Restriction site variation and structural analysis of the chloroplast DNA of Isoetes in North America

This study applied data from chloroplast DNA to systematic problems in Isoetes (Isoetaceae), a non-seed bearing vascular plant. Recent studies using allozyme electrophoresis have suggested that the population biology and patterns of divergence in Isoetes are significantly different than what might be expected in a supposedly relict genus. They have also raised questions regarding whether current traditional classifications of the genus accurately reflect phylogenetic relationships. This study examined a group of poorly understood plants for which molecular systematic data is uniquely suitable for addressing systematic problems. Examination of the chloroplast DNA structure provided the first complete restriction site maps of the chloroplast genome of a lycopod, the quillwort Isoetes melanopoda. The Isoetes chloroplast genome shares significant features with those of two non-vascular plants, the bryophytes Marchantia (liverwort) and Physcomitrella (moss). The Isoetes chloroplast genome can be distinguished by several features: (1) its inverted repeat (IR) is several kb larger than the IR of either of the bryophytes but is significantly smaller than the IR of most vascular plants, (2) the small single copy region (SSC) has a large (5-8 kb) region of extra genetic material of unknown origin, and (3) the large single copy region (LSC) appears to have several small inversions, although these could not be accurately characterized because of the size of the probes used (2-4 kb). Low levels of chloroplast DNA restriction site sequence divergence (0.00%-0.32%) among members of Isoetes supported a lack of divergence among Isoetes in North America. Phylogenetic analysis based on the principle of parsimony suggests that the North American taxa do not form a monophyletic group. Three groups of North American species were supported. The distribution of morphological characters among these groups suggests that many of these characters have been derived numerous times in the evolution of Isoetes. In addition, the chloroplast DNA restriction site data provided evidence regarding the origins of polyploid taxa.