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Figure 5 | BMC Evolutionary Biology

Figure 5

From: A simplified explanation for the frameshift mutation that created a novel C-terminal motif in the APETALA3 gene lineage

Figure 5

Nucleotide ancestral character state reconstructions and evolutionary scenarios. A, The MP ancestral character state reconstructions for the pre- and post-frameshift nodes (A1 and A2, respectively, as indicated to the right) of the recovered phylogeny (Fig. 2). These nucleotide sequences were recovered with the accelerated transitions (ACCTRAN) setting. Under the delayed transitions (DELTRAN) setting, the inferred sequences were identical to those shown in B. In the schematic phylogeny to the right, the star indicates the euAP3/TM6 duplication node and the red branch denotes the timing of the frameshift event. B, The MP ancestral character state reconstructions for an alternative topology where the Pachysandra loci predate the euAP3/TM6 duplication (again indicated by a star on the schematic phylogeny to the right). In this case, the frameshift occurred along the red branch immediately following the duplication event. Node B1 represents the duplication while B2 represents the ancestor of the euAP3 clade. The sequences recovered with the ACCTRAN and DELTRAN settings were identical. C. Evolutionary scenario that minimizes the number of non-synonymous changes associated with the frameshift event. Each line represents stepwise changes that would have occurred during the transition from the sequence indicated as 'node B1' to that denoted 'node B2.' Under this model, four nucleotide changes occurred before the frameshift (line 'pre-FS') and two after (line 'node B2'), but only one of these changes was non-synonymous (indicated by red asterisk). D. Evolutionary scenario that maximizes the number of non-synonymous changes associated with the frameshift event. Again, each line represents stepwise changes that would have occurred during the transition from the sequence indicated as 'node B1' to that denoted 'node B2.' Under this model, three nucleotide changes occurred before the frameshift (line 'pre-FS') and three after (line 'node B2'), but all of these changes were non-synonymous (indicated by red asterisks). Scenarios in C and D are both based on the reconstructions shown in B. All nucleotide changes are indicated with red letters. FS = frameshift.

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