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Figure 3. Assignment of Putative Retention Mechanisms Based on Molecular Changes in the Coding RegionWe assigned a retention mechanism to paralogs based on the results of three analyses. The first one compared a model with no change in the ka/ks ratio after duplication (Model A in which the ka/ks ratio on all branches is indicated by R0) to a model with a higher ka/ks ratio after duplication (Model B with ka/ks ratio R1 > R0). The second one compared a model with no difference in the nonsynonymous substitution rate (Model B, in which R0 and R1 are nonsynonymous rates on each branch) to a model with different rates of nonsynonymous substitution in each paralog (Model C in which R0, R1, and R2 are nonsynonymous rates on each branch), with the stipulation that the paralog with the higher nonsynonymous rate also have a higher ka/ks ratio than the slower paralog and a higher ka/ks ratio than the diploid lineage. The third analysis tested for complementarity of amino acid substitution in each paralog.In the table in the figure, a minus sign (−) indicates either no significant difference between the models or no significant complementarity of nonsynonymous substitutions. A plus sign (+) indicates a significant improvement in likelihood of the more parameterized model or significant complementarity of nonsynonymous substitution. An asterisk (*) denotes the caveat that an increased substitution ratio could stem from relaxed purifying selection and therefore be a consequence of rather than a cause for retention. Image published in: Chain FJ and Evans BJ (2006) Copyright: © 2006 Chain and Evans. This image is reproduced with permission of the journal and the copyright holder. This is an open-access article distributed under the terms of the Creative Commons Attribution license Larger Image Printer Friendly View

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