Evolution of the chloroplast genome and polymorphic ITS regions in Allium subg. Melanocrommyum

Relationships based on PCR-RFLPs of non-coding regions of cpDNA indicate th at some of the largest subgenera of the genus Allium and five of the larges t sections of the Central Asian subg. Melanocrommyum are artificial. Intern ested synapomorphic mutations without homoplasy were found only in the chlo roplast genomes of plants of subg. Melanocrommyum that occur in the border region of Tajikistan, Uzbekistan, Afghanistan, and Kyrgyzstan. Eighteen of 49 plants surveyed were polymorphic for their ITS regions. Even plants that had identical chloroplast genomes were polymorphic for nuclear ribosomal r egions. These individuals had markedly different frequencies of ITS variant s that were detected with various restriction enzymes. The geographic parti tioning of chloroplast haplotypes and the fact that the ITS variants could not be ordered hierarchically can readily be envisioned to result from gene flow. Processes such as concerted evolution and parallel morphological evo lution may also be partly responsible for the disconcordance of mutations i n the chloroplast and nuclear genome. However, the chimeric nature of the n uclear ribosomal regions indicates that concerted evolution is not the domi nating process in Allium subg. Melanocrommyum.