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This thesis has focused on the evolutionary history of Isoetes (Isoetales, Lycopsida), its phylogeny, megaspore morphology and evolutionary path through deep time. With a broadened sampling of species to include more of the worldwide diversity of the genus compared to previous work an unexpected sister to the rest of the genus was found. Isoetes wormaldii Sim is a critically endangered species from the southeastern Cape region in South Africa, which grows in ponds and slow-moving streams. There are only a few, small populations, and they are very sensitive to habitat changes. The rest of Isoetes is divided into five major clades, which show complex and not readily understandable biogeographic patterns, and by which processes the species came to live in their current locations in the world is often a conundrum. The age of the extant Isoetes is intriguing as it could potentially explain some of the baffling geographic distributions. Analyses based on whole chloroplast genomes and nuclear cistrons found that the choice of clock model and which genome dataset the dating analysis is based on matter greatly when trying to date the genus as the results were highly inconsistent. The solution to the dating analysis woes might be dependent on finding new bases, e.g., fossil evidence, for age calibrations which would require the morphology of Isoetes to be better understood. Our study of megaspore morphology found substantial differences among species of Isoetes in both ornamentation and surface texture/structure. While no major clade within the genus could be unambiguously defined by their spore morphology there are some characteristics of smaller clades and patterns of ornamentation and surface texture across the phylogeny. Our tentative hypothesis is that a pustulate megaspore ornamentation and a cobwebby texture are ancestral features in the megaspore of Isoetes.

Premise: The isoetalean lineage has a rich fossil record that extends to the Devonian, but the age of the living clade is unclear. Recent results indicate that it is young, from the Cenozoic, whereas earlier work based on less data from a denser taxon sampling yielded Mesozoic median ages. Methods: We analyzed node ages in Isoetes using two genomic data sets (plastome and nuclear ribosomal cistron), three clock models implemented in MrBayes (ILN, WN, and TK02 models), and a conservative approach to calibration. Results: While topological results were consistently resolved in Isoetes estimated crown group ages range from the latest Paleozoic (mid-Permian) to the Mesozoic depending on data type and clock model. The oldest estimates were retrieved using the autocorrelated TK02 clock model. An (early) Cenozoic age was only obtained under one specific condition (plastome data analyzed with the uncorrelated ILN clock model). That same plastome data set also yielded the oldest (mid-Permian) age estimate when analyzed with the autocorrelated TK02 clock model. Adding the highly divergent, recently established sister species Isoetes wormaldii to the data set approximately doubled the average median node depth to the Isoetes crown group. Conclusions: There is no consistent support for a Cenozoic origin of the living clade Isoetes. We obtained seemingly well-founded, yet strongly deviating results depending on data type and clock model. The single most important future improvement is probably to add calibration points, which requires an improved understanding of the isoetalean fossil record or alternative bases for calibration.