Additional file 1:

Binned rates of synonymous substitution per site (Ks) of paralog α of gene fragments greater than 200 bp suggest that Ks is lower in the early stage than in the later stage. Ks values were calculated using a free ratio model on the phylogeny depicted in Fig. 1B in which Ks is estimated independently for each branch. The early stage of evolution (blue bars) corresponds with the paralog α lineage between node 1 and 3 and the later stage of evolution (red bars) corresponds with the XLα lineage between node 3 and XLα.

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Additional file 2:

Information about sequence data including gene acronym, length in base pairs (bp), and Genbank accession numbers, and results of model based analysis of individual fragments. Gene acronyms refer to the name of one Xenopus paralog or, if a name was not available, an acronym of a closely related named homolog. Xenopus borealis sequences less than 50 bp in length were not submitted to Genbank and are available upon request (AUR). Species and paralog abbreviations are the same as in Fig. 1. Discontinuous fragments of the same paralog have separate accession numbers. For each fragment, the likelihood of a null (Ho) and alternative (Ha) model of evolution is listed for two tests that correspond with the combined analyses presented in Tables 1 and 2. If the P value is greater than 0.05 the null model is not rejected. For the first test, in which the alternative model has a different Ka/Ks ratio in the early and later stages of duplicate gene evolution, the estimated Ka/Ks ratios are listed. Note that the null model of no difference between these ratios is not rejected for most fragments.

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Additional file 3:

supplementary methods.

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Additional file 4:

No correlation between expression divergence and (A) Ka, (B) Ks, or (C) Ka/Ks (R² ≅ 0.0002 and P > 0.50 for all correlations). Expression divergence is quantified by ln(1+R)/(1-R) where R is the Pearson correlation coefficient between each paralogous expression profile [69]. In (C) two outliers that have a Ka/Ks ratio over 1 are excluded. There also is not a significant correlation between the Ka/Ks ratio and ln(1+R)/(1-R) (data not shown). Ka/Ks ratios were calculated from complete or large fragments of expressed X. laevis paralogs; the average length of these sequences was 1119 bp.

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