Transcriptional regulatory divergence underpinning species-specific learned vocalization in songbirds

Abstract

Learning of most motor skills is constrained in a species-specific manner. However, the proximate mechanisms underlying species-specific learned behaviors remain poorly understood. Songbirds acquire species-specific songs through learning, which is hypothesized to depend on species-specific patterns of gene expression in functionally specialized brain regions for vocal learning and production, called song nuclei. Here, we leveraged two closely related songbird species, zebra finch, owl finch, and their interspecific first-generation (F1) hybrids, to relate transcriptional regulatory divergence between species with the production of species-specific songs. We quantified genome-wide gene expression in both species and compared this with allele-specific expression in F1 hybrids to identify genes whose expression in song nuclei is regulated by species divergence in either cis- or trans-regulation. We found that divergence in transcriptional regulation altered the expression of approximately 10% of total transcribed genes and was linked to differential gene expression between the two species. Furthermore, trans-regulatory changes were more prevalent than cis-regulatory and were associated with synaptic formation and transmission in song nucleus RA, the avian analog of the mammalian laryngeal motor cortex. We identified brain-derived neurotrophic factor (BDNF) as an upstream mediator of trans-regulated genes in RA, with a significant correlation between individual variation in BDNF expression level and species-specific song phenotypes in F1 hybrids. This was supported by the fact that the pharmacological overactivation of BDNF receptors altered the expression of its trans-regulated genes in the RA, thus disrupting the learned song structures of adult zebra finch songs at the acoustic and sequence levels. These results demonstrate functional neurogenetic associations between divergence in region-specific transcriptional regulation and species-specific learned behaviors.

The tyranny of phylogeny—A plea for a less dogmatic stance on two‐species comparisons

“…For instance, the identity of differentially expressed genes of androgen and oestrogen‐responsive sites in a motor nucleus of the song control system in brains of canaries ( Serinus canaria ) and zebra finches ( Taeniopygia guttata ) seems to be species‐specific: they express different types of genes to regulate a similar motor output, singing behavior. [ 43 ] Even among zebra finch relatives, the estrildid finches, the type of genes expressed in the song control nuclei during singing differs substantially, [ 44 ] suggesting strong diversification even among close relatives within the songbird clade.…”

Temporal Profile of Brain Gene Expression After Prey Catching Conditioning in an Anuran Amphibian

“…The gene fosb is expected to show an early peak like c-fos (Nestler, 2015) but instead showed only high upregulation at 4 h in B. orientalis. Homer1, which is integral to the regulation of synaptic changes induced by LTP (Chowdhury and Hell, 2018), was not differentially expressed at any time-point after conditioning in B. orientalis, and neither was bdnf, a gene coding for an important neurotrophic factor associated with neurogenesis and longterm memory in mammals and song learning in birds (Lu et al, 2008;Wang et al, 2019). Therefore, despite observing important similarities in IEG expression between B. orientalis and other vertebrates, there were notable differences in that some IEGs showed different temporal patterns of expression while others were not engaged by the learning task used in the present study.…”

Neurogenomic insights into the behavioral and vocal development of the zebra finch

“…By tapping into the existing genetic and behavioral diversity of wild and captive lineages in zebra finches (e.g. Forstmeier et al, 2007 ; Knief et al, 2015 ) to perform comparative avian genomic analyses ( Jarvis et al, 2014 ; Feng et al, 2020 ), interspecific hybridization studies ( Woolley and Sakata, 2019 ; Wang et al, 2019 ), and direct genetic manipulations ( Liu et al, 2015 ; London, 2020 ), the zebra finch shall continue to serve as a focal subject of integrative research into human language-like vocal culture ( Hyland Bruno et al, 2021 ), auditory learning ( Theunissen et al, 2004 ), acoustically-mediated social bonding ( Tokarev et al, 2017 ), and genetic ( Balakrishnan et al, 2010 ) and behavioral (e.g. song) variability ( Lansverk et al, 2019 ; see Box 1 ).…”