The origins of acoustic communication in vertebrates

Formant analysis of vertebrate vocalizations: achievements, pitfalls, and promises

When applied to vertebrate vocalizations, source-filter theory, initially developed for human speech, has revolutionized our understanding of animal communication, resulting in major insights into the form and function of animal sounds. However, animal calls and human nonverbal vocalizations can differ qualitatively from human speech, often having more chaotic and higher-frequency sources, making formant measurement challenging. We review the considerable achievements of the "formant revolution" in animal vocal communication research, then highlight several important methodological problems in formant analysis. We offer concrete recommendations for effectively applying source-filter theory to non-speech vocalizations and discuss promising avenues for future research in this area.Brief Formants (vocal tract resonances) play key roles in animal communication, offering researchers exciting promise but also potential pitfalls.

Nonlinear phenomena in mammalian vocal communication: an introduction and scoping review

Nonlinear phenomena (NLP) are common elements of mammalian vocalizations. Resulting from irregular sound production, they contribute to perceived harshness and are often present in calls conveying urgency or arousal. Initially dismissed as by-products of vocal production, NLP are increasingly recognized for their adaptive potential. However, NLP have never been the subject of a comprehensive review across vertebrate taxa. Here, we introduce NLP and examine developments in NLP studies in mammals. We found 220 papers published between 1962 and 2023, with publication rates increasing with time. The studies covered a wide range of taxonomic groups but were dominated by artiodactyls, carnivores, bats, rodents and primates. Tinbergen's questions offer a framework for future investigations, highlighting that while much research has been conducted on adaptive function, our understanding is still lacking in terms of ontogeny, mechanisms and evolution. The existing literature is a testimony to the importance of NLP in animal vocalizations. With the use of novel tools for analysis and playback studies, NLP research can become more cohesive and impactful, fostering better understanding among researchers. We look forward to a new age of NLP research, which we anticipate will lead to a paradigm shift in our understanding of vocal communication in mammals.This article is part of the theme issue 'Nonlinear phenomena in vertebrate vocalizations: mechanisms and communicative functions'.

Wind farm noise negatively impacts the calling behavior of three frogs in Caatinga dry forests

Acoustic signals play a fundamental role in the lives of anurans. With the increasing prevalence of wind farms in Caatinga ecosystems, our goal was to assess whether the noise generated by this energy source poses a threat to anuran communication. We analyzed acoustic parameters of the advertisement calls from 181 adult males, of the species Scinax pachycrus, Scinax x-signatus, and Physalaemus cicada. Call activity was recorded across noise gradients in 19 temporary ponds with similar vegetation structures, distributed in two wind farms. Our results revealed a significant relationship between wind turbine noise and changes in acoustic parameters of the three species, distinctly influencing their spectral and temporal parameters of the advertisement calls. Dominant frequency, frequency range of Scinax pachycrus were affected by the noise, decreasing in noisier temporary ponds, while Scinax x-signatus decreased call amplitude and call pulses. On the other hand, Physalaemus cicada showed changes only in temporal variables, with reductions in call duration and call pulses, and an increase in call rate to cope whit noise in temporary ponds. Therefore, noise pollution becomes particularly concerning for the anurans of the Caatinga, as the areas of greatest interest for wind power generation overlap with priority areas for biodiversity conservation.

Understanding speech in "noise" or free energy minimization in the soundscapes of the anthropocene

Listening to speech in the presence of irrelevant sounds is ubiquitous in the modern world, but is generally acknowledged to be both effortful and unpleasant. Here we argue that this problem arises largely in circumstances that our human auditory system has not evolved to accommodate. The soundscapes of the Anthropocene are frequently characterized by an overabundance of sound sources, the vast majority of which are functionally irrelevant to a given listener. The problem of listening to speech in such environments must be solved by an auditory system that is not optimized for this task. Building on our previous work linking attention to effortful listening and incorporating an active inference approach, we argue that the answers to these questions have implications not just for the study of human audition. They are also significant for the development and broad awareness of hearing aids and cochlear implants, as well as other auditory technologies such as earbuds, immersive auditory environments, and systems for human-machine interaction.

Gharial acoustic signaling: Novel underwater pops are temporally based, context-dependent, seasonally stable, male-specific, and individually distinctive

Gharials (Gavialis gangeticus) produce a sudden, high amplitude, pulsatile, underwater sound called a POP. In this study, gharial POPs ranged from 9 to 55 ms, and were clearly audible on land and water, at ≥500 m. POPs were only performed underwater by adult males possessing a sex-specific, cartilaginous narial excrescence, termed the ghara. We recorded 130 POP events of seven wild adult males in 115 km stretch of the Chambal River during 2017-2019, using hydrophones and aerial mics. A POP event occurs when a male produces a single or double or triple POP, each with a specific duration and timing. A POP event was incorporated into a complex, multi-modal breathing display, typically performed by each male during the breeding season. Key features of this novel gharial POP signal are documented here for the first time. These include its incorporation into a complex breathing display, its reliance on temporal rather than spectral elements, its dependence on a specific social context, its stability within an individual, and its individually distinctive patterning specific to a particular male. The breathing display consisted of sub-audible vibrations (SAV) preceding each POP, then a stereotyped exhalation-inhalation-exhalation sequence, concluding with bubbling and submergence. In our study, 96% of the variation in POP signal parameters was explained by POP signal timings (92%) and number of POPs (4%), and only 2% was related to spectral features. Each POP event was performed in a specific social setting. Two behavioral contexts were examined: ALERT and PATROL. In each context, male identities were examined using Discriminant Function Analysis (DFA). Within each context, each of the seven males exhibited distinctive POP patterns that were context-specific and denoted a male's identity and his location. POP signal features were stable for individual males, from 1 year to the next. Overall, the seven males showed POP patterns that were individually specific, with minimal overlap amongst males, yet these were remarkably diverse. The stereotypy of POP patterns, based on temporal versus frequency difference was best characterized statistically using DFA metrics, rather than Beecher's Information Statistic, MANOVA, or Discriminant Score computations. Our field observations indicated that audiences of gharial, located nearby, and/or in the distance, responded immediately to POPs by orienting in the signal direction. Extensive auditory studies of crocodylians indicate that their capacity for auditory temporal discrimination and neural processing in relation to locating a sound target is on par with that of birds. How the POP sound is produced and broadcast loudly in both water and air has received little study to date. We briefly summarize existing reports on ghara anatomy, ontogeny, and paleontology. Finally, preliminary observations made in a clear underwater zoo enclosure indicate that jaw claps performed entirely underwater produce POP sounds. Simultaneous bubble clouds emanating from the base of the ghara are suggestive of cavitation phenomena associated with loud high volume sounds such as shrimp snaps and seal/walrus claps. We discuss the likelihood that the adult male's ghara plays an essential role in the production of the non-vocal underwater POP, a sexually dimorphic acoustic signal unique to gharial.

