Song evolution, speciation, and vocal learning in passerine birds

Parental developmental experience affects vocal learning in offspring

Cultural and genetic inheritance combine to enable rapid changes in trait expression, but their relative importance in determining trait expression across generations is not clear. Birdsong is a socially learned cognitive trait that is subject to both cultural and genetic inheritance, as well as being affected by early developmental conditions. We sought to test whether early-life conditions in one generation can affect song acquisition in the next generation. We exposed one generation (F1) of nestlings to elevated corticosterone (CORT) levels, allowed them to breed freely as adults, and quantified their son's (F2) ability to copy the song of their social father. We also quantified the neurogenetic response to song playback through immediate early gene (IEG) expression in the auditory forebrain. F2 males with only one corticosterone-treated parent copied their social father's song less accurately than males with two control parents. Expression of ARC in caudomedial nidopallium (NCM) correlated with father-son song similarity, and patterns of expression levels of several IEGs in caudomedial mesopallium (CMM) in response to father song playback differed between control F2 sons and those with a CORT-treated father only. This is the first study to demonstrate that developmental conditions can affect social learning and neurogenetic responses in a subsequent generation.

Auditory discrimination learning and acoustic cue weighing in female zebra finches with localized FoxP1 knockdowns

Rare disruptions of the transcription factor FOXP1 are implicated in a human neurodevelopmental disorder characterized by autism and/or intellectual disability with prominent problems in speech and language abilities. Avian orthologues of this transcription factor are evolutionarily conserved and highly expressed in specific regions of songbird brains, including areas associated with vocal production learning and auditory perception. Here, we investigated possible contributions of FoxP1 to song discrimination and auditory perception in juvenile and adult female zebra finches. They received lentiviral knockdowns of FoxP1 in one of two brain areas involved in auditory stimulus processing, HVC (proper name) or CMM (caudomedial mesopallium). Ninety-six females, distributed over different experimental and control groups were trained to discriminate between two stimulus songs in an operant Go/Nogo paradigm and subsequently tested with an array of stimuli. This made it possible to assess how well they recognized and categorized altered versions of training stimuli and whether localized FoxP1 knockdowns affected the role of different features during discrimination and categorization of song. Although FoxP1 expression was significantly reduced by the knockdowns, neither discrimination of the stimulus songs nor categorization of songs modified in pitch, sequential order of syllables or by reversed playback were affected. Subsequently, we analyzed the full dataset to assess the impact of the different stimulus manipulations for cue weighing in song discrimination. Our findings show that zebra finches rely on multiple parameters for song discrimination, but with relatively more prominent roles for spectral parameters and syllable sequencing as cues for song discrimination.NEW & NOTEWORTHY In humans, mutations of the transcription factor FoxP1 are implicated in speech and language problems. In songbirds, FoxP1 has been linked to male song learning and female preference strength. We found that FoxP1 knockdowns in female HVC and caudomedial mesopallium (CMM) did not alter song discrimination or categorization based on spectral and temporal information. However, this large dataset allowed to validate different cue weights for spectral over temporal information for song recognition.

Body size shapes song in honeyeaters

Birdsongs are among the most distinctive animal signals. Their evolution is thought to be shaped simultaneously by habitat structure and by the constraints of morphology. Habitat structure affects song transmission and detectability, thus influencing song (the acoustic adaptation hypothesis), while body size and beak size and shape necessarily constrain song characteristics (the morphological constraint hypothesis). Yet, support for the acoustic adaptation and morphological constraint hypotheses remains equivocal, and their simultaneous examination is infrequent. Using a phenotypically diverse Australasian bird clade, the honeyeaters (Aves: Meliphagidae), we compile a dataset consisting of song, environmental, and morphological variables for 163 species and jointly examine predictions of these two hypotheses. Overall, we find that body size constrains song frequency and pace in honeyeaters. Although habitat type and environmental temperature influence aspects of song, that influence is indirect, likely via effects of environmental variation on body size, with some evidence that elevation constrains the evolution of song peak frequency. Our results demonstrate that morphology has an overwhelming influence on birdsong, in support of the morphological constraint hypothesis, with the environment playing a secondary role generally via body size rather than habitat structure. These results suggest that changing body size (a consequence of both global effects such as climate change and local effects such as habitat transformation) will substantially influence the nature of birdsong.

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.

The impacts of fine-tuning, phylogenetic distance, and sample size on big-data bioacoustics

Vocalizations in animals, particularly birds, are critically important behaviors that influence their reproductive fitness. While recordings of bioacoustic data have been captured and stored in collections for decades, the automated extraction of data from these recordings has only recently been facilitated by artificial intelligence methods. These have yet to be evaluated with respect to accuracy of different automation strategies and features. Here, we use a recently published machine learning framework to extract syllables from ten bird species ranging in their phylogenetic relatedness from 1 to 85 million years, to compare how phylogenetic relatedness influences accuracy. We also evaluate the utility of applying trained models to novel species. Our results indicate that model performance is best on conspecifics, with accuracy progressively decreasing as phylogenetic distance increases between taxa. However, we also find that the application of models trained on multiple distantly related species can improve the overall accuracy to levels near that of training and analyzing a model on the same species. When planning big-data bioacoustics studies, care must be taken in sample design to maximize sample size and minimize human labor without sacrificing accuracy.

