The effect of tandem substitutions on the correlation between synonymous and nonsynonymous rates in rodents

Nonsynonymous substitutions in DNA cause amino acid substitutions while syn onymous substitutions in DNA leave amino acids unchanged. The cause of the correlation between the substitution rates at nonsynonymous (K-A) and synon ymous (K-S) sites in mammals is a contentious issue, and one that impacts o n many aspects of molecular evolution. Here we use a large set of orthologo us mammalian genes to investigate the causes of the K-A-K-S correlation in rodents. The strength of the K-A-K-S correlation exceeds the neutral theory expectation when substitution rates are estimated using algorithmic method s, but not when substitution rates are estimated by maximum likelihood. Irr espective of this methodological uncertainty the strength of the K-A-K-S co rrelation appears mostly due to tandem substitutions, an excess of which is generated by substitutional nonindependence. Doublet mutations cannot expl ain the excess of tandem synonymous-nonsynonymous substitutions, and substi tution patterns indicate that selection on silent sites is the likely cause . We find no evidence for selection on codon usage. The nature of the relat ionship between synonymous divergence and base composition is unclear becau se we find a significant correlation if we use maximum-likelihood methods b ut not if we use algorithmic methods. Finally, we find that K-S is reduced at the start of genes, which suggests that selection for RNA structure may affect silent sites in mammalian protein-coding genes.