The roles of different gene expression regulators in acoustic variation in the intermediate horseshoe bat revealed by long-read and short-read RNA sequencing data

Gene expression changes contribute greatly to phenotypic variations in nature. Studying patterns of regulators of gene expression is important to fully understand the molecular mechanism underlying phenotypic variations. In horseshoe bats, the cochleae are finely tuned to echoes of call frequency. Here, using 2 recently diverged subspecies of the intermediate horseshoe bat (Rhinolophus affinis hainanus and R. a. himalayanus) with great acoustic variations as the system, we aim to explore relative roles of different regulators of gene expression (differential gene expression, alternative splicing (AS) and long non-coding RNAs (lncRNAs)) in phenotypic variation with a combination of Illumina short-read and Nanopore long-read RNA-seq data from the cochlea. Compared to R. a. hainanus, R. a. himalayanus exhibited much more upregulated differentially expressed genes (DEGs) and multiple of them may play important roles in the maintenance and damage repair of auditory hair cells. We identified 411 differentially expressed lncRNAs and their target DEGs upregulated in R. a. himalayanus were also mainly involved in a protective mechanism for auditory hair cells. Using 3 different methods of AS analysis, we identified several candidate alternatively spliced genes (ASGs) that expressed different isoforms which may be associated with acoustic divergence of the 2 subspecies. We observed significantly less overlap than expected between DEGs and ASGs, supporting complementary roles of differential gene expression and AS in generating phenotypic variations. Overall, our study highlights the importance of a combination of short-read and long-read RNA-seq data in examining the regulation of gene expression changes responsible for phenotypic variations.

Peripheral hearing sensitivity is similar between the sexes in a benthic turtle species despite the larger body size of males

Sexually dimorphic hearing sensitivity has evolved in many vertebrate species, and the sex with a larger body size typically shows more sensitive hearing. However, generalizing this association is controversial. Research on sexually dimorphic hearing sensitivity contributes to an understanding of auditory sense functions, adaptations, and evolution among species. Therefore, the hypothesized association between body size and hearing needs further validation, especially in specific animal groups. In this study, we assessed hearing sensitivity by measuring auditory brainstem responses (ABRs) in both sexes of 3-year-old Chinese softshell turtles (Pelodiscus sinensis). In this species, male bodies are larger than those of female, and individuals spend most of their lives in the mud at the bottom of freshwater habitats. We found that for both sexes, the hearing sensitivity bandwidth was 0.2-0.9 kHz. Although males were significantly larger than females, no significant differences in ABR thresholds or latencies were found between males and females at the same stimulus frequency. These results indicate that P. sinensis hearing is only sensitive to low-frequency (typically <0.9 kHz) sound signals and that sexually dimorphic hearing sensitivity is not a trait that has evolved in P. sinensis. Physiological and environmental reasons may account for P. sinensis acoustic communication via low-frequency sound signals and the lack of sexually dimorphic hearing sensitivity in these benthic turtles. The results of this study refine our understanding of the adaptation and evolution of the vertebrate auditory system.

Sound evidence for biodiversity monitoring

Bioacoustics and artificial intelligence facilitate ecological studies of animal populations.

Hidden social complexity behind vocal and acoustic communication in non-avian reptiles

Social interactions are inevitable in the lives of most animals, since most essential behaviours require interaction with conspecifics, such as mating and competing for resources. Non-avian reptiles are typically viewed as solitary animals that predominantly use their vision and olfaction to communicate with conspecifics. Nevertheless, in recent years, evidence is mounting that some reptiles can produce sounds and have the potential for acoustic communication. Reptiles that can produce sound have an additional communicative channel (in addition to visual/olfactory channels), which could suggest they have a higher communicative complexity, the evolution of which is assumed to be driven by the need of social interactions. Thus, acoustic reptiles may provide an opportunity to unveil the true social complexity of reptiles that are usually thought of as solitary. This review aims to reveal the hidden social interactions behind the use of sounds in non-avian reptiles. Our review suggests that the potential of vocal and acoustic communication and the complexity of social interactions may be underestimated in non-avian reptiles, and that acoustic reptiles may provide a great opportunity to uncover the coevolution between sociality and communication in non-avian reptiles. This article is part of the theme issue 'The power of sound: unravelling how acoustic communication shapes group dynamics'.

Context-driven communication during deep-sea foraging in a social toothed whale

Social deep-diving odontocetes face the challenge of balancing near-surface proximity to oxygen and group members with foraging in the deep sea. Individuals rely on conspecifics for critical life functions, such as predator defence, but disperse during foraging to feed individually. To understand the role of social acoustic mediation during foraging in deep-diving toothed whales, we investigated the context of social burst-pulse call production in Risso's dolphin (Grampus griseus) using biologgers. Dolphins produced context-specific burst pulses predominantly during daytime foraging, preceding or following foraging dives and in the early descent of daytime deep dives. Individuals applied differential short and long burst-pulse calls intended for either near-surface receivers (horizontal transmission) or deep-foraging receivers (vertical transmission). Our results show that deep-diving toothed whales are reliant on acoustic communication during certain foraging contexts, to relay information including foraging conditions or an individual's location. Moreover, they accentuate the importance of maintaining acoustic contact with conspecifics, specifically when dispersed during deeper foraging. It also signifies that our oceanic top predators may be specifically vulnerable to the current strong increase in anthropogenic noise. Potential masking of the signals from group members communicating at a distance could undermine their social cohesion, and hence their capacity to maintain vital life functions.

Network analysis reveals context-dependent structural complexity of social calls in serrate-legged small treefrogs

Vocal communication plays an important role in survival, reproduction, and animal social association. Birds and mammals produce complex vocal sequence to convey context-dependent information. Vocalizations are conspicuous features of the behavior of most anuran species (frogs and toads), and males usually alter their calling strategies according to ecological context to improve the attractiveness/competitiveness. However, very few studies have focused on the variation of vocal sequence in anurans. In the present study, we used both conventional method and network analysis to investigate the context-dependent vocal repertoire, vocal sequence, and call network structure in serrate-legged small treefrogs Kurixalus odontotarsus. We found that male K. odontotarsus modified their vocal sequence by switching to different call types and increasing repertoire size in the presence of a competitive rival. Specifically, compared with before and after the playback of advertisement calls, males emitted fewer advertisement calls, but more aggressive calls, encounter calls, and compound calls during the playback period. Network analysis revealed that the mean degree, mean closeness, and mean betweenness of the call networks significantly decreased during the playback period, which resulted in lower connectivity. In addition, the increased proportion of one-way motifs and average path length also indicated that the connectivity of the call network decreased in competitive context. However, the vocal sequence of K. odontotarsus did not display a clear small-world network structure, regardless of context. Our study presents a paradigm to apply network analysis to vocal sequence in anurans and has important implications for understanding the evolution and function of sequence patterns.