Species-specific song responses emerge as a by-product of tuning to the local dialect

Oscine birds preferentially respond to certain sounds over others from an early age, which focuses subsequent learning onto sexually relevant songs.^1,2,3 Songs vary both across species and, due to cultural evolution, among populations of the same species. As a result, early song responses are expected to be shaped by selection both to avoid the fitness costs of cross-species learning⁴ and to promote learning of population-typical songs.⁵ These sources of selection are not mutually exclusive but can result in distinct geographic patterns of song responses in juvenile birds: if the risks of interspecific mating are the main driver of early song discrimination, then discrimination should be strongest where closely related species co-occur.⁴ In contrast, if early discrimination primarily facilitates learning local songs, then it should be tuned to songs typical of the local dialect.^5,6,7 Here, we experimentally assess the drivers of song discrimination in nestling pied flycatchers (Ficedula hypoleuca). We first demonstrate that early discrimination against the songs of the closely related collared flycatcher (F. albicollis) is not strongly affected by co-occurrence. Second, across six European populations, we show that nestlings' early song responses are tuned to their local song dialect and that responses to the songs of collared flycatchers are similarly weak as to those of other conspecific dialects. Taken together, these findings provide clear experimental support for the hypothesis that cultural evolution, in conjunction with associated learning predispositions, drives the emergence of pre-mating reproductive barriers.

Evolutionary endocrinology and the problem of Darwin's tangled bank

Like Darwin's tangled bank of biodiversity, the endocrine mechanisms that give rise to phenotypic diversity also exhibit nearly endless forms. This tangled bank of mechanistic diversity can prove problematic as we seek general principles on the role of endocrine mechanisms in phenotypic evolution. A key unresolved question is therefore: to what degree are specific endocrine mechanisms re-used to bring about replicated phenotypic evolution? Related areas of inquiry are booming in molecular ecology, but behavioral traits are underrepresented in this literature. Here, I leverage the rich comparative tradition in evolutionary endocrinology to evaluate whether and how certain mechanisms may be repeated hotspots of behavioral evolutionary change. At one extreme, mechanisms may be parallel, such that evolution repeatedly uses the same gene or pathway to arrive at multiple independent (or, convergent) origins of a particular behavioral trait. At the other extreme, the building blocks of behavior may be unique, such that outwardly similar phenotypes are generated via lineage-specific mechanisms. This review synthesizes existing case studies, phylogenetic analyses, and experimental evolutionary research on mechanistic parallelism in animal behavior. These examples show that the endocrine building blocks of behavior have some elements of parallelism across replicated evolutionary events. However, support for parallelism is variable among studies, at least some of which relates to the level of complexity at which we consider sameness (i.e. pathway vs. gene level). Moving forward, we need continued experimentation and better testing of neutral models to understand whether, how - and critically, why - mechanism A is used in one lineage and mechanism B is used in another. We also need continued growth of large-scale comparative analyses, especially those that can evaluate which endocrine parameters are more or less likely to undergo parallel evolution alongside specific behavioral traits. These efforts will ultimately deepen understanding of how and why hormone-mediated behaviors are constructed the way that they are.

Gaia as Solaris: An Alternative Default Evolutionary Trajectory

Now that we know that Earth-like planets are ubiquitous in the universe, as well as that most of them are much older than the Earth, it is justified to ask to what extent evolutionary outcomes on other such planets are similar, or indeed commensurable, to the outcomes we perceive around us. In order to assess the degree of specialty or mediocrity of our trajectory of biospheric evolution, we need to take into account recent advances in theoretical astrobiology, in particular (i) establishing the history of habitable planets' formation in the Galaxy, and (ii) understanding the crucial importance of "Gaian" feedback loops and temporal windows for the interaction of early life with its physical environment. Hereby we consider an alternative macroevolutionary pathway that may result in tight functional integration of all sub-planetary ecosystems, eventually giving rise to a true superorganism at the biospheric level. The blueprint for a possible outcome of this scenario has been masterfully provided by the great Polish novelist Stanisław Lem in his 1961 novel Solaris. In fact, Solaris offers such a persuasive and powerful case for an "extremely strong" Gaia hypothesis that it is, arguably, high time to investigate it in a discursive astrobiological and philosophical context. In addition to novel predictions in the domain of potentially detectable biosignatures, some additional cognitive and heuristic benefits of studying such extreme cases of functional integration are briefly discussed.

The dynamics of introgression across an avian radiation

Hybridization and resulting introgression can play both a destructive and a creative role in the evolution of diversity. Thus, characterizing when and where introgression is most likely to occur can help us understand the causes of diversification dynamics. Here, we examine the prevalence of and variation in introgression using phylogenomic data from a large (1300+ species), geographically widespread avian group, the suboscine birds. We first examine patterns of gene tree discordance across the geographic distribution of the entire clade. We then evaluate the signal of introgression in a subset of 206 species triads using Patterson's D‐statistic and test for associations between introgression signal and evolutionary, geographic, and environmental variables. We find that gene tree discordance varies across lineages and geographic regions. The signal of introgression is highest in cases where species occur in close geographic proximity and in regions with more dynamic climates since the Pleistocene. Our results highlight the potential of phylogenomic datasets for examining broad patterns of hybridization and suggest that the degree of introgression between diverging lineages might be predictable based on the setting in which they occur.

