We searched our orthologous data set for loci involved in hearing, including those linked to deafness and/or ear development. All GO annotations for each gene in our data set were obtained by searching the DAVID 6.7 database (http://david.abcc.ncifcrf.gov) (47), and we identified a total of 104 hearing-related genes with the annotations containing the words “auditory,” “sound,” or “ear” (table S2). After identifying convergent and divergent substitutions, we compared the ratios of the number of convergent substitutions to the number of divergent substitutions between branches I and II and branches I and III as well as between branches I and IV and branches I and V, respectively. We also used the bootstrap approach to test whether the C/D value of hearing genes is significantly different from that of nonhearing genes for the same number as hearing genes for each branch pair examined for convergence.

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