Rhythmic properties of Sciaena umbra calls across space and time in the Mediterranean Sea

In animals, the rhythmical properties of calls are known to be shaped by physical constraints and the necessity of conveying information. As a consequence, investigating rhythmical properties in relation to different environmental conditions can help to shed light on the relationship between environment and species behavior from an evolutionary perspective. Sciaena umbra (fam. Sciaenidae) male fish emit reproductive calls characterized by a simple isochronous, i.e., metronome-like rhythm (the so-called R-pattern). Here, S. umbra R-pattern rhythm properties were assessed and compared between four different sites located along the Mediterranean basin (Mallorca, Venice, Trieste, Crete); furthermore, for one location, two datasets collected 10 years apart were available. Recording sites differed in habitat types, vessel density and acoustic richness; despite this, S. umbra R-calls were isochronous across all locations. A degree of variability was found only when considering the beat frequency, which was temporally stable, but spatially variable, with the beat frequency being faster in one of the sites (Venice). Statistically, the beat frequency was found to be dependent on the season (i.e. month of recording) and potentially influenced by the presence of soniferous competitors and human-generated underwater noise. Overall, the general consistency in the measured rhythmical properties (isochrony and beat frequency) suggests their nature as a fitness-related trait in the context of the S. umbra reproductive behavior and calls for further evaluation as a communicative cue.

Midbrain node for context-specific vocalisation in fish

Vocalizations communicate information indicative of behavioural state across divergent social contexts. Yet, how brain regions actively pattern the acoustic features of context-specific vocal signals remains largely unexplored. The midbrain periaqueductal gray (PAG) is a major site for initiating vocalization among mammals, including primates. We show that PAG neurons in a highly vocal fish species (Porichthys notatus) are activated in distinct patterns during agonistic versus courtship calling by males, with few co-activated during a non-vocal behaviour, foraging. Pharmacological manipulations within vocally active PAG, but not hindbrain, sites evoke vocal network output to sonic muscles matching the temporal features of courtship and agonistic calls, showing that a balance of inhibitory and excitatory dynamics is likely necessary for patterning different call types. Collectively, these findings support the hypothesis that vocal species of fish and mammals share functionally comparable PAG nodes that in some species can influence the acoustic structure of social context-specific vocal signals.

Characterization of the vocal behavior of the miniature and transparent fish model, Danionella cerebruma)

Danionella cerebrum has recently been proposed as a promising model to investigate the structure and function of the adult vertebrate brain, including the development of vocal-auditory neural pathways. This genetically tractable and transparent cypriniform is highly vocal, but limited information is available on its acoustic behavior and underlying biological function. Our main goal was to characterize the acoustic repertoire and diel variation in sound production of D. cerebrum, as well as to investigate the relationship between vocal behavior and reproduction. Sound recordings demonstrated high vocal activity, with sounds varying from short sequences of pulses known as "bursts" (comprising up to 15 pulses) to notably longer sounds, termed "long bursts", which extended up to 349 pulses with over 2.7 s. Vocal activity peaked at midday and it was very low at night with only a few bursts. While the number of pulses was higher during the daytime, the interpulse interval was longer at night. In addition, calling time was positively associated with the number of viable eggs, suggesting that acoustic communication is important for reproduction. These preliminary findings reveal the potential of using D. cerebrum to investigate vocal plasticity and the implications for sexual selection and reproduction in a novel vertebrate model for neuroscience.

Vocal complexity in a socially complex corvid: gradation, diversity and lack of common call repertoire in male rooks

Vocal communication is widespread in animals, with vocal repertoires of varying complexity. The social complexity hypothesis predicts that species may need high vocal complexity to deal with complex social organization (e.g. have a variety of different interindividual relations). We quantified the vocal complexity of two geographically distant captive colonies of rooks, a corvid species with complex social organization and cognitive performances, but understudied vocal abilities. We quantified the diversity and gradation of their repertoire, as well as the inter-individual similarity at the vocal unit level. We found that males produced call units with lower diversity and gradation than females, while song units did not differ between sexes. Surprisingly, while females produced highly similar call repertoires, even between colonies, each individual male produced almost completely different call repertoires from any other individual. These findings question the way male rooks communicate with their social partners. We suggest that each male may actively seek to remain vocally distinct, which could be an asset in their frequently changing social environment. We conclude that inter-individual similarity, an understudied aspect of vocal repertoires, should also be considered as a measure of vocal complexity.

Convergent Anuran Middle Ear Loss Lacks a Universal, Adaptive Explanation

INTRODUCTION

Shared selection pressures often explain convergent trait loss, yet anurans (frogs and toads) have lost their middle ears at least 38 times with no obvious shared selection pressures unifying "earless" taxa. Anuran tympanic middle ear loss is especially perplexing because acoustic communication is dominant within Anura and tympanic middle ears enhance airborne hearing in most tetrapods.

METHODS

Here, we use phylogenetic comparative methods to examine whether particular geographic ranges, microhabitats, activity patterns, or aspects of acoustic communication are associated with anuran tympanic middle ear loss.

RESULTS

Although we find some differences between the geographic ranges of eared and earless species on average, there is plenty of overlap between the geographic distributions of eared and earless species. Additionally, we find a higher prevalence of diurnality in earless species, but not all earless species are diurnal. We find no universal adaptive explanation for the many instances of anuran tympanic middle ear loss.

CONCLUSION

The puzzling lack of universally shared selection pressures among earless species motivates discussion of alternative hypotheses, including genetic or developmental constraints, and the possibility that tympanic middle ear loss is maladaptive.

Vocal tract shape variation contributes to individual vocal identity in African penguins

Variation in formant frequencies has been shown to affect social interactions and sexual competition in a range of avian species. Yet, the anatomical bases of this variation are poorly understood. Here, we investigated the morphological correlates of formants production in the vocal apparatus of African penguins. We modelled the geometry of the supra-syringeal vocal tract of 20 specimens to generate a population of virtual vocal tracts with varying dimensions. We then estimated the acoustic response of these virtual vocal tracts and extracted the centre frequency of the first four predicted formants. We demonstrate that: (i) variation in length and cross-sectional area of vocal tracts strongly affects the formant pattern, (ii) the tracheal region determines most of this variation, and (iii) the skeletal size of penguins does not correlate with the trachea length and consequently has relatively little effect on formants. We conclude that in African penguins, while the variation in vocal tract geometry generates variation in resonant frequencies supporting the discrimination of conspecifics, such variation does not provide information on the emitter's body size. Overall, our findings advance our understanding of the role of formant frequencies in bird vocal communication.