A machine learning approach for classifying and quantifying acoustic diversity

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

A Call to Expand Avian Vocal Development Research

Birds are our best models to understand vocal learning – a vocal production ability guided by auditory feedback, which includes human language. Among all vocal learners, songbirds have the most diverse life histories, and some aspects of their vocal learning ability are well-known, such as the neural substrates and vocal control centers, through vocal development studies. Currently, species are classified as either vocal learners or non-learners, and a key difference between the two is the development period, extended in learners, but short in non-learners. But this clear dichotomy has been challenged by the vocal learning continuum hypothesis. One way to address this challenge is to examine both learners and canonical non-learners and determine whether their vocal development is dichotomous or falls along a continuum. However, when we examined the existing empirical data we found that surprisingly few species have their vocal development periods documented. Furthermore, we identified multiple biases within previous vocal development studies in birds, including an extremely narrow focus on (1) a few model species, (2) oscines, (3) males, and (4) songs. Consequently, these biases may have led to an incomplete and possibly erroneous conclusions regarding the nature of the relationships between vocal development patterns and vocal learning ability. Diversifying vocal development studies to include a broader range of taxa is urgently needed to advance the field of vocal learning and examine how vocal development patterns might inform our understanding of vocal learning.

The Bogert effect, a factor in evolution

Behavior is one of the major architects of evolution: by behaviorally modifying how they interact with their environments, organisms can influence natural selection, amplifying it in some cases and dampening it in others. In one of the earliest issues of Evolution, Charles Bogert proposed that regulatory behaviors (namely thermoregulation) shield organisms from selection and limit physiological evolution. Here, I trace the history surrounding the origin of this concept (now known as the "Bogert effect" or "behavioral inertia"), and its implications for physiological and evolutionary research throughout the 20th century. A key follow-up study in the early 21st century galvanized renewed interest in Bogert's classic ideas, and established a focus on slowdowns in the rate of evolution in response to regulatory behaviors. I illustrate recent progress on the Bogert effect in evolutionary research, and discuss the ecological variables that predict whether and how strongly the phenomenon unfolds. Based on these discoveries, I provide hypotheses for the Bogert effect across several scales: patterns of trait evolution within and among groups of species, spatial effects on the phenomenon, and its importance for speciation. I also discuss the inherent link between behavioral inertia and behavioral drive through an empirical case study linking the phenomena. Modern comparative approaches can help put the macroevolutionary implications of behavioral buffering to the test: I describe progress to date, and areas ripe for future investigation. Despite many advances, bridging microevolutionary processes with macroevolutionary patterns remains a persistent gap in our understanding of the Bogert effect, leaving wide open many avenues for deeper exploration.

Ecology and behavior predict an evolutionary trade-off between song complexity and elaborate plumages in antwrens (Aves, Thamnophilidae)

The environment can impose constraints on signal transmission properties such that signals should evolve in predictable directions (Sensory Drive Hypothesis). However, behavioral and ecological factors can limit investment in more than one sensory modality leading to a trade-off in use of different signals (Transfer Hypothesis). In birds, there is mixed evidence for both sensory drive and transfer hypothesis. Few studies have tested sensory drive while also evaluating the transfer hypothesis, limiting understanding of the relative roles of these processes in signal evolution. Here, we assessed both hypotheses using acoustic and visual signals in male and female antwrens (Thamnophilidae), a species-rich group that inhabits diverse environments and exhibits behaviors, such as mixed-species flocking, that could limit investment in different signal modalities. We uncovered significant effects of habitat (sensory drive) and mixed-species flocking behavior on both sensory modalities, and we revealed evolutionary trade-offs between song and plumage complexity, consistent with the transfer hypothesis. We also showed sex- and trait-specific responses in visual signals that suggest both natural and social selection play an important role in the evolution of sexual dimorphism. Altogether, these results support the idea that environmental (sensory drive) and behavioral pressures (social selection) shape signal evolution in antwrens.

Ongoing production of low-fitness hybrids limits range overlap between divergent cryptic species

Contact zones between recently diverged taxa provide opportunities to examine the causes of reproductive isolation and the processes that determine whether two species can coexist over a broad region. The Pacific wren (Troglodytes pacificus) and winter wren (Troglodytes hiemalis) are two morphologically similar songbirds that started diverging about 4 million years ago, older than most sister species pairs of temperate songbirds. The ranges of these species come into narrow contact in western Canada, where the two species remain distinct. To assess evidence for differentiation, hybridization and introgression in this system, we examined variation in over 250,000 single nucleotide polymorphism markers distributed across the genome. The two species formed highly divergent genetic clusters, consistent with long-term differentiation. In a set of 75 individuals, two first-generation hybrids (i.e., F₁ 's) were detected, indicating only moderate levels of assortative mating between these taxa. We found no recent backcrosses or other evidence of recent breeding success of F₁ 's, indicating very low or zero fitness of F₁  hybrids. Examination of genomic variation shows evidence for only a single backcrossing event many generations ago. The moderate rate of hybridization combined with very low F₁  hybrid fitness is expected to result in a population sink in the contact zone, largely explaining the narrow overlap of the two species. If such dynamics are common in nature, they could explain the narrow range overlap often observed between pairs of closely related species.

