revealed the most rapid nucleotide substitution rate in the grass family, followed by families in the orders Orchidales, Liliales, Bromeliales, and Arecales (represented by the palms). Rates of synonymous nucleotide substitution in grass rbcL sequences exceed rates in other monocot sequences by as little as 130% and by as much as 800%.
Bousquet et al. (1992b) reported extensive rate variation among 15 rbcL sequences representing monocot, dicot, and gymnosperm taxa. They concluded that missense rate variation is more extensive than synonymous rate variation. This result differs with that reported by Gaut et al. (1992). The differences between these studies can probably be ascribed to the wide phylogenetic range of taxa surveyed. The relatively narrow monocot comparisons included few missense substitutions; the paucity of nonsynonymous substitutions may have made detection of missense rate heterogeneity difficult. On the other hand, the study of Bousquet et al. (1992b) may have underestimated synonymous rate variation because some of their sequence comparisons had probably been saturated for synonymous substitutions.
Clearly a simple stochastically constant molecular clock does not hold for the rbcL locus; however, there may be a generation-time effect (Li, 1993). While it is difficult to estimate generation times in most plant taxa, the monocot sequences show a clear negative correlation between the minimum generation time and substitution rates (Gaut et al., 1992). Given that rate variation in monocot sequences is largely synonymous (and therefore presumably close to neutral) and that rate variation is correlated with minimum generation time, rate variation at the rbcL locus of monocot taxa is consistent with neutral predictions. The conclusions of Bousquet et al. (1992b) are not as straightforward, but their results do indicate clear differences in substitution rates among annual and perennial taxa, a result not inconsistent with a generation-time effect. Bousquet et al. (1992b) also speculate that speciation rates influence substitution rates. Other factors hypothesized to contribute to rate variation among evolutionary lineages include polymerase fidelity (Wu and Li, 1985; Li et al., 1985), selection (Gillespie, 1986), and G + C content (Bulmer et al., 1991).
What is the pattern of rate variation at other chloroplast loci? If rate variation is predominantly a function of an evolutionary factor that affects the whole genome (like, presumably, the generation-time effect), then one would expect to find similar patterns of rate variation in most chloroplast loci. Conversely, widely divergent patterns of rate variation among chloroplast loci would argue for locus-specific factors (like selection) as the motive force behind substitution rate variation. Ideally, one should sample chloroplast loci from the taxa used in the rbcL studies to directly compare patterns of rate variation among loci. Unfortunately,