Diatoms are crucially important to the global ecosystem due to their role in regulating the world’s carbon and silicon cycles, and their production of large amounts of organic material in aquatic environments. They are thought to comprise ca. 100,000 species, although some estimates suggest that there could be over a million. Despite their importance and high species diversity, little is known about their phylogeny due to technical issues that hinder the reconstruction of their relationships. However, owing to a new technique that allows for DNA to be amplified from a single isolated cell, it is possible to explore diatom relationships with extensive taxonomic sampling. This thesis aims to demonstrate that the integration of molecular data and morphological characters can provide a new paradigm for future phylogenetic and taxonomic studies of diatoms, especially among closely related and taxonomically complex groups. To achieve this, I examined common species from two naviculoid diatom genera, Frustulia and Navicula using sequence data from three molecular markers (rbcL, atpB, 18S), traditional and fine-scale morphological characters, and frustule shape. The molecular markers rbcL and atpB evolved at a similar rate and performed well at reconstructing species-level phylogenies, whereas 18S was more conserved and best used for resolving relationships at higher taxonomic levels. Hidden diversity was uncovered in what have traditionally been thought as well-circumscribed taxa, and three new species were described. The methods used here show promise for the future of diatom systematics.

Hybridization is an important mechanism in diversification. It often makes taxonomy difficult. Lack of strong supported intrageneric classification in genus Pteris (Pteridaceae) could be caused by natural hybridization. Most hybridization documnted in Pteris was based on limited evidence. This study focuses on Pteris cadieri complex, the taxon with putative hybridization. The species complex displayed significant morphological variation and was associated with hybrid origin. Reproductive biology revealed variation in spore number per sporangium, spore size, spore shape and apogamous reproduction, which imply its hybrid origin. Cytology analysis using chromosome counting and flow cytometry identified diploids, triploids, and tetraploids. CpDNA and nuclear DNA supported that Pteris cadieri complex is hybrid origin: paternal and maternal lineages were inferred and 11 taxa were identified. Furthermore, comparing materials form Hainan and Taiwan, , it is clear that the species complex is composed by taxa arisen from multiple hybridization. Systematic inconsistency existed between chloroplast and nuclear phylogenies in Pteris impled that other taxa might have involved in hybridization events, in addition to the Pteris cadieri complex. Hybridization may be very common in Pteris. To infer intrageneric taxonomy of Pteris, effect of reticulate evolution should never be neglected. Finally, based on morphological and evolutionary traits, the taxonomy of Pteris cadieri complex is revised. There are Pteris cadieri Christ, Pteris dimorpha Copel. var. dimorpha, Pteris dimorpha var. plumbea (Christ) Y.-S. Chao, H.-Y. Liu & W.-L. Chiou, Pteris grevilleana Wall. ex Agardh var. grevilleanan, Pteris grevilleana Wall. ex Agardh var. ornata Alderw., and Pteris hainanensis Ching.

<p><i>Echiochilon</i>, <i>Ogastemma</i> and <i>Sericostoma</i> are revised resulting in the recognition of 15 species of <i>Echiochilon</i> and one <i>Ogastemma</i> species. Several species are placed in synonymy and three new species are described, <i>E. baricum</i>, <i>E. callianthum</i> and <i>E. cyananthum</i>. The single species of <i>Sericostoma</i> is shown to be nested within <i>Echiochilon</i>.</p><p>The plastid <i>atpB</i> gene was sequenced for <i>Echiochilon</i> and <i>Ogastemma</i> from the Old World and <i>Antiphytum</i> from the New World, plus for a selection of 33 other Boraginaceae taxa. They were analysed together with selected outgroup taxa to give a framework of the tribes of Boraginoideae. The analysis gave support for establishing the new tribe Echiochileae for <i>Antiphytum</i>, <i>Echiochilon</i> and <i>Ogastemma</i>, and for merging the traditionally accepted tribe Eritrichieae with Cynoglosseae. The ITS region was sequenced for all but one species of <i>Echiochilon</i> and for representatives of <i>Antiphytum</i> and <i>Ogastemma</i>. Phylogenetic analysis of Echiochilon revealed that the strongly zygomorphic-flowered species form a paraphyletic group. The morphological data gave results fairly congruent with the ITS phylogeny.</p><p>Biogeographic interpretations of the ITS and <i>atpB</i> phylogenies indicated a trans-Atlantic dispersal of <i>Antiphytum</i> as the most plausible explanation to the Old/New World disjunction. Analyses using DIVA (Dispersal Vicariance Analysis) of the distributions of the <i>Echiochilon</i> species indicated an ancestor to <i>Echiochilon</i> with a wide distribution over northern Africa and Arabia to India.</p>

Echiochilon, Ogastemma and Sericostoma are revised resulting in the recognition of 15 species of Echiochilon and one Ogastemma species. Several species are placed in synonymy and three new species are described, E. baricum, E. callianthum and E. cyananthum. The single species of Sericostoma is shown to be nested within Echiochilon. The plastid atpB gene was sequenced for Echiochilon and Ogastemma from the Old World and Antiphytum from the New World, plus for a selection of 33 other Boraginaceae taxa. They were analysed together with selected outgroup taxa to give a framework of the tribes of Boraginoideae. The analysis gave support for establishing the new tribe Echiochileae for Antiphytum, Echiochilon and Ogastemma, and for merging the traditionally accepted tribe Eritrichieae with Cynoglosseae. The ITS region was sequenced for all but one species of Echiochilon and for representatives of Antiphytum and Ogastemma. Phylogenetic analysis of Echiochilon revealed that the strongly zygomorphic-flowered species form a paraphyletic group. The morphological data gave results fairly congruent with the ITS phylogeny. Biogeographic interpretations of the ITS and atpB phylogenies indicated a trans-Atlantic dispersal of Antiphytum as the most plausible explanation to the Old/New World disjunction. Analyses using DIVA (Dispersal Vicariance Analysis) of the distributions of the Echiochilon species indicated an ancestor to Echiochilon with a wide distribution over northern Africa and Arabia to India.