An Unbiased Molecular Approach Using 3'-UTRs Resolves the Avian Family-Level Tree of Life

Presumably, due to a rapid early diversification, major parts of the higher-level phylogeny of birds are still resolved controversially in different analyses or are considered unresolvable. To address this problem, we produced an avian tree of life, which includes molecular sequences of one or several species of ∼90% of the currently recognized family-level taxa (429 species, 379 genera) including all 106 family-level taxa of the nonpasserines and 115 of the passerines (Passeriformes). The unconstrained analyses of noncoding 3-prime untranslated region (3′-UTR) sequences and those of coding sequences yielded different trees. In contrast to the coding sequences, the 3′-UTR sequences resulted in a well-resolved and stable tree topology. The 3′-UTR contained, unexpectedly, transcription factor binding motifs that were specific for different higher-level taxa. In this tree, grebes and flamingos are the sister clade of all other Neoaves, which are subdivided into five major clades. All nonpasserine taxa were placed with robust statistical support including the long-time enigmatic hoatzin (Opisthocomiformes), which was found being the sister taxon of the Caprimulgiformes. The comparatively late radiation of family-level clades of the songbirds (oscine Passeriformes) contrasts with the attenuated diversification of nonpasseriform taxa since the early Miocene. This correlates with the evolution of vocal production learning, an important speciation factor, which is ancestral for songbirds and evolved convergent only in hummingbirds and parrots. As 3′-UTR-based phylotranscriptomics resolved the avian family-level tree of life, we suggest that this procedure will also resolve the all-species avian tree of life

Defining the multidimensional phenotype: New opportunities to integrate the behavioral ecology and behavioral neuroscience of vocal learning

Vocal learning has evolved independently in several lineages. This complex cognitive trait is commonly treated as binary: species either possess or lack it. This view has been a useful starting place to examine the origins of vocal learning, but is also incomplete and potentially misleading, as specific components of the vocal learning program - such as the timing, extent and nature of what is learned - vary widely among species. In our review we revive an idea first proposed by Beecher and Brenowitz (2005) by describing six dimensions of vocal learning: (1) which vocalizations are learned, (2) how much is learned, (3) when it is learned, (4) who it is learned from, (5) what is the extent of the internal template, and (6) how is the template integrated with social learning and innovation. We then highlight key examples of functional and mechanistic work on each dimension, largely from avian taxa, and discuss how a multi-dimensional framework can accelerate our understanding of why vocal learning has evolved, and how brains became capable of this important behaviour.

Species diversification and ecomorphological evolution in the radiation of tanagers (Passeriformes: Thraupidae)

Ecological opportunity is hypothesized to cause an early burst of species diversification and trait evolution followed by a slowdown in diversification rates as niches are filled. Nonetheless, few studies have tested these predictions empirically with ecomorphological data at the large spatial scales relevant to most of biodiversity. Tanagers (Passeriformes: Thraupidae), the largest family of songbirds, show an early burst of species diversification and provide an excellent opportunity to test one of the hallmarks of adaptive radiation: rapid ecomorphological evolution. Here, we test for an early-burst pattern of a resource-exploiting trait (bill morphology) across the radiation of tanagers using a time-calibrated molecular phylogeny and high-resolution three-dimensional surface scans of bill structure from museum study skins. Using recently developed methods of multivariate trait evolution, we find evidence for a rapid burst of bill shape evolution early in the radiation of tanagers, followed by a subsequent decrease in rates toward the present. Likewise, we show that morphological disparity is distributed among (rather than within) subclades, indicating that most of the observed bill shape disparity evolved early in the radiation of tanagers and has slowed through time. The diversification dynamics of tanagers match patterns expected from adaptive radiation and the filling of ecomorphospace.

The burgeoning reach of animal culture

Culture can be defined as all that is learned from others and is repeatedly transmitted in this way, forming traditions that may be inherited by successive generations. This cultural form of inheritance was once thought specific to humans, but research over the past 70 years has instead revealed it to be widespread in nature, permeating the lives of a diversity of animals, including all major classes of vertebrates. Recent studies suggest that culture's reach may extend also to invertebrates-notably, insects. In the present century, the reach of animal culture has been found to extend across many different behavioral domains and to rest on a suite of social learning processes facilitated by a variety of selective biases that enhance the efficiency and adaptiveness of learning. Far-reaching implications, for disciplines from evolutionary biology to anthropology and conservation policies, are increasingly being explored.

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.

Male-biased sexual selection, but not sexual dichromatism, predicts speciation in birds

Sexual selection is thought to shape phylogenetic diversity by affecting speciation or extinction rates. However, the net effect of sexual selection on diversification is hard to predict because many of the hypothesized effects on speciation or extinction have opposing signs and uncertain magnitudes. Theoretical work also suggests that the net effect of sexual selection on diversification should depend strongly on ecological factors, though this prediction has seldom been tested. Here, we test whether variation in sexual selection can predict speciation and extinction rates across passerine birds (up to 5812 species, covering most genera) and whether this relationship is mediated by environmental factors. Male-biased sexual selection, and specifically sexual size dimorphism, predicted two of the three measures of speciation rates that we examined. The link we observed between sexual selection and speciation was independent of environmental variability, though species with smaller ranges had higher speciation rates. There was no association between any proxies of sexual selection and extinction rate. Our findings support the view that male-biased sexual selection, as measured by frequent predictors of male-male competition, has shaped diversification in the largest radiation of birds.

