Comparison of the evolution of ribulose-1, 5-biphosphate carboxylase (rbcL) and atpB-rbcL noncoding spacer sequences in a recent plant group, the tribe Rubieae (Rubiaceae).

Plastid sequences of the atpB-rbcL spacer and rbcL gene itself were used to evaluate their respective potential in reconstructing the phylogeny of 15 taxa from the tribe Rubieae (Rubiaceae). From our previous analyses using the atpB-rbcL spacer, the 15 selected taxa represent most of the variability of the tribe. Since this group is considered to be relatively recent (Upper Tertiary), it should allow the study of early dynamics of nucleotide substitutions in recent divergences. The results show that the spacer and rbcL inferred phylogenies are not totally congruent; the spacer trees are more similar to interpretations of morphological data. A comparative analysis of the pattern of nucleotide substitution of these two sequences in the Rubieae shows that (1) the overall rate of substitution is similar in the spacer and in rbcL, and the rate of synonymous substitution in rbcL is much higher; (2) the level of homoplasy is higher in rbcL than in the spacer matrix which shows a higher phylogenetic structure; and (3) the pattern of transition and transversion substitutions is different in the two sequences, and is not linear in rbcL. As a result of these observations, we suggest that (1) the spacer is evolving relatively slowly because of unsuspected, and phylogenetically important, selective constraints on its sequence; and (2) in the rbcL sequence, many sites, free of constraint, are changing at high rate, and some of these sites seem to have undergone multiple substitutions even in this recent tribe. This could explain the high level of homoplasy found in Rubieae rbcL sequences.