Nocturnal selective pressures on the evolution of human musicality as a missing piece of the adaptationist puzzle

Human musicality exhibits the necessary hallmarks for biological adaptations. Evolutionary explanations focus on recurrent adaptive problems that human musicality possibly solved in ancestral environments, such as mate selection and competition, social bonding/cohesion and social grooming, perceptual and motor skill development, conflict reduction, safe time-passing, transgenerational communication, mood regulation and synchronization, and credible signaling of coalition and territorial/predator defense. Although not mutually exclusive, these different hypotheses are still not conceptually integrated nor clearly derived from independent principles. I propose The Nocturnal Evolution of Human Musicality and Performativity Theory in which the night-time is the missing piece of the adaptationist puzzle of human musicality and performing arts. The expansion of nocturnal activities throughout human evolution, which is tied to tree-to-ground sleep transition and habitual use of fire, might help (i) explain the evolution of musicality from independent principles, (ii) explain various seemingly unrelated music features and functions, and (iii) integrate many ancestral adaptive values proposed. The expansion into the nocturnal niche posed recurrent ancestral adaptive challenges/opportunities: lack of luminosity, regrouping to cook before sleep, imminent dangerousness, low temperatures, peak tiredness, and concealment of identity. These crucial night-time features might have selected evening-oriented individuals who were prone to acoustic communication, more alert and imaginative, gregarious, risk-taking and novelty-seeking, prone to anxiety modulation, hedonistic, promiscuous, and disinhibited. Those night-time selected dispositions may have converged and enhanced protomusicality into human musicality by facilitating it to assume many survival- and reproduction-enhancing roles (social cohesion and coordination, signaling of coalitions, territorial defense, antipredatorial defense, knowledge transference, safe passage of time, children lullabies, and sexual selection) that are correspondent to the co-occurring night-time adaptive challenges/opportunities. The nocturnal dynamic may help explain musical features (sound, loudness, repetitiveness, call and response, song, elaboration/virtuosity, and duetting/chorusing). Across vertebrates, acoustic communication mostly occurs in nocturnal species. The eveningness chronotype is common among musicians and composers. Adolescents, who are the most evening-oriented humans, enjoy more music. Contemporary tribal nocturnal activities around the campfire involve eating, singing/dancing, storytelling, and rituals. I discuss the nocturnal integration of musicality's many roles and conclude that musicality is probably a multifunctional mental adaptation that evolved along with the night-time adaptive landscape.

Context-dependent activation of a social behavior brain network during learned vocal production

Neural activation in brain regions for vocal control is social context dependent. This context-dependent brain activation reflects social context-appropriate vocal behavior but has unresolved mechanisms. Studies of non-vocal social behaviors in multiple organisms suggest a functional role for several evolutionarily conserved and highly interconnected brain regions. Here, we use neural activity-dependent gene expression to evaluate the functional connectivity of this social behavior network within zebra finches in non-social and social singing contexts. We found that activity in one social behavior network region, the medial preoptic area (POM), was strongly associated with the amount of non-social undirected singing in zebra finches. In addition, in all regions of the social behavior network and the paraventricular nucleus (PVN), a higher percentage of EGR1 expression was observed during a social female-directed singing context compared to a non-social undirected singing context. Furthermore, we observed distinct patterns of significantly correlated activity between regions of the social behavior network during non-social undirected and social female-directed singing. Our results suggest that non-social vs. social contexts differentially activate this social behavior network and PVN. Moreover, neuronal activity within this social behavior network, PVN, and POM may alter context-appropriate vocal production.

Trait-based species richness: ecology and macroevolution

Understanding the origins of species richness patterns is a fundamental goal in ecology and evolutionary biology. Much research has focused on explaining two kinds of species richness patterns: (i) spatial species richness patterns (e.g. the latitudinal diversity gradient), and (ii) clade-based species richness patterns (e.g. the predominance of angiosperm species among plants). Here, I highlight a third kind of richness pattern: trait-based species richness (e.g. the number of species with each state of a character, such as diet or body size). Trait-based richness patterns are relevant to many topics in ecology and evolution, from ecosystem function to adaptive radiation to the paradox of sex. Although many studies have described particular trait-based richness patterns, the origins of these patterns remain far less understood, and trait-based richness has not been emphasised as a general category of richness patterns. Here, I describe a conceptual framework for how trait-based richness patterns arise compared to other richness patterns. A systematic review suggests that trait-based richness patterns are most often explained by when each state originates within a group (i.e. older states generally have higher richness), and not by differences in transition rates among states or faster diversification of species with certain states. This latter result contrasts with the widespread emphasis on diversification rates in species-richness research. I show that many recent studies of spatial richness patterns are actually studies of trait-based richness patterns, potentially confounding the causes of these patterns. Finally, I describe a plethora of unanswered questions related to trait-based richness patterns.

Sexual Signals Persist over Deep Time: Ancient Co-option of Bioluminescence for Courtship Displays in Cypridinid Ostracods

Although the diversity, beauty, and intricacy of sexually selected courtship displays command the attention of evolutionists, the longevity of these traits in deep time is poorly understood. Population-based theory suggests sexual selection could either lower or raise extinction risk, resulting in high or low persistence of lineages with sexually selected traits. Furthermore, empirical studies that directly estimate the longevity of sexually selected traits are uncommon. Sexually selected signals-including bioluminescent courtship-originated multiple times during evolution, allowing the empirical study of their longevity after careful phylogenetic and divergence time analyses. Here, we estimate the first transcriptome-based molecular phylogeny and divergence times of Cypridinidae. We report extreme longevity of bioluminescent courtship, a trait important in mate choice and probably under sexual selection. Our relaxed-clock estimates of divergence times coupled with stochastic character mapping show luminous courtship evolved only once in Cypridinidae-in a Sub-Tribe, we name Luxorina-at least 151 millions of years ago from cypridinid ancestors that used bioluminescence only in antipredator displays, defining a Tribe we name Luminini. This time-calibrated molecular phylogeny of cypridinids will serve as a foundation for integrative and comparative studies on the biochemistry, molecular evolution, courtship, diversification, and ecology of cypridinid bioluminescence. The persistence of luminous courtship for hundreds of millions of years suggests that sexual selection did not cause a rapid loss of associated traits, and that rates of speciation within the group exceeded extinction risk, which may contribute to the persistence of a diverse clade of signaling species. [Ancestral state reconstruction; Biodiversity; co-option; divergence time estimates; macroevolution; Ostracoda; phylogenomics; sexual selection.].