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

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

Differential geographic patterns in song components of male Albert's lyrebirds

Geographic variation in bird song has received much attention in evolutionary studies, yet few consider components within songs that may be subject to different constraints and follow different evolutionary trajectories. Here, we quantify patterns of geographic variation in the socially transmitted "whistle" song of Albert's lyrebirds (Menura alberti), an oscine passerine renowned for its remarkable vocal abilities. Albert's lyrebirds are confined to narrow stretches of suitable habitat in Australia, allowing us to map likely paths of cultural transmission using a species distribution model and least cost paths. We use quantitative methods to divide the songs into three components present in all study populations: the introductory elements, the song body, and the final element. We compare geographic separation between populations with variation in these components as well as the full song. All populations were distinguishable by song, and songs varied according to the geographic distance between populations. However, within songs, only the introductory elements and song body could be used to distinguish among populations. The song body and final element changed with distance, but the introductory elements varied independently of geographic separation. These differing geographic patterns of within-song variation are unexpected, given that the whistle song components are always produced in the same sequence and may be perceived as a temporally discrete unit. Knowledge of such spatial patterns of within-song variation enables further work to determine possible selective pressures and constraints acting on each song component and provides spatially explicit targets for preserving cultural diversity. As such, our study highlights the importance for science and conservation of investigating spatial patterns within seemingly discrete behavioral traits at multiple levels of organization.

Ecological and morphological determinants of evolutionary diversification in Darwin's finches and their relatives

Darwin's finches are a classic example of adaptive radiation, a process by which multiple ecologically distinct species rapidly evolve from a single ancestor. Such evolutionary diversification is typically explained by adaptation to new ecological opportunities. However, the ecological diversification of Darwin's finches following their dispersal to Galápagos was not matched on the same archipelago by other lineages of colonizing land birds, which diversified very little in terms of both species number and morphology. To better understand the causes underlying the extraordinary variation in Darwin's finches, we analyze the evolutionary dynamics of speciation and trait diversification in Thraupidae, including Coerebinae (Darwin's finches and relatives) and, their closely related clade, Sporophilinae. For all traits, we observe an early pulse of speciation and morphological diversification followed by prolonged periods of slower steady-state rates of change. The primary exception is the apparent recent increase in diversification rate in Darwin's finches coupled with highly variable beak morphology, a potential key factor explaining this adaptive radiation. Our observations illustrate how the exploitation of ecological opportunity by contrasting means can produce clades with similarly high diversification rate yet strikingly different degrees of ecological and morphological differentiation.

Avian Diversity: Speciation, Macroevolution, and Ecological Function

The origin, distribution, and function of biological diversity are fundamental themes of ecology and evolutionary biology. Research on birds has played a major role in the history and development of these ideas, yet progress was for many decades limited by a focus on patterns of current diversity, often restricted to particular clades or regions. Deeper insight is now emerging from a recent wave of integrative studies combining comprehensive phylogenetic, environmental, and functional trait data at unprecedented scales. We review these empirical advances and describe how they are reshaping our understanding of global patterns of bird diversity and the processes by which it arises, with implications for avian biogeography and functional ecology. Further expansion and integration of data sets may help to resolve longstanding debates about the evolutionary origins of biodiversity and offer a framework for understanding and predicting the response of ecosystems to environmental change.

Heterogeneous relationships between rates of speciation and body size evolution across vertebrate clades

Several theories predict that rates of phenotypic evolution should be related to the rate at which new lineages arise. However, drawing general conclusions regarding the coupling between these fundamental evolutionary rates has been difficult due to the inconsistent nature of previous results combined with uncertainty over the most appropriate methodology with which to investigate such relationships. Here we propose and compare the performance of several different approaches for testing associations between lineage-specific rates of speciation and phenotypic evolution using phylogenetic data. We then use the best-performing method to test relationships between rates of speciation and body size evolution in five major vertebrate clades (amphibians, birds, mammals, ray-finned fish and squamate reptiles) at two phylogenetic scales. Our results provide support for the long-standing view that rates of speciation and morphological evolution are generally positively related at broad macroevolutionary scales, but they also reveal a substantial degree of heterogeneity in the strength and direction of these associations at finer scales across the vertebrate tree of life.

Evolution of communication signals and information during species radiation

Communicating species identity is a key component of many animal signals. However, whether selection for species recognition systematically increases signal diversity during clade radiation remains debated. Here we show that in woodpecker drumming, a rhythmic signal used during mating and territorial defense, the amount of species identity information encoded remained stable during woodpeckers’ radiation. Acoustic analyses and evolutionary reconstructions show interchange among six main drumming types despite strong phylogenetic contingencies, suggesting evolutionary tinkering of drumming structure within a constrained acoustic space. Playback experiments and quantification of species discriminability demonstrate sufficient signal differentiation to support species recognition in local communities. Finally, we only find character displacement in the rare cases where sympatric species are also closely related. Overall, our results illustrate how historical contingencies and ecological interactions can promote conservatism in signals during a clade radiation without impairing the effectiveness of information transfer relevant to inter-specific discrimination.

Animal signals often encode information on the emitter’s species identity. Using woodpecker drumming as a model, here the authors show that limited signal divergence during a clade radiation does not impair species discrimination, as long as the signals are adapted to local ecological requirements.

