d) eyes opening correlated with the early (9-12 d) emergence of mature vocal patterns of USV calls. The mature vocal patterns included a prominent shift in percentages of chevron and upward contours of fundamental frequency (f0) and the changes in the acoustic variables of USV calls. Call duration was the longest at 1-4 d, significantly shorter at 9-12 d and did not between 9-12-d and older age classes. The maximum fundamental frequency (f0max) decreased with increase of age class, from about 50 kHz in neonates to about 40 kHz in adults. These ontogenetic pathways of USV duration and f0max (towards shorter and lower-frequency USV calls) were reminiscent of those in laboratory mice Mus musculus.

Longitudinal analysis of ultrasonic vocalizations in mice from infancy to adolescence: Insights into the vocal repertoire of three wild-type strains in two different social contexts

Ultrasonic vocalizations (USV) are emitted by mice under certain developmental, social and behavioral conditions. The analysis of USV can be used as a reliable measure of the general affective state, for testing the efficacy of pharmacological compounds and for investigating communication in mutant mice with predicted social or communication deficits. Social and communication studies in mice have focused mainly on the investigation of USV emitted by neonatal pups after separation from the dam and during social interaction between adult males and females. Longitudinal USV analysis among the different developmental states remained uninvestigated. In our study, we first recorded USV from three inbred mouse strains C57BL/6N, DBA/2 and FVB/N during the neonatal stages after separation from the littermates and then during a reunion with one littermate. Our results revealed significant strain-specific differences in the numbers and categories of USV calls. In addition, the USV profiles seemed to be sensitive to small developmental progress during infancy. By following these mice to the adolescent stage and measuring USV in the three-chamber social test, we found that USV profiles still showed significant differences between these strains in the different trials of the test. To study the effects of social context on USV characteristics, we measured USV emitted by another cohort of adolescent mice during the direct social interaction test. To this end, this study provides a strategy for evaluating novel mouse mutants in behavioral questions relevant to disorders with deficits in communication and sociability and emphasizes the important contribution of genetics and experimental contexts on the behavioral outcome.

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.