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We are broadly interested in how genomic features that are unique to a given species or lineage may be associated with behavioral phenotypes uniquely expressed by that species or lineage. We discuss how we utilize comparative genomics to identify novel genes or paralogs uniquely present in a given species or lineage of interest. Our strategy relies extensively on local and comparative genomic alignments of gene predictions using the BLAST-like alignment tool (BLAT), in conjunction with extensive and thorough examination of alignments and synteny to verify or disprove orthology. Follow-ups include examination of conserved domains and gene expression analysis in relevant brain circuits. We have successfully employed this strategy to identify novel genes that are uniquely present in songbirds, a vocal learning group, and expressed in their vocal control circuitry. We expect our strategy to be applicable to other models, and that its systematic application will significantly improve gene annotations in newly assembled genomes of interest.

Publisher Summary This chapter describes the way the analysis of immediate-early gene (IEG) expression has been used to map vocal communication areas in the brain of songbirds and other avian groups. IEGs are genes that are rapidly and transiently induced in neuronal cells when these undergo depolarization. While some IEGs code for proteins that exert direct effects on neuronal cell function, several others encode transcription factors thought to modulate neuronal function indirectly by triggering gene regulatory cascades. Although the function of the IEG response is not yet fully understood, the analysis of induced IEG expression can be used to identify patterns of brain activation associated with specific stimuli or behaviors. The chapter focuses on zenk , the IEG for which most data in birds are currently available. The comparative zenk expression analysis has revealed several striking similarities in the organization of brain systems for vocal communication in independent avian vocal learning orders.