Generation, Coordination, and Evolution of Neural Circuits for Vocal Communication

In many species, vocal communication is essential for coordinating social behaviors including courtship, mating, parenting, rivalry, and alarm signaling. Effective communication requires accurate production, detection, and classification of signals, as well as selection of socially appropriate responses. Understanding how signals are generated and how acoustic signals are perceived is key to understanding the neurobiology of social behaviors. Here we review our long-standing research program focused on Xenopus, a frog genus which has provided valuable insights into the mechanisms and evolution of vertebrate social behaviors. In Xenopus laevis, vocal signals differ between the sexes, through development, and across the genus, reflecting evolutionary divergence in sensory and motor circuits that can be interrogated mechanistically. Using two ex vivo preparations, the isolated brain and vocal organ, we have identified essential components of the vocal production system: the sexually differentiated larynx at the periphery, and the hindbrain vocal central pattern generator (CPG) centrally, that produce sex- and species-characteristic sound pulse frequencies and temporal patterns, respectively. Within the hindbrain, we have described how intrinsic membrane properties of neurons in the vocal CPG generate species-specific vocal patterns, how vocal nuclei are connected to generate vocal patterns, as well as the roles of neurotransmitters and neuromodulators in activating the circuit. For sensorimotor integration, we identified a key forebrain node that links auditory and vocal production circuits to match socially appropriate vocal responses to acoustic features of male and female calls. The availability of a well supported phylogeny as well as reference genomes from several species now support analysis of the genetic architecture and the evolutionary divergence of neural circuits for vocal communication. Xenopus thus provides a vertebrate model in which to study vocal communication at many levels, from physiology, to behavior, and from development to evolution. As one of the most comprehensively studied phylogenetic groups within vertebrate vocal communication systems, Xenopus provides insights that can inform social communication across phyla.

Independent evolution of song diversity and song motor performance in canaries, goldfinches and allies indicates clade-specific trade-offs in birdsong

The diversity and the motor performance of birdsongs can both be sexually selected. In wood warblers, most species with high motor performance sing a greater proportion of trills, presumably to advertise performance, and thus have lower syllable diversity. We tested if this trade-off between motor performance and syllable diversity extends to canaries, goldfinches and allies, a clade with much longer and more varied songs. We assembled a molecular phylogeny and inferred song motor performance based on the speed of frequency modulation either in trills or in within-song intervals. The two metrics of performance were positively, but only mildly, related across species. While performance evaluated in intervals had high phylogenetic signal, performance evaluated in trills changed independently of phylogeny and was constrained by body size. Species in densely vegetated habitats sang fewer trills, but did not differ in motor performance. Contrary to wood warblers, song motor performance did not predict the proportion of trilled syllables nor within-song syllable diversity, perhaps because large differences in the song duration of canaries, goldfinches and allies prevent trills from severely compromising syllable diversity. Opposed results in wood warblers and in these finches indicate the existence of clade-specific trade-offs in the evolution of birdsong.

The phylogenetic significance of the morphology of the syrinx, hyoid and larynx, of the southern cassowary, Casuarius casuarius (Aves, Palaeognathae)

BACKGROUND

Palaeognathae is a basal clade within Aves and include the large and flightless ratites and the smaller, volant tinamous. Although much research has been conducted on various aspects of palaeognath morphology, ecology, and evolutionary history, there are still areas which require investigation. This study aimed to fill gaps in our knowledge of the Southern Cassowary, Casuarius casuarius, for which information on the skeletal systems of the syrinx, hyoid and larynx is lacking - despite these structures having been recognised as performing key functional roles associated with vocalisation, respiration and feeding. Previous research into the syrinx and hyoid have also indicated these structures to be valuable for determining evolutionary relationships among neognath taxa, and thus suggest they would also be informative for palaeognath phylogenetic analyses, which still exhibits strong conflict between morphological and molecular trees.

RESULTS

The morphology of the syrinx, hyoid and larynx of C. casuarius is described from CT scans. The syrinx is of the simple tracheo-bronchial syrinx type, lacking specialised elements such as the pessulus; the hyoid is relatively short with longer ceratobranchials compared to epibranchials; and the larynx is comprised of entirely cartilaginous, standard avian anatomical elements including a concave, basin-like cricoid and fused cricoid wings. As in the larynx, both the syrinx and hyoid lack ossification and all three structures were most similar to Dromaius. We documented substantial variation across palaeognaths in the skeletal character states of the syrinx, hyoid, and larynx, using both the literature and novel observations (e.g. of C. casuarius). Notably, new synapomorphies linking Dinornithiformes and Tinamidae are identified, consistent with the molecular evidence for this clade. These shared morphological character traits include the ossification of the cricoid and arytenoid cartilages, and an additional cranial character, the articulation between the maxillary process of the nasal and the maxilla.

CONCLUSION

Syrinx, hyoid and larynx characters of palaeognaths display greater concordance with molecular trees than do other morphological traits. These structures might therefore be less prone to homoplasy related to flightlessness and gigantism, compared to typical morphological traits emphasised in previous phylogenetic studies.