Machine learning and statistical classification of birdsong link vocal acoustic features with phylogeny

Birdsong is a longstanding model system for studying evolution and biodiversity. Here, we collected and analyzed high quality song recordings from seven species in the family Estrildidae. We measured the acoustic features of syllables and then used dimensionality reduction and machine learning classifiers to identify features that accurately assigned syllables to species. Species differences were captured by the first 3 principal components, corresponding to basic frequency, power distribution, and spectrotemporal features. We then identified the measured features underlying classification accuracy. We found that fundamental frequency, mean frequency, spectral flatness, and syllable duration were the most informative features for species identification. Next, we tested whether specific acoustic features of species' songs predicted phylogenetic distance. We found significant phylogenetic signal in syllable frequency features, but not in power distribution or spectrotemporal features. Results suggest that frequency features are more constrained by species' genetics than are other features, and are the best signal features for identifying species from song recordings. The absence of phylogenetic signal in power distribution and spectrotemporal features suggests that these song features are labile, reflecting learning processes and individual recognition.

Evolution of stridulatory mechanisms: vibroacoustic communication may be common in leaf-footed bugs and allies (Heteroptera: Coreoidea)

Intra- and interspecific communication is crucial to fitness via its role in facilitating mating, territoriality and defence. Yet, the evolution of animal communication systems is puzzling-how do they originate and change over time? Studying stridulatory morphology provides a tractable opportunity to deduce the origin and diversification of a communication mechanism. Stridulation occurs when two sclerotized structures rub together to produce vibratory and acoustic (vibroacoustic) signals, such as a cricket 'chirp'. We investigated the evolution of stridulatory mechanisms in the superfamily Coreoidea (Hemiptera: Heteroptera), a group of insects known for elaborate male fighting behaviours and enlarged hindlegs. We surveyed a large sampling of taxa and used a phylogenomic dataset to investigate the evolution of stridulatory mechanisms. We identified four mechanisms, with at least five evolutionary gains. One mechanism, occurring only in male Harmostini (Rhopalidae), is described for the first time. Some stridulatory mechanisms appear to be non-homoplastic apomorphies within Rhopalidae, while others are homoplastic or potentially homoplastic within Coreidae and Alydidae, respectively. We detected no losses of these mechanisms once evolved, suggesting they are adaptive. Our work sets the stage for further behavioural, evolutionary and ecological studies to better understand the context in which these traits evolve and change.

Two pup vocalization types are genetically and functionally separable in deer mice

Vocalization is a widespread social behavior in vertebrates that can affect fitness in the wild. Although many vocal behaviors are highly conserved, heritable features of specific vocalization types can vary both within and between species, raising the questions of why and how some vocal behaviors evolve. Here, using new computational tools to automatically detect and cluster vocalizations into distinct acoustic categories, we compare pup isolation calls across neonatal development in eight taxa of deer mice (genus Peromyscus) and compare them with laboratory mice (C57BL6/J strain) and free-living, wild house mice (Mus musculus domesticus). Whereas both Peromyscus and Mus pups produce ultrasonic vocalizations (USVs), Peromyscus pups also produce a second call type with acoustic features, temporal rhythms, and developmental trajectories that are distinct from those of USVs. In deer mice, these lower frequency "cries" are predominantly emitted in postnatal days one through nine, whereas USVs are primarily made after day 9. Using playback assays, we show that cries result in a more rapid approach by Peromyscus mothers than USVs, suggesting a role for cries in eliciting parental care early in neonatal development. Using a genetic cross between two sister species of deer mice exhibiting large, innate differences in the acoustic structure of cries and USVs, we find that variation in vocalization rate, duration, and pitch displays different degrees of genetic dominance and that cry and USV features can be uncoupled in second-generation hybrids. Taken together, this work shows that vocal behavior can evolve quickly between closely related rodent species in which vocalization types, likely serving distinct functions in communication, are controlled by distinct genetic loci.

At the root of the mammalian mind: The sensory organs, brain and behavior of pre-mammalian synapsids

All modern mammals are descendants of the paraphyletic non-mammaliaform Synapsida, colloquially referred to as the "mammal-like reptiles." It has long been assumed that these mammalian ancestors were essentially reptile-like in their morphology, biology, and behavior, i.e., they had a small brain, displayed simple behavior, and their sensory organs were unrefined compared to those of modern mammals. Recent works have, however, revealed that neurological, sensory, and behavioral traits previously considered typically mammalian, such as whiskers, enhanced olfaction, nocturnality, parental care, and complex social interactions evolved before the origin of Mammaliaformes, among the early-diverging "mammal-like reptiles." In contrast, an enlarged brain did not evolve immediately after the origin of mammaliaforms. As such, in terms of paleoneurology, the last "mammal-like reptiles" were not significantly different from the earliest mammaliaforms. The abundant data and literature published in the last 10 years no longer supports the "three pulses" scenario of synapsid brain evolution proposed by Rowe and colleagues in 2011, but supports the new "outside-in" model of Rodrigues and colleagues proposed in 2018, instead. As Mesozoic reptiles were becoming the dominant taxa within terrestrial ecosystems, synapsids gradually adapted to smaller body sizes and nocturnality. This resulted in a sensory revolution in synapsids as olfaction, audition, and somatosensation compensated for the loss of visual cues. This altered sensory input is aligned with changes in the brain, the most significant of which was an increase in relative brain size.

Diversity of Underwater Vocalizations in Chinese Soft-Shelled Turtle (Pelodiscus sinensis)

Sound communication is important for underwater species. The wild population of the Chinese soft-shelled turtle (Pelodiscus sinensis) is listed as vulnerable. However, its vocalization, which can serve as the basis for ecological and evolutionary research, has not been studied. Here, we performed underwater recordings of 23 Chinese soft-shelled turtles of different ages and sexes and identified 720 underwater calls. The turtle calls were manually divided into 10 call types according to visual and aural inspection properties. The similarity test indicated that the manual division was reliable. We described the acoustic properties of the calls and the statistical analysis showed that the peak frequency of calls was significantly different between adult females and males, and also between subadults and adults. Similar to other aquatic turtles that prefer to live in deep water, Chinese soft-shelled turtles have a high vocal diversity and many harmonic calls, indicating that this highly aquatic species developed a variety of vocalizations to enhance their underwater communication, which helped them adapt to the complex and dim underwater environment. Furthermore, the turtles showed a tendency for vocalization to become more diverse with age.

