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Primary functional classes of the regulated genes were (i) efflux pumps, (ii) stress response, (iii) fatty acid, lipid, and derivatives biosynthesis, and (iv) hexose transport, ergosterol biosynthesis, and thiamine biosynthesis (Table 1).
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Within each schema (comprised of many functional classes of genes), each gene is assigned to a primary functional class.
Given our limited sampling, our primary goal was to identify functional classes of genes under positive selection, and it appears that the signal in H is not strong enough to independently confirm the dN/ dS results.
In group IV, we also observed genes related to primary metabolism that mainly belonged to the functional classes of "energy metabolism", "lipid metabolism", and "transcription".
In group II (table 1), we also observed genes related to primary metabolism that mainly belonged to the functional classes of "purines, pyrimidines, nucleosides, and nucleotides".
Gene definitions and functional classes were added manually by using FASTA analyses of the primary automated comparisons.
As we said before, this non-primary, associative auditory area has been shown to differentially respond to the functional classes of starlings' songs [38].
Specifically, our primary analysis uses a subset of Gene Ontology (GO) biological process terms that correspond to broad functional classes ("Informative Terms" [ 25], see Materials and Methods for more details).
The functional classes of these genes refer to the functional classes in (Additional file 3: Table S2).
Representative genes belonging to these functional classes are described below.
Next, the genes were annotated according to functional classes.
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