Features of Recent Codon Evolution: A Comparative Polymorphism-Fixation Study

Abstract

Features of amino-acid and codon changes can provide us important insights on protein evolution. So far, investigators have often examined mutation patterns at either interspecies fixed substitution or intraspecies nucleotide polymorphism level, but not both. Here, we performed a unique analysis of a combined set of intra-species polymorphisms and inter-species substitutions in human codons. Strong difference in mutational pattern was found at codon positions 1, 2, and 3 between the polymorphism and fixation data. Fixation had strong bias towards increasing the rarest codons but decreasing the most frequently used codons, suggesting that codon equilibrium has not been reached yet. We detected strong CpG effect on CG-containing codons and subsequent suppression by fixation. Finally, we detected the signature of purifying selection against A∣U dinucleotides at synonymous dicodon boundaries. Overall, fixation process could effectively and quickly correct the volatile changes introduced by polymorphisms so that codon changes could be gradual and directional and that codon composition could be kept relatively stable during evolution.

Roles for Synonymous Codon Usage in Protein Biogenesis

“…For example, CG dinucleotide pairs have an increased mutational susceptibility in methylated eukaryotic genomes (99). As a result, in the human genome NCG is rarely used to encode amino acids encoded by NCN codons (149). Synonymous codon usage within coding sequences can also alter the stability of mRNA structure, affecting cell physiology.…”

Advantages of an easy-to-use DNA extraction method for minimal-destructive analysis of collection specimens

“… These two partitions appeared to be appropriate from all we know about the different evolutionary rates and selection pressures of the different codon positions and protein-coding genes compared to non-protein-coding genes [ 108 – 111 ]. …”

“…The splitting of H. centralasiae into two branches separated by other species, including H. siehei, could suggest two mitochondrial lineages within this species, with the paralectotype (MTD-TW 9228) showing one mitochondrial lineage and the two samples FN386551 and FN386553 representing another lineage. The origin and species status of Hyles svetlana is not yet clear and is still discussed [115,116], but the grouping in the cluster including some H. siehei and the H. centralasiae paralectotype could These two partitions appeared to be appropriate from all we know about the different evolutionary rates and selection pressures of the different codon positions and protein-coding genes compared to non-protein-coding genes [108][109][110][111].…”