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Figure 4 | BMC Evolutionary Biology

Figure 4

From: Retrotransposition and mutation events yield Rap1 GTPases with differential signalling capacity

Figure 4

Codon evolution model of Rap1 retrogenes. A. The phylogenetic tree depicts the evolution of mammalian Rap1A orthologs and the two mouse Rap1A retrogenes. To check whether the two retrogenes are functional, we compute ω-ratios of non-synonymous to synonymous substitutions with the clades model of PAML. We assume one ω1-ratio for the left part of the tree whereas the evolution of recently emerged retrogenes is modelled by an individual ω2-value. Table shows the estimated ω-values and their standard deviations as computed by PAML. The amino acid sequences of mammalian Rap1A orthologs are fully conserved and the ML estimate ω1 = 0.0001 is too close to zero for PAML to compute a standard deviation. B. The evolution of the two mouse Rap1A retrogenes involved a retrotransposition event and a subsequent duplication event. Vertical edge lengths in the tree dendrogram were computed by the PAML software and scale with the expected number of neutral synonymous substitutions under the 2-clades codon evolution model. Leaves and internal nodes are annotated with the four codons at positions 9, 35, 59, 96, where non-synonymous subsitutions occured. Codons at internal nodes were reconstructed by applying the Maximum Parsimony principle to single nucleotide substitutions. It can be hypothesized, that non-synonymous (T35 M) and synonymous (T35T) mutations at codon 35 observed in mRap1A-retro1 and mRap1A-retro2, respectively, result from deaminations of methylated CpG dinucleotide. Non-synonymous mutations are highlighted in cyan.

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