Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae)

We examine rate heterogeneity among evolutionary lineages of the grassfamily at two plasmid loci, ndhF and rbcL, and we introduce a method todetermine whether patterns of rate heterogeneity are correlated betweenloci. We show both that rates of synonymous evolution are heterogeneousamong grass lineages and that are heterogeneity is correlated between lociat synonymous sites. At nonsynonymous sites, the pattern of rateheterogeneity is not correlated between loci, primarily due to an aberrantpattern of rate heterogeneity at nonsynonymous sites of rbcL. We comparepatterns of synonymous rate heterogeneity to predictors based on thegeneration time effect and the speciation rate hypotheses. Although thereis some evidence for generation time effects, neither generation timeeffects nor speciation rates appear to be sufficient to explain patterns ofrate heterogeneity in the grass plastid sequences.