Capturing the Effects of Domestication on Vocal Learning Complexity

The genomics of the domestication syndrome in a songbird model species

Many domesticated animals share a syndromic phenotype marked by a suite of traits that include more variable patterns of coloration, reduced stress, aggression, and altered risk-taking and exploratory behaviors relative to their wild counterparts. Roughly 150 years after Darwin's pioneering insight into this phenomenon, reasonable progress has been made in understanding the evolutionary and biological basis of the so-called domesticated phenotype in mammals. However, the extent to which these processes are paralleled in non-mammalian domesticates is scant. Here, we address this knowledge gap by investigating the genetic basis of the domesticated phenotype in the Bengalese finch, a songbird frequently found in pet shops and a popular animal model in the study of learned vocal behaviors. Using whole-genome sequencing and population genomic approaches, we identify strain-specific selection signals in the Bengalee finch and its wild munia ancestor. Our findings suggest that, like in mammals, the evolution of the domestication syndrome in avian species involves a shift in the selective regime, capable of altering brain circuits favoring the dynamic modulation of motivation and reward sensitivity over augmented aggression and stress responses.

Domestication effects on crowing in chickens: variation between wild and captive red junglefowl and domestic white Leghorn and the genetic architecture of crowing vocalizations

The crowing of the male chicken is a charismatic example of vocal display in a bird. It is regarded as the main territorial announcement of the ancestral red junglefowl. The call has been preserved throughout domestication, although several of its elements have been altered. To assess these alterations, we assayed crowing spectrograms from wild and captive-held red junglefowl populations from India, along with two red junglefowl populations held in long-term captivity in Sweden, and a domestic white Leghorn breed. We find consistent differences between the different Indian red junglefowl and the domestic white Leghorn for a range of characteristics, including the duration of the last syllable and the number of formants and their frequency in the last and second-to-last syllable. To analyse the genetic architecture of crowing vocalization, we performed a quantitative trait loci (QTL) experiment using a wild × domestic advanced intercross to identify QTL that explained a large percentage of the variation present for the duration of the last syllable and the number of formants in the second to last syllable. With this study we thus demonstrate consistent differences in red junglefowl and white Leghorn chickens and identify a relatively simple genetic architecture for some of these traits.This article is part of the theme issue 'Unravelling domestication: multi-disciplinary perspectives on human and non-human relationships in the past, present and future'.

The evolution of human music in light of increased prosocial behavior: a new model

Together with language, music is perhaps our most distinctive behavioral trait. Following the lead of evolutionary linguistic research, different hypotheses have been proposed to explain why only humans perform music and how this ability might have evolved in the species. In this paper, we advance a new model of music evolution that builds on the theory of self-domestication, according to which the human phenotype is, at least in part, the outcome of a process similar to mammal domestication, triggered by a progressive reduction in reactive aggression levels in response to environmental changes. In the paper, we specifically argue that changes in aggression management through the course of human cultural evolution can account for the behaviors conducive to the emergence and evolution of music. We hypothesize 4 stages in the evolutionary development of music under the influence of environmental changes and evolution of social organization: starting from musilanguage, 1) proto-music gave rise to 2) personal and private forms of timbre-oriented music, then to 3) small-group ensembles of pitch-oriented music, at first of indefinite and then definite pitch, and finally to 4) collective (tonal) music. These stages parallel what has been hypothesized for languages and encompass the diversity of music types and genres described worldwide. Overall, music complexity emerges in a gradual fashion under the effects of enhanced abilities for cultural niche construction, resulting from the stable trend of reduction in reactive aggression towards the end of the Pleistocene, leading to the rise of hospitality codes, and succeeded by the increase in proactive aggression from the beginning of the Holocene onward. This paper addresses numerous controversies in the literature on the evolution of music by providing a clear structural definition of music, identifying its structural features that distinguish it from oral language, and summarizing the typology of operational functions of music and formats of its transmission. The proposed framework of structural approach to music arms a researcher with means to identify and comparatively analyze different schemes of tonal organization of music, placing them in the context of human social and cultural evolution. Especially valuable is the theory of so-called "personal song", described and analyzed here from ethological, social, cultural, cognitive, and musicological perspectives. Personal song seems to constitute a remnant of the proto-musical transition from animal communication to human music as we know it today. We interlink the emergence of personal song with the evolution of kinship, placing both of them on the timeline of cultural evolution - based on totality of ethnographic, archaeological, anthropological, genetic, and paleoclimatic data.

Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements

Vocal production learning ("vocal learning") is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from the Egyptian fruit bat (Rousettus aegyptiacus) with analyses of the genomes of 215 placental mammals. First, we identified a set of proteins evolving more slowly in vocal learners. Then, we discovered a vocal motor cortical region in the Egyptian fruit bat, an emergent vocal learner, and leveraged that knowledge to identify active cis-regulatory elements in the motor cortex of vocal learners. Machine learning methods applied to motor cortex open chromatin revealed 50 enhancers robustly associated with vocal learning whose activity tended to be lower in vocal learners. Our research implicates convergent losses of motor cortex regulatory elements in mammalian vocal learning evolution.

What made us "hunter-gatherers of words"

This paper makes three interconnected claims: (i) the "human condition" cannot be captured by evolutionary narratives that reduce it to a recent 'cognitive modernity', nor by narratives that eliminates all cognitive differences between us and out closest extinct relatives, (ii) signals from paleogenomics, especially coming from deserts of introgression but also from signatures of positive selection, point to the importance of mutations that impact neurodevelopment, plausibly leading to temperamental differences, which may impact cultural evolutionary trajectories in specific ways, and (iii) these trajectories are expected to affect the language phenotypes, modifying what is being learned and how it is put to use. In particular, I hypothesize that these different trajectories influence the development of symbolic systems, the flexible ways in which symbols combine, and the size and configurations of the communities in which these systems are put to use.

A chromosome-level reference genome and pangenome for barn swallow population genomics

Insights into the evolution of non-model organisms are limited by the lack of reference genomes of high accuracy, completeness, and contiguity. Here, we present a chromosome-level, karyotype-validated reference genome and pangenome for the barn swallow (Hirundo rustica). We complement these resources with a reference-free multialignment of the reference genome with other bird genomes and with the most comprehensive catalog of genetic markers for the barn swallow. We identify potentially conserved and accelerated genes using the multialignment and estimate genome-wide linkage disequilibrium using the catalog. We use the pangenome to infer core and accessory genes and to detect variants using it as a reference. Overall, these resources will foster population genomics studies in the barn swallow, enable detection of candidate genes in comparative genomics studies, and help reduce bias toward a single reference genome.

Did Dog Domestication Contribute to Language Evolution?

Different factors seemingly account for the emergence of present-day languages in our species. Human self-domestication has been recently invoked as one important force favoring language complexity mostly via a cultural mechanism. Because our self-domestication ultimately resulted from selection for less aggressive behavior and increased prosocial behavior, any evolutionary or cultural change impacting on aggression levels is expected to have fostered this process. Here, we hypothesize about a parallel domestication of humans and dogs, and more specifically, about a positive effect of our interaction with dogs on human self-domestication, and ultimately, on aspects of language evolution, through the mechanisms involved in the control of aggression. We review evidence of diverse sort (ethological mostly, but also archeological, genetic, and physiological) supporting such an effect and propose some ways of testing our hypothesis.