Context-dependent activation of a social behavior brain network associates with learned vocal production

In zebra finches, an avian brain network for vocal control undergoes context-dependent patterning of song-dependent activation. Previous studies in zebra finches also implicate the importance of dopaminergic input in producing context-appropriate singing behavior. In mice, it has been shown that oxytocinergic neurons originated in the paraventricular nucleus of the hypothalamus (PVN) synapse directly onto dopamine neurons in the ventral tegmental area (VTA), implicating the necessity of oxytocin signaling from the PVN for producing a context-appropriate song. Both avian and non-avian axonal tract-tracing studies indicate high levels of PVN innervation by the social behavior network. Here, we hypothesize that the motivation for PVN oxytocin neurons to trigger dopamine release originates in the social behavior network, a highly conserved and interconnected collection of six regions implicated in various social and homeostatic behaviors. We found that expression of the neuronal activity marker EGR1 was not strongly correlated with song production in any of the regions of the social behavior network. However, when EGR1 expression levels were normalized to the singing rate, we found significantly higher levels of expression in the social behavior network regions except the medial preoptic area during a social female-directed singing context compared to a non-social undirected singing context. Our results suggest neuronal activity within the male zebra finch social behavior network influences the synaptic release of oxytocin from PVN onto dopaminergic projection neurons in the VTA, which in turn signals to the vocal control network to allow for context-appropriate song production.

Evolution of sexually selected traits across animals

Sexual selection is thought to be a major driver of phenotypic diversity and diversification in animals, but large-scale evolutionary patterns in sexually selected (SS) traits remain largely unknown. Here, we survey and analyze the evolution of these traits across animal phylogeny. We find that female mate choice appears to be the most widespread mechanism of sexual selection, but male-male competition appears to be almost as frequent in chordates and male mate choice is also common in arthropods. Among sensory types, tactile traits appear to be most widespread whereas auditory traits are relatively uncommon. Rather than being ubiquitous or randomly distributed across animals, most of these different types of SS traits are confined to clades in arthropods and chordates, which form “hotspots” for the evolution of these diverse trait types. Thus, different sensory types show accelerated rates of evolution in these clades. Moreover, different types of SS traits are strongly correlated with each other in their evolution across animals. Finally, despite the intensive interest in the role of sexual selection in speciation, we find only limited support for the idea that SS traits drive large-scale patterns of diversification and species richness across all animals.

Chinese striped-neck turtles vocalize underwater and show differences in peak frequency among different age and sex groups

Background

Turtle vocalizations play an important role throughout their lives by expressing individual information (position, emotion, or physiological status), reflecting mating preferences, and synchronizing incubation. The Chinese striped-neck turtle (Mauremys sinensis) is one of the most widely distributed freshwater turtles in China, whose wild population is critically endangered. However, its vocalization has not been studied, which can be the basis for behavioral and ecological studies.

Methods

Five different sex-age groups of turtles were recorded underwater in a soundproof room. Cluster analysis and principal component analysis for classification of Chinese striped-neck turtle calls were unreasonable. The turtle calls were manually sought using visual and aural inspection of the recordings in Raven Pro 1.5 software and classified according to differences perceived through auditory inspection and the morphological characteristics of the spectrograms. The results of similarity analysis verified the reliability of manual classification. We compared the peak frequency of the calls among different age and sex groups.

Results

We identified ten M. sinensis call types, displayed their spectra and waveforms, and described their auditory characteristics. Most calls produced by the turtles were low-frequency. Some high-frequency call types, that are common in other turtle species were also produced. Similar to other turtles, the Chinese striped-neck turtle generates harmonic vocalizations. Courtship behaviors were observed when one of the call types occurred in the mixed-sex group. Adult females produced more high-frequency call types, and subadult males had higher vocalizations than other groups. These results provide a basis for future research on the function of vocalizations, field monitoring, and conservation of this species.

Human Auditory Ecology: Extending Hearing Research to the Perception of Natural Soundscapes by Humans in Rapidly Changing Environments

Research in hearing sciences has provided extensive knowledge about how the human auditory system processes speech and assists communication. In contrast, little is known about how this system processes "natural soundscapes," that is the complex arrangements of biological and geophysical sounds shaped by sound propagation through non-anthropogenic habitats [Grinfeder et al. (2022). Frontiers in Ecology and Evolution. 10: 894232]. This is surprising given that, for many species, the capacity to process natural soundscapes determines survival and reproduction through the ability to represent and monitor the immediate environment. Here we propose a framework to encourage research programmes in the field of "human auditory ecology," focusing on the study of human auditory perception of ecological processes at work in natural habitats. Based on large acoustic databases with high ecological validity, these programmes should investigate the extent to which this presumably ancestral monitoring function of the human auditory system is adapted to specific information conveyed by natural soundscapes, whether it operate throughout the life span or whether it emerges through individual learning or cultural transmission. Beyond fundamental knowledge of human hearing, these programmes should yield a better understanding of how normal-hearing and hearing-impaired listeners monitor rural and city green and blue spaces and benefit from them, and whether rehabilitation devices (hearing aids and cochlear implants) restore natural soundscape perception and emotional responses back to normal. Importantly, they should also reveal whether and how humans hear the rapid changes in the environment brought about by human activity.

High acoustic diversity and behavioral complexity of katydids in the Mesozoic soundscape

Acoustic communication has played a key role in the evolution of a wide variety of vertebrates and insects. However, the reconstruction of ancient acoustic signals is challenging due to the extreme rarity of fossilized organs. Here, we report the earliest tympanal ears and sound-producing system (stridulatory apparatus) found in exceptionally preserved Mesozoic katydids. We present a database of the stridulatory apparatus and wing morphology of Mesozoic katydids and further calculate their probable singing frequencies and analyze the evolution of their acoustic communication. Our suite of analyses demonstrates that katydids evolved complex acoustic communication including mating signals, intermale communication, and directional hearing, at least by the Middle Jurassic. Additionally, katydids evolved a high diversity of singing frequencies including high-frequency musical calls, accompanied by acoustic niche partitioning at least by the Late Triassic, suggesting that acoustic communication might have been an important driver in the early radiation of these insects. The Early-Middle Jurassic katydid transition from Haglidae- to Prophalangopsidae-dominated faunas coincided with the diversification of derived mammalian clades and improvement of hearing in early mammals, supporting the hypothesis of the acoustic coevolution of mammals and katydids. Our findings not only highlight the ecological significance of insects in the Mesozoic soundscape but also contribute to our understanding of how acoustic communication has influenced animal evolution.

