Chloroplast Dna Polymorphism At The Intrageneric Level And Plant Phylogenies

Times Cited: 32; International audience; Analysis of chloroplast DNA (cpDNA) sequences is a tool which is being used more and more frequently in plant systematics and evolution. The recent development of polymerase chain reaction (PCR) has enabled sequencing the rbcL gene for a great number of species and to infer phylogemies at higher taxonomic levels. However this gene reaches its lower limits of resolution in resolving relationships among closely related genera. The analysis of non-coding regions, which display higher mutation rates than coding regions, extends the resolution of the molecule. Here we report a high variability in divergence rates for two non-coding regions of the chloroplast genome. Thirty-six species belonging to 10 different genera were sampled and indicated divergence rates that varied 5-8 fold. In order to explain this heterogeneity, three non-exclusive hypotheses involving sampling bias, age of common ancestor and variants of the molecular clock, are proposed and discussed. The potential utility of these two non-coding regions in resolving phylogenetic relationships differs among genera.