INTRALINEAGE VARIATION IN THE PATTERN OF RBCL NUCLEOTIDE SUBSTITUTION

Variation in chloroplast rbcL sequences was studied in representative species of four different lineages: the tribe Rubieae (Rubiaceae), and the genera Drosera (Droseraceae), Nothofagus (Nothofagaceae) and Ilex (Aquifoliaceae). Each lineage has its particular non-overlapping set of rbcL polymorphic sites, indicating that common unconstrained rbcL s ites are not shared. Large differences in the rate and pattern of nucl eotide substitution are observed among the four lineages. The genus Il ex has the lowest rate of substitution, the lowest transition/transver sion ratio, the lowest synonymous/ replacement ratio and the lowest nu mber of substitutions at the third codon position. An apparent relatio nship of these measures to the age of the lineages is observed. The AT content and codon use among the four lineages are very similar and, apparently, cannot account for the observed differences in patterns of nucleotide substitution. However, the A+T content of the two bases im mediately flanking the polymorphic sites is higher in Ilex than in the other lineages. This could be correlated with the transversion/transi tion bias observed in Ilex. The particularly low synonymous/replacemen t ratio found in Ilex could also be explained by the small population sizes of species in this genus.