Abstract
Two new Isoetes from South America are described and contrasted with morphologically similar and sympatric species. The first of these species, I. baculata, represents a relictual morphotype within the Isoetaceae as indicated by the presence of completely laminate leaves. The other species, I. eshbaughii, is unique in forming desiccation resistant foliar gemmae which are completely enclosed by sclerified scales. Analyses on the distribution of alate leaves and scales, as well as peripheral fibrous bundles and sporangial pigmentation, show that there are nested sets of species within the Isoetaceae which represent major phylogenetic lineages. The pattern of character nesting suggests an historical transition from a primitively aquatic habit to a seasonally amphibious one, with subsequent parallel reversions back to aquatic zones. These habitat changes have resulted in convergent morphologies which are in large part responsible for the previous confusion regarding the evolution of the genus and the dependence on megaspore morphology as the sole basis of infrageneric classification. A major advantage of the proposed phylogeny is that the demarcation of major lineages now allows for the establishment of functional ingroups and outgroups, and thus provides a frame of reference from which additional phylogenetic hypotheses can be formulated.

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