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. 2009 May 25;1:85–98. doi: 10.1093/gbe/evp010

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© The Author(s) 2009. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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FIG. 8.— — Evolution of binding site number for transcription factors in the methionine pathway of yeast. Clades are marked by a letter at their root and a bracket with the mean binding site number and the V/m ratio above the corresponding species names. For some species the binding site numbers are also given above the name. The whole-genome duplication of the E clade is marked by WGD. For CBF1 (A), the likelihood model estimates a half-life of 57.3 My. There also seems to be a significant decrease in the binding site density in stem lineage of the G clade. GCN4 (B) has with 84.1 My, the longest estimated half-life and a significant loss of binding sites in the D clade. MET30/31 (C) has an estimated half-life of 24.2 My and like CBF1 a significant binding site loss in the G clade. BAS1 (D) has an estimated half-life of 22.7 My. RTG1/3 (E) has in the F clade a V/m ratio close to 1 (0.84), suggesting equilibrium within the 20 Mio years time frame of the F clade. This makes the estimation of the rate parameters difficult and yields to the shortest half-life of only 30.900 years.