How phenotypic matching based on neutral mating cues enables speciation in locally adapted populations

Maynard Smith's (American Naturalist, 1966, 100, 637) suggestion that in some cases a prerequisite for speciation is the existence of local ecological adaptations has not received much attention to date. Here, we test the hypothesis using a model like that of Maynard Smith but differing in the way animals disperse between niches. In previous studies, males disperse randomly between niches but females stay put in their natal niche. As a first step toward generalizing the model, we here analyze the case that equal proportions of the two sexes disperse between niches before breeding. Supporting Maynard Smith's (1966) hypothesis, we find that once local adaptations are established, a neutral mating cue at an independent locus can rapidly enable speciation in populations with a suitable mechanism for phenotype matching. We find that stable ecological polymorphisms are relatively insensitive to the strength of selection, but depend crucially on the extent of dispersal between niches, with a threshold of ~5% if population sizes in two niches are equal. At higher levels of dispersal, ecological differentiation is lost. These results contrast with those of earlier studies and shed light on why parapatric speciation is limited by the extent of gene flow. Our testable model provides a candidate explanation for the rapid speciation rates, diversity of appearance and occurrence of "species flocks" observed among some African cichlids and neotropical birds and may also have implications for the occurrence of punctuational change on phylogenies.

Character displacement of a learned behaviour and its implications for ecological speciation

Cultural evolution may accelerate population divergence and speciation, though most support for this hypothesis is restricted to scenarios of allopatric speciation driven by random cultural drift. By contrast, the role of cultural evolution in non-allopatric speciation (i.e. speciation with gene flow) has received much less attention. One clade in which cultural evolution may have figured prominently in speciation with gene flow includes the conifer-seed-eating finches in the red crossbill (Loxia curvirostra) complex. Here we focus on Cassia crossbills (Loxia sinesciuris; an ecotype recently split taxonomically from red crossbills) that learn social contact calls from their parents. Previous work found that individuals modify their calls throughout life such that they become increasingly divergent from a closely related, sympatric red crossbill ecotype. This open-ended modification of calls could lead to character displacement if it causes population-level divergence in call structure that, in turn, reduces (maladaptive) heterospecific flocking. Heterospecific flocking is maladaptive because crossbills use public information from flockmates to assess resource quality, and feeding rates are depressed when flockmates differ in their ability to exploit a shared resource (i.e. when flockmates are heterospecifics). We confirm the predictions of character displacement by documenting substantial population-level divergence in Cassia crossbill call structure over just two decades and by using field experiments to demonstrate that Cassia and red crossbills differentially respond to these evolved differences in call structure, reducing heterospecific flock formation. Moreover, because crossbills choose mates from within flocks, a reduction in heterospecific flocking should increase assortative mating and may have been critical for speciation of Cassia crossbills in the face of ongoing gene flow in as few as 5000 years. Our results provide evidence for a largely neglected yet potentially widespread mechanism by which reproductive isolation can evolve between sympatric lineages as a byproduct of adaptive cultural evolution.

The reach of gene-culture coevolution in animals

Culture (behaviour based on socially transmitted information) is present in diverse animal species, yet how it interacts with genetic evolution remains largely unexplored. Here, we review the evidence for gene-culture coevolution in animals, especially birds, cetaceans and primates. We describe how culture can relax or intensify selection under different circumstances, create new selection pressures by changing ecology or behaviour, and favour adaptations, including in other species. Finally, we illustrate how, through culturally mediated migration and assortative mating, culture can shape population genetic structure and diversity. This evidence suggests strongly that animal culture plays an important evolutionary role, and we encourage explicit analyses of gene-culture coevolution in nature.

Song Feature Specific Analysis of Isolate Song Reveals Interspecific Variation in Learned Components

Studies of avian vocal development without exposure to conspecific song have been conducted in many passerine species, and the resultant isolate song is often interpreted to represent an expression of the genetic code for conspecific song. There is wide recognition that vocal learning exists in oscine songbirds, but vocal learning has only been thoroughly investigated in a few model species, resulting in a narrow view of birdsong learning. By extracting acoustic signals from published spectrograms, we have reexamined the findings of isolate studies with a universally applicable semi-automated quantitative analysis regimen. When song features were analyzed in light of three different production aspects (respiratory, syringeal, and central programming of sequence), all three show marked interspecific variability in how close isolate song features are to normal. This implies that song learning mechanisms are more variable than is commonly recognized. Our results suggest that the interspecific variation shows no readily observable pattern reflecting phylogeny, which has implications for understanding the mechanisms behind the evolution of avian vocal communication. We emphasize that song learning in passerines provides an excellent opportunity to investigate the evolution of a complex, plastic trait from a phylogenetic perspective.

Sexual selection predicts the rate and direction of colour divergence in a large avian radiation

Sexual selection is proposed to be a powerful driver of phenotypic evolution in animal systems. At macroevolutionary scales, sexual selection can theoretically drive both the rate and direction of phenotypic evolution, but this hypothesis remains contentious. Here, we find that differences in the rate and direction of plumage colour evolution are predicted by a proxy for sexual selection intensity (plumage dichromatism) in a large radiation of suboscine passerine birds (Tyrannida). We show that rates of plumage evolution are correlated between the sexes, but that sexual selection has a strong positive effect on male, but not female, interspecific divergence rates. Furthermore, we demonstrate that rapid male plumage divergence is biased towards carotenoid-based (red/yellow) colours widely assumed to represent honest sexual signals. Our results highlight the central role of sexual selection in driving avian colour divergence, and reveal the existence of convergent evolutionary responses of animal signalling traits under sexual selection.

