Synonymous codon usage and selection on proteins
  Selection pressures on proteins are usually measured by comparing homologous nucleotide sequences (Zuckerkandl and Pauling 1965). Recently we introduced a novel method, termed `volatility', to estimate selection pressures on protein sequences from their synonymous codon usage (Plotkin and Dushoff 2003, Plotkin et al 2004a). Here we provide a theoretical foundation for this approach. We derive the expected frequencies of synonymous codons as a function of the strength of selection, the mutation rate, and the effective population size. We analyze the conditions under which we can expect to draw inferences from biased codon usage, and we estimate the time scales required to establish and maintain such a signal. Our results indicate that, over a broad range of parameters, synonymous codon usage can reliably distinguish between negative selection, positive selection, and neutrality. While the power of volatility to detect negative selection depends on the population size, there is no such dependence for the detection of positive selection. Furthermore, we show that phenomena such as transient hyper-mutators in microbes can improve the power of volatility to detect negative selection, even when the typical observed neutral site heterozygosity is low. 
Joshua B. Plotkin, Jonathan Dushoff, Michael M. Desai, Hunter B.   Fraser