RESTRICTION DATA FROM CHLOROPLAST DNA FOR PHYLOGENETIC RECONSTRUCTION - IS THERE ONLY ONE ACCURATE WAY OF SCORING

Information from the same restriction analysis of chloroplast DNA of 33 taxa of Rubiaceae was scored in four different ways, two of which were based on fragments, and two on restriction sites, and they were subsequently analysed with Wagner parsimony. The methods resulted in different phylogenetic trees. The inherent differences between the methods relate to the amount of non-homologous characters and dependent characters, but none of the methods will systematically bias the resulting cladograms. The fragment analyses are much less time-consuming, but probably less accurate, than the site analyses. The choice of method is dependent on a trade-off between accuracy and resources (time). One important recommendation is made: all phylogenetic analyses of chloroplast DNA data should be accompanied by a data matrix and contain information on how the matrix was compiled.