Chloroplast DNA restriction site variation and phylogeny of the Berberidaceae

Comparative restriction site mapping of the chloroplast genome was performe d to examine phylogenetic relationships among 27 species representing 16 ge nera of the Berberidaceae and two outgroups. Chloroplast genomes of the spe cies included in this study showed no major structural rearrangements (i.e. , they are collinear to tobacco cpDNA) except for the extension of the inve rted repeat in species of Berberis and Mahonia. Excluding several regions t hat exhibited severe length variation, a total of 501 phylogenetically info rmative sites was mapped for ten restriction enzymes. The strict consensus tree of 14 equally parsimonious trees indicated that some berberidaceous ge nera (Berberis, Mahonia, Diphylleia) are not monophyletic. To explore phylo genetic utility of different parsimony methods phylogenetic trees were gene rated using Wagner, Dollo, and weighted parsimony for a reduced data set th at included 18 species. One of the most significant results was the recogni tion of the four chromosomal groups, which were strongly supported regardle ss of the parsimony method used. The most notable difference among the tree s produced by the three parsimony methods was the relationships among the f our chromosomal groups. The cpDNA trees also strongly supported a close rel ationship of several generic pairs (e.g., Berberis-Mahonia, Epimedium-Vanco uveria, etc.). Maximum likelihood values were computed for the four differe nt tree topologies of the chromosomal groups, two Wagner, one Dollo, and on e weighted topology. The results indicate that the weighted tree has the hi ghest likelihood value. The lowest likelihood value was obtained for the Do llo tree, which had the highest bootstrap and decay values. Separate analys es using only the Inverted Repeat (IR) region resulted in a tree that is id entical to the weighted tree. Poor resolution and/or support for the relati onships among the four chromosomal lineages of the Berberidaceae indicate t hat they may have radiated from an ancestral stock in a relatively short ev olutionary time.