Comparative genomics of two Empidonax flycatchers reveal candidate genes for bird song production

Whole-genome-level comparisons of sister taxa that vary in phenotype against a background of high genomic similarity can be used to identify the genomic regions that might underlie their phenotypic differences. In wild birds, this exploratory approach has detected markers associated with plumage coloration, beak and wing morphology, and complex behavioral traits like migration. Here, we use genomic comparisons of two closely related suboscine flycatchers (Empidonax difficilis and E. occidentalis) and their hybrids to search for candidate genes underlying their variation in innate vocal signals. We sequenced the genomes of 20 flycatchers that sang one of two species-specific pure song types and 14 putative hybrid individuals with intermediate song types. In the resulting genomic comparisons, we found six areas of high differentiation that may be associated with variation in nonlearned songs. These narrow regions of genomic differentiation contain a total of 67 described genes, of which three have been previously associated with forms of language impairment and dyslexia in humans and 18 are known to be differentially expressed in the song nuclei regions of the avian brain compared with adjacent parts of the avian brain. This natural experiment therefore may help identify loci associated with song differences that merit further study across bird lineages with both learned and innate vocalizations.

Automated summary

Comparing the genomes of closely related suboscine flycatchers and their hybrids, researchers identified six regions of high genomic differentiation that may be associated with variation in nonlearned songs. These regions contain a total of 67 described genes, three of which have been linked to language impairment and dyslexia in humans, and 18 are known to be differentially expressed in the avian song nuclei regions. This study provides insights into the genetic basis of innate vocal signals and can guide further research on vocal differences in various bird lineages.