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. 2010 Feb 16;10:45. doi: 10.1186/1471-2148-10-45

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Copyright ©2010 Marcussen et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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d_Nand d_Sestimated for NRPD2/E2-a and NRPD2/E2-b along individual branches in the Violaceae phylogeny. Values of d_N(above branches) and d_S(below branches) along each branch were estimated by using the free-ratio model using the CodeML program in PAML [49]. For the branches drawn with bold lines, d_N/d_Swas larger than 1 (p = 0.010) under a 2-rate model, which suggests that positive selection acted on these lineages. Branches collapsing in a MP phylogenetic analysis of the 54 bp region are indicated with broken lines. NRPD2/E2 duplication in the common ancestor of Allexis and Viola is indicated. Only species names are shown for Viola, and non-Viola taxon names are shown in boldface. Pseudogenes are indicated with capital letters.