Molecular Evolution Activities
 

This is a comprehensive bibliography (under construction) of primary and secondary sources on the neutral theory of molecular evolution. It currently covers the period 1973-2001.

Author :

Smith, N. G.;Hurst, L. D.

Year :

1999

Title :

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

Journal :

Genetics

Volume :

153

Issue :

3

Pages :

1395-402

Short Title :

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

Custom 3 :

20014929

Abstract :

Nonsynonymous substitutions in DNA cause amino acid substitutions while synonymous substitutions in DNA leave amino acids unchanged. The cause of the correlation between the substitution rates at nonsynonymous (K(A)) and synonymous (K(S)) sites in mammals is a contentious issue, and one that impacts on many aspects of molecular evolution. Here we use a large set of orthologous 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 methods, but not when substitution rates are estimated by maximum likelihood. Irrespective of this methodological uncertainty the strength of the K(A)-K(S) correlation appears mostly due to tandem substitutions, an excess of which is generated by substitutional nonindependence. Doublet mutations cannot explain the excess of tandem synonymous-nonsynonymous substitutions, and substitution patterns indicate that selection on silent sites is the likely cause. We find no evidence for selection on codon usage. The nature of the relationship between synonymous divergence and base composition is unclear because we find a significant correlation if we use maximum-likelihood methods but 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.
 -- contributed by John Beatty, March 29, 2002