What factors explain variation in the pace and trajectory of evolutionary divergence between lineages? Here, the authors show that a proxy measure for sexual selection intensity predicts both the rate and direction of plumage colour evolution in a diverse radiation of New World passerine birds.

Speciation Rate Is Independent of the Rate of Evolution of Morphological Size, Shape, and Absolute Morphological Specialization in a Large Clade of Birds

Whether ecological differences between species evolve in parallel with lineage diversification is a fundamental issue in evolutionary biology. These processes might be connected if conditions that favor the proliferation of species, such as release from competitors, facilitate the evolution of novel ecological relationships. Despite this, phylogenetic studies do not consistently identify such a connection. Conversely, if higher diversity caused species to become increasingly specialized ecologically, then lineage diversification might become dissociated from ecological diversification. In this analysis, we ask whether the rate of lineage diversification in a large clade of birds is correlated with morphological specialization and with rates of morphological evolution. We find that morphological variation is related to species richness within clades but that rates of morphological evolution are decoupled from the rate of lineage diversification. Additionally, morphological specialization within lineages is independent of the rate at which lineages diversify, with the results apparently robust against false negative inference. This dissociation is likely a consequence of the major ecomorphological differences between avian clades arising early in their evolutionary history, with comparatively little variation added subsequently, while avian diversification has been driven predominantly by geographic isolation and sexual selection. Accordingly, biodiversity appears to be limited by the extent to which taxa can subdivide exploited regions of ecological space and not just overall ecological opportunity.

Elevational differentiation accelerates trait evolution but not speciation rates in Amazonian birds

The importance of ecologically mediated divergent selection in accelerating trait evolution has been poorly studied in the most species-rich biome of the planet, the continental Neotropics. We performed macroevolutionary analyses of trait divergence and diversification rates across closely related pairs of Andean and Amazonian passerine birds, to assess whether the difference in elevational range separating species pairs - a proxy for the degree of ecological divergence - influences the speed of trait evolution and diversification rates. We found that elevational differentiation is associated with faster divergence of song frequency, a trait important for pre-mating isolation, and several morphological traits, which may contribute to extrinsic post-mating isolation. However, elevational differentiation did not increase recent speciation rates, possibly due to early bursts of diversification during the uplift of the eastern Andes followed by a slow-down in speciation rate. Our results suggest that ecological differentiation may speed up trait evolution, but not diversification of Neotropical birds.

Genomic divergence in allopatric Northern Cardinals of the North American warm deserts is linked to behavioral differentiation

Biogeographic barriers are considered important in initiating speciation through geographic isolation, but they rarely indiscriminately and completely reduce gene flow across entire communities. Explicitly demonstrating which factors are associated with gene-flow levels across barriers would help elucidate how speciation is initiated and isolation maintained. Here, we investigated the association of behavioral isolation on population differentiation in Northern Cardinals (Cardinalis cardinalis) distributed across the Cochise Filter Barrier, a region of transitional habitat which separates the Sonoran and Chihuahuan deserts of North America. Using genomewide markers, we modeled demographic history by fitting the data to isolation and isolation-with-migration models. The best-fit model indicated that desert populations diverged in the Pleistocene with low, historic, and asymmetric gene flow across the barrier. We then tested behavioral isolation using reciprocal call-broadcast experiments to compare song recognition between deserts, controlling for song dialect changes within deserts. We found that male Northern Cardinals in both deserts were most aggressive to local songs and failed to recognize across-barrier songs. A correlation of genomic differentiation and strong song discrimination is consistent with a model where speciation is initiated across a barrier and maintained by behavioral isolation.

Assortative Mating by an Obliquely Transmitted Local Cultural Trait Promotes Genetic Divergence: A Model

The effect of learned culture (e.g., birdsong dialects and human languages) on genetic divergence is unclear. Previous theoretical research suggests that because oblique learning allows phenotype transmission from individuals with no offspring to an unrelated individual in the next generation, the effect of sexual selection on the learned trait is masked. However, I propose that migration and spatially constrained learning can form statistical associations between cultural and genetic traits, which may allow selection on the cultural traits to indirectly affect the genetic traits. Here, I build a population genetic model that allows such statistical associations to form and find that sexual selection and divergent selection on the cultural trait can indeed help maintain genetic divergence through such statistical associations, while selection against genetic hybrids does not affect cultural trait divergence. Furthermore, I find that even when the cultural trait changes over time due to drift and mutation, it can still help maintain genetic divergence. These results suggest the role of obliquely transmitted traits in evolution may be underrated, and the lack of one-to-one associations between cultural and genetic traits may not be sufficient to disprove the role of culture in genetic divergence.

Behavioral Isolation and Incipient Speciation in Birds

Behavioral changes, such as those involved in mating, foraging, and migration, can generate reproductive barriers between populations. Birds, in particular, are known for their great diversity in these behaviors, and so behavioral isolation is often proposed to be the major driver of speciation. Here, we review empirical evidence to evaluate the importance of behavioral isolation in the early stages of avian speciation. Experimentally measured mating preferences indicate that changes in mating behavior can result in premating barriers, with their strength depending on the extent of divergence in mating signals. Differences in migratory and foraging behavior also can play important roles in generating reproductive barriers in the early stages of speciation. However, because premating behavioral isolation is imperfect, extrinsic postzygotic barriers, in the form of selection against hybrids having intermediate phenotypes, also play an important role in avian diversification, especially in completing the speciation process.