data for these kinds of studies are not yet available. As a first step in the analysis of rate variation among chloroplast loci, Gaut et al. (1993) examined rate heterogeneity among a number of chloroplast loci from three taxa (maize, rice, and tobacco, using Marchantia as an outgroup). Comparison of sequence data from the maize and rice chloroplast genomes revealed little rate heterogeneity (using tobacco as an outgroup). However, comparisons of sequence data from rice and tobacco (using Marchantia as the outgroup) revealed much heterogeneity: significant deviation from a molecular clock was detected at 14 of 40 loci. All 14 loci have accelerated substitution rates in rice relative to tobacco, suggesting concerted rate increases in the rice lineage. In addition, 17 loci had nonsignificantly accelerated rates in rice, while the remaining 9 loci had nonsignificantly slower rates in rice, relative to tobacco.
Interestingly, many of the 14 loci that exhibit significant rate heterogeneity between rice and tobacco lineages encode protein products of related function. For example, three of the four loci that encode RNA polymerase subunits demonstrate rate heterogeneity between rice and tobacco lineages. Further analysis of RNA polymerase genes suggests rate acceleration with subsequent rate deceleration (B. S. Gaut, unpublished data), perhaps indicating the episodic rate pattern thought to result from selective pressures (Gillespie, 1986).
The question of site-dependent probabilities of amino acid replacement can be addressed in considerable detail by using the very large rbcL data base. This large data base may be used to ask whether models of nucleotide substitution provide an acceptable fit to the data, and it is even more important to ask whether the pattern of accepted amino acid change provides useful information on protein adaptation. The three-dimensional structure of the RuBisCo protein has been determined for a wide phylogenetic range of species (Chapman et al., 1988; Knight et al., 1989; Schneider et al., 1990). The pattern of amino acid replacement can be mapped onto the physical structure to identify major constraints in molecular change. Such an analysis, when placed in a phylogenetic context, may also help to identify amino acid replacement of functional importance.
The large subunit of RuBisCo contains two domains: (i) a carboxyl-terminal C domain that includes (a) an α/β-barrel consisting of alternating α-helices and β-strands, with the parallel β-strands forming an interior barrel; (b) an interior extension with an α-helix followed by a pair of antiparallel β-strands; and (c) a terminal extension of two to four