For most of the schools a coefficients of divergence (COD) values varied from spatial homogeneity to moderate spatial heterogeneity.
Type I and type II functional divergence between clusters of the Actinopterygii CYP3 family was examined using DIVERGE v2.0 [40], which can be used to determine whether the coefficients of divergence θI and θII are significantly >0.
Tests for types-I and -II divergence based upon the relevant coefficients of divergence, which correspond to the probability that a specific site has undergone type-I or -II divergence in a pairwise comparison, were proposed by Gu [ 21, 22, 48].
Type-I and type-II functional divergence among large or small subunit groups was examined using the DIVERGE software [ 48], which implements the tests suggested by Gu [ 22, 47] that can be used to determine whether the coefficients of divergence (θI and θII) are significantly greater than zero.
To test if the cluster-specific residues in SAP30 and SAP30L are indicative of type-I divergence, we estimated the coefficient of functional divergence, which measures the difference in the evolutionary rate at amino acid sites between gene clusters.
We applied this approach to full length protein sequences to estimate the pairwise coefficient of functional divergence (type-I functional divergence or θI) between all FFRPs.
To test if 'cluster-specific' residues are functionally divergent we estimated the coefficient of functional divergence, which measures the difference in evolutionary rate at amino acid sites between gene clusters.
The Akirin1 and Akirin2 clades were defined as separate clusters and the coefficient of functional divergence and posterior probability for functional divergence at each site in the alignment were estimated using the Gu99 algorithm [ 28].
The coefficient of functional divergence and the posterior probability for the functional divergence were calculated for each position in the alignment.