Why are animals conspicuously colored? Evolution of sexual versus warning signals in land vertebrates

Conspicuous colors (e.g., red, yellow, blue) have evolved numerous times across animals. But the function of this coloration can differ radically among species. Many species use this coloration as a sexual signal to conspecifics, whereas others use it as a warning signal to predators. Why do different species evolve conspicuous coloration in association with one function as opposed to the other? We address this question in terrestrial vertebrates (tetrapods) using phylogenetic approaches, and test whether day-night activities of species help determine these patterns. Using phylogenetic logistic regression, we found that conspicuous, sexually dimorphic coloration is significantly associated with diurnal lineages (e.g., many birds and lizards). By contrast, the evolution of warning signals was significantly associated with large-scale clades that were ancestrally nocturnal (e.g., snakes, amphibians), regardless of the current diel activity of species. Overall, we show that the evolution of conspicuous coloration as warning signals or sexual signals is influenced by the ecology of species, both recently and in the ancient past.

Cortical adaptation of the night monkey to a nocturnal niche environment: a comparative non-invasive T1w/T2w myelin study

Night monkeys (Aotus) are the only genus of monkeys within the Simian lineage that successfully occupy a nocturnal environmental niche. Their behavior is supported by their sensory organs' distinctive morphological features; however, little is known about their evolutionary adaptations in sensory regions of the cerebral cortex. Here, we investigate this question by exploring the cortical organization of night monkeys using high-resolution in-vivo brain MRI and comparative cortical-surface T1w/T2w myeloarchitectonic mapping. Our results show that the night monkey cerebral cortex has a qualitatively similar but quantitatively different pattern of cortical myelin compared to the diurnal macaque and marmoset monkeys. T1w/T2w myelin and its gradient allowed us to parcellate high myelin areas, including the middle temporal complex (MT +) and auditory cortex, and a low-myelin area, Brodmann area 7 (BA7) in the three species, despite species differences in cortical convolutions. Relative to the total cortical-surface area, those of MT + and the auditory cortex are significantly larger in night monkeys than diurnal monkeys, whereas area BA7 occupies a similar fraction of the cortical sheet in all three species. We propose that the selective expansion of sensory areas dedicated to visual motion and auditory processing in night monkeys may reflect cortical adaptations to a nocturnal environment.

Convergent and divergent neural circuit architectures that support acoustic communication

Vocal communication is used across extant vertebrates, is evolutionarily ancient, and been maintained, in many lineages. Here I review the neural circuit architectures that support intraspecific acoustic signaling in representative anuran, mammalian and avian species as well as two invertebrates, fruit flies and Hawaiian crickets. I focus on hindbrain motor control motifs and their ties to respiratory circuits, expression of receptors for gonadal steroids in motor, sensory, and limbic neurons as well as divergent modalities that evoke vocal responses. Hindbrain and limbic participants in acoustic communication are highly conserved, while forebrain participants have diverged between anurans and mammals, as well as songbirds and rodents. I discuss the roles of natural and sexual selection in driving speciation, as well as exaptation of circuit elements with ancestral roles in respiration, for producing sounds and driving rhythmic vocal features. Recent technical advances in whole brain fMRI across species will enable real time imaging of acoustic signaling partners, tying auditory perception to vocal production.

Common evolutionary origin of acoustic communication in choanate vertebrates

Acoustic communication, broadly distributed along the vertebrate phylogeny, plays a fundamental role in parental care, mate attraction and various other behaviours. Despite its importance, comparatively less is known about the evolutionary roots of acoustic communication. Phylogenetic comparative analyses can provide insights into the deep time evolutionary origin of acoustic communication, but they are often plagued by missing data from key species. Here we present evidence for 53 species of four major clades (turtles, tuatara, caecilian and lungfish) in the form of vocal recordings and contextual behavioural information accompanying sound production. This and a broad literature-based dataset evidence acoustic abilities in several groups previously considered non-vocal. Critically, phylogenetic analyses encompassing 1800 species of choanate vertebrates reconstructs acoustic communication as a homologous trait, and suggests that it is at least as old as the last common ancestor of all choanate vertebrates, that lived approx. 407 million years before present.

Determinants of variability in signature whistles of the Mediterranean common bottlenose dolphin

One of the most studied aspects of animal communication is the acoustic repertoire difference between populations of the same species. While numerous studies have investigated the variability of bottlenose dolphin whistles between populations, very few studies have focused on the signature whistles alone and the factors underlying differentiation of signature whistles are still poorly understood. Here we describe the signature whistles produced by six distinct geographical units of the common bottlenose dolphin (Tursiops truncatus) in the Mediterranean Sea and identify the main determinants of their variability. Particularly, the influence of the region (proxy of genetic distance), the geographic site, and the environmental (sea bottom-related) and demographical (population-related) conditions on the acoustic structure of signature whistles was evaluated. The study provides the first evidence that the genetic structure, which distinguishes the eastern and western Mediterranean bottlenose dolphin populations has no strong influence on the acoustic structure of their signature whistles, and that the geographical isolation between populations only partially affected whistle variability. The environmental conditions of the areas where the whistles developed and the demographic characteristics of the belonging populations strongly influenced signature whistles, in accordance with the "acoustic adaptation hypothesis" and the theory of signature whistle determination mediated by learning.

Comparative transcriptome analysis provides insights into the molecular mechanisms of high-frequency hearing differences between the sexes of Odorrana tormota

Background

Acoustic communication is important for the survival and reproduction of anurans and masking background noise is a critical factor for their effective acoustic communication. Males of the concave-eared frog (Odorrana tormota) have evolved an ultrasonic communication capacity to avoid masking by the widespread background noise of local fast-flowing streams, whereas females exhibit no ultrasonic sensitivity. However, the molecular mechanisms underlying the high-frequency hearing differences between the sexes of O. tormota are still poorly understood.

Results

In this study, we sequenced the brain transcriptomes of male and female O. tormota, and compared their differential gene expression. A total of 4,605 differentially expressed genes (DEGs) between the sexes of O. tormota were identified and eleven of them were related to auditory based on the annotation and enrichment analysis. Most of these DEGs in males showed a higher expression trend than females in both quantity and expression quantity. The highly expressed genes in males were relatively concentrated in neurogenesis, signal transduction, ion transport and energy metabolism, whereas the up-expressed genes in females were mainly related to the growth and development regulation of specific auditory cells.

Conclusions

The transcriptome of male and female O. tormota has been sequenced and de novo assembled, which will provide gene reference for further genomic studies. In addition, this is the first research to reveal the molecular mechanisms of sex differences in ultrasonic hearing between the sexes of O. tormota and will provide new insights into the genetic basis of the auditory adaptation in amphibians during their transition from water to land.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08536-2.

