weed); this was despite normal loadings of total DNA in these two lanes and strong hybridization with all chloroplast probes used. To explore this, portions of several mt protein and rRNA genes were PCR-amplified from both taxa and sequenced (Y.C., C.L.P., Y.-L.Q., and J.D.P., unpublished work). In all cases, the genes are exceptionally divergent. Most critically, in the case of the protein genes, most of the enhanced divergence is confined to synonymous sites. This indicates that the neutral point mutation rate, the rate of occurrence of nucleotide substitutions irrespective of selection, is markedly enhanced in both genera. To illustrate this effect for cob and cox2, Fig. 4 shows phylogenetic trees constructed with third codon positions only. Most third position changes are silent, and therefore the extremely long branch lengths leading to the Pelargonium and Plantago sequences in each tree graphically illustrate the high point mutation rate in these two distantly unrelated angiosperms.
Analysis of chloroplast and nuclear gene sequences from both plants indicates that these two genomes are not undergoing accelerated evolution (consistent with the strong hybridization of chloroplast probes mentioned above). Thus, the mutation rate increases in these two plants are restricted to their mitochondrial genomes. This distinguishes these cases of rate variation from those reported by Eyre-Walker and Gaut (1997), in which all three genomes of grasses were shown to exhibit higher rates of synonymous substitution than in palms. Another distinction is the magnitude of the rate variation: Grasses and palms differ only several-fold in their (plant-wide) substitution rates, whereas Pelargonium and Plantago