Heterogeneity of three molecular data partition phylogenies of mints related to M. x piperita (Mentha; Lamiaceae).

Phylogenetic reconstructions with molecular tools are now widely used, thanks to advances in IPCIR and sequencing technologies. The choice of the molecular target still remains a problem because too few comparative data are available. This is particularly true for hybrid taxa, where differential introgression of genome parts leads to incongruity between data sets. We have studied the potential of three data partitions to reconstruct the phylogeny of mints related to M. x piperita. These included nuclear DNA (ITS), chloroplast DNA (non-coding regions tmL intron, intergenic spacers trnL-trnF, and psbA-trnH), and AFLIP and ISSR, markers. The taxonomic sampling was composed of hybrids, diploid and polyploid genomes. Since the genealogy of cultivated mint hybrids is known, they represent a model group to compare the usefulness of various molecular markers for phylogeny inference. Incongruities between ITS, chloroplast DNA, and AFLIP-ISSR phylogenetic trees were recorded, although DNA fingerprinting data were congruent with morphological classification. Evidence of chloroplast capture events was obtained for M. x piperita. Direct sequencing of ITS led to biased results because of the existence of pseuclogenes. Sequencing of cloned ITS further failed to provide evidence of the existence of the two parental copy types for M. x piperita, a sterile hybrid that has had no opportunity for concerted evolution of ITS copies. AFLP-ISSIR data clustered M. x piperita with the parent that had the largest genome. This study sheds light on differential of introgression of different genome regions in mint hybrids.