Relative rates of nucleotide substitution in frogs

Abstract

Accurate estimation of relative mutation rates of mitochondrial DNA (mtDNA) and single-copy nuclear DNA (scnDNA) within lineages contributes to a general understanding of molecular evolutionary processes and facilitates making demographic inferences from population genetic data. The rate of divergence at synonymous sites ( K(s)) may be used as a surrogate for mutation rate. Such data are available for few organisms and no amphibians. Relative to mammals and birds, amphibian mtDNA is thought to evolve slowly, and the K(s) ratio of mtDNA to scnDNA would be expected to be low as well. Relative K(s) was estimated from a mitochondrial gene, ND2, and a nuclear gene, c-myc, using both "approximate" and likelihood methods. Three lineages of congeneric frogs were studied and this ratio was found to be approximately 16, the highest of previously reported ratios. No evidence of a low K(s) in the nuclear gene was found: c-myc codon usage was not biased, the K(s) was double the intron divergence rate, and the absolute K(s) was similar to estimates obtained here for other genes from other frog species. A high K(s) in mitochondrial vs. nuclear genes was unexpected in light of previous reports of a slow rate of mtDNA evolution in amphibians. These results highlight the need for further investigation of the effects of life history on mutation rates.