HybridMouse: A Hybrid Convolutional-Recurrent Neural Network-Based Model for Identification of Mouse Ultrasonic Vocalizations

Mice use ultrasonic vocalizations (USVs) to convey a variety of socially relevant information. These vocalizations are affected by the sex, age, strain, and emotional state of the emitter and can thus be used to characterize it. Current tools used to detect and analyze murine USVs rely on user input and image processing algorithms to identify USVs, therefore requiring ideal recording environments. More recent tools which utilize convolutional neural networks models to identify vocalization segments perform well above the latter but do not exploit the sequential structure of audio vocalizations. On the other hand, human voice recognition models were made explicitly for audio processing; they incorporate the advantages of CNN models in recurrent models that allow them to capture the sequential nature of the audio. Here we describe the HybridMouse software: an audio analysis tool that combines convolutional (CNN) and recurrent (RNN) neural networks for automatically identifying, labeling, and extracting recorded USVs. Following training on manually labeled audio files recorded in various experimental conditions, HybridMouse outperformed the most commonly used benchmark model utilizing deep-learning tools in accuracy and precision. Moreover, it does not require user input and produces reliable detection and analysis of USVs recorded under harsh experimental conditions. We suggest that HybrideMouse will enhance the analysis of murine USVs and facilitate their use in scientific research.

Size of Snake Eyes Correlates With Habitat Types and Diel Activity Patterns

Eye size influences visual acuity, sensitivity, and temporal resolution and is a result of vertebrate adaptation to the environment. The habitats of snake species are diverse, ranging from fossorial, terrestrial, arboreal, to aquatic. They also demonstrate a variety of behavioral and physiological characteristics, such as activity time, feeding patterns, and prey detection. In this study, we comparatively investigated how the relative eye size (i.e., eye diameter vs. head width) associated with the ecological (i.e., habitat), behavioral (i.e., diel activity pattern, foraging strategy), and physiological traits (i.e., the presence of pits), respectively, across six snake families from Taiwan. Among the traits we examined, we found that terrestrial and/or diurnal snakes tended to exhibit the larger relative eye size, indicating the evolutionary responses of eye size to changes in habitat types and activity patterns, respectively, while no evidence of how foraging strategies and the presence of pits affected snake eye size was found. Our findings not only shed light on the adaptive significance of the visual system in diversifying the behaviors and the environments exploited in snakes, but also underline the interactive effects of multidimensional evolutionary attributes (e.g., behavior, ecology, physiology and phylogeny) on the evolution of optimal visual performance.

Vocalizations of the Sepia short-tailed Opossum Monodelphis adusta (Thomas, 1897, Didelphimorphia: Didelphidae)

As part of their behavior, various groups of species, including marsupials and other mammals, have evolved vocalizations, with varying degrees of complexity, for different communication purposes. Despite the growing interest in the bioacoustics of species, there are groups in which the study in this field is still unknown. A clear example is the genus Monodelphis, the most diverse group of didelphid marsupials. In this work we present the first description of the vocalizations of Monodelphis adusta, the only species of the genus registered in Ecuador, which shows the ability to produce audible phrases with different numbers of syllables.

Evolutionary and Allometric Insights into Anuran Auditory Sensitivity and Morphology

As species change through evolutionary time, the neurological and morphological structures that underlie behavioral systems typically remain coordinated. This is especially important for communication systems, in which these structures must remain coordinated both within and between senders and receivers for successful information transfer. The acoustic communication of anurans ("frogs") offers an excellent system to ask when and how such coordination is maintained, and to allow researchers to dissociate allometric effects from independent correlated evolution. Anurans constitute one of the most speciose groups of vocalizing vertebrates, and females typically rely on vocalizations to localize males for reproduction. Here, we compile and compare data on various aspects of auditory morphology, hearing sensitivity, and call-dominant frequency across 81 species of anurans. We find robust, phylogenetically independent scaling effects of body size for all features measured. Furthermore, after accounting for body size, we find preliminary evidence that morphological evolution beyond allometry can correlate with hearing sensitivity and dominant frequency. These data provide foundational results regarding constraints imposed by body size on communication systems and motivate further data collection and analysis using comparative approaches across the numerous anuran species.

Amphibian behavioral diversity offers insights into evolutionary neurobiology

Recent studies have served to emphasize the unique placement of amphibians, composed of more than 8000 species, in the evolution of the brain. We provide an overview of the three amphibian orders and their respective ecologies, behaviors, and brain anatomy. Studies have probed the origins of independently evolved parental care strategies in frogs and the biophysical principles driving species-specific differences in courtship vocalization patterns. Amphibians are also important models for studying the central control of movement, especially in the context of the vertebrate origin of limb-based locomotion. By highlighting the versatility of amphibians, we hope to see a further adoption of anurans, urodeles, and gymnophionans as model systems for the evolution and neural basis of behavior across vertebrates.

Speciation across the Tree of Life

Much of what we know about speciation comes from detailed studies of well-known model systems. Although there have been several important syntheses on speciation, few (if any) have explicitly compared speciation among major groups across the Tree of Life. Here, we synthesize and compare what is known about key aspects of speciation across taxa, including bacteria, protists, fungi, plants, and major animal groups. We focus on three main questions. Is allopatric speciation predominant across groups? How common is ecological divergence of sister species (a requirement for ecological speciation), and on what niche axes do species diverge in each group? What are the reproductive isolating barriers in each group? Our review suggests the following patterns. (i) Based on our survey and projected species numbers, the most frequent speciation process across the Tree of Life may be co-speciation between endosymbiotic bacteria and their insect hosts. (ii) Allopatric speciation appears to be present in all major groups, and may be the most common mode in both animals and plants, based on non-overlapping ranges of sister species. (iii) Full sympatry of sister species is also widespread, and may be more common in fungi than allopatry. (iv) Full sympatry of sister species is more common in some marine animals than in terrestrial and freshwater ones. (v) Ecological divergence of sister species is widespread in all groups, including ~70% of surveyed species pairs of plants and insects. (vi) Major axes of ecological divergence involve species interactions (e.g. host-switching) and habitat divergence. (vii) Prezygotic isolation appears to be generally more widespread and important than postzygotic isolation. (viii) Rates of diversification (and presumably speciation) are strikingly different across groups, with the fastest rates in plants, and successively slower rates in animals, fungi, and protists, with the slowest rates in prokaryotes. Overall, our study represents an initial step towards understanding general patterns in speciation across all organisms.