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The striking difference in percentage estimates between nucleotide and amino acid levels could be explained by saturation of more variable codon positions in the former.
Nevertheless, RRT results showed that conserved codon positions also contribute significantly to neobatrachian-specific rate acceleration, displaying similar trends to those experienced by more variable codon positions (see Additional file 3).
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Translation of the protein-coding genes COI and PTPN12 did not reveal stop codons or frame-shift mutations, and third codon positions were more variable than first and second codon positions as expected in functional genes.
Existing start codons are more variable: ATT is found in cytb, nad3, cox2 and cox3; nand anad4ad4 start with ATG; atp6 begins with ATA and nad6 with ATC.
The nucleotide substitution rates of the first and second codon positions of PCGs are always lower but more variable within each gene than the third codon positions (see Additional file 3B), which is most likely because of the different selective constraints on the different genes [ 46].
Mutations of other codons have much more variable phenotypes with more variable severity and (anterior posterior) gradient of LIS and more consistent hypoplasia of the corpus callosum and cerebellum.
Shorter genes in bacteria tend to have more variable expression levels, and selective pressure on codon usage is also higher in shorter genes [ 22].
More specifically, we controlled for both the equilibrium GC composition at all codon position (GC*) and the equilibrium GC at the third-codon position (GC3*), the latter being markedly more variable than the former (Gibson et al. 2005).
Therefore, a third codon position nucleotide in a loop is more variable than that in a helix.
Of the three codon positions, third position nucleotides were systematically more variable than those of first and second positions as measured by percentage of sites that were variable and the percentages of sites that were parsimony informative (data not shown).
All proteins contained spikes of variable codons scattered throughout, although there were stretches of lower variability with fewer spikes even in the generally more variable proteins Env and Nef.
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