Ferns are one of the three main clades of vascular plants. They have few easily studied morphological characters, reflected in a historically unstable classification. The fern genus Woodsia is known to have a complex evolutionary history including numerous polyploid taxa and hybrids. It is a cosmopolitan group of small rock loving ferns mainly found in montane areas. This thesis aims at analyzing the patterns of diploid and polyploid evolution in Woodsia and to resolve and classify the relationships of Woodsiaceae and the other families in the large fern clade Eupolypods II. The Eupolypods II family relationships were inferred with DNA sequences from 81 specimens representing all major lineages. This resulted in the first well supported phylogeny of this clade and revealed Woodsiaceae to be non-monophyletic. The genera previously placed in this family were reclassified into five new or resurrected families. Swedish fern genera that have changed family classification are Woodsia (hällebräknar), now in the monogeneric family Woodsiaceae, Athyrium (majbräknar), now  in Athyriaceeae and Cystopteris (stenbräknar) and Gymnocarpium (ekbräknar) now in Cystopteridaceae. To analyze the evolution of Woodsia, phylogenies were produced from five plastid and two nuclear regions sequenced from 188 specimens. The results show that most taxa in Woodsia are polyploid. Polyploidization is the most common mode of speciation in the genus with an estimated polyploid speciation rate of 54%. The polyploids are mostly young and many of the polyploid taxa seem to have formed multiple times. The results also address several taxonomic and biogeographic questions. In the process of the work we made methodological advancements and developed 20 new low copy nuclear marker regions as well as a software pipeline for finding primers in transcriptome datasets. The alignment editor software AliView was developed for handling the increasing size datasets in a user friendly way. In conclusion this thesis provides new insights into the complexities of the evolution of a fern genus in which much of the diversity is accommodated in young species formed through polyploidization. It provides a framework of phylogenetic relationships at different levels that both answers long standing questions and generates new ones.

Genome duplication plays a significant role in plant evolution. Formation of new polyploids is generally considered to be rare. Nevertheless, under natural conditions mixed-ploidy populations occur in relatively large numbers. Only the observations in the cytotype contact zone can identify all the factors affecting the stability or instability of the population. Number of research focusing on study of cytotype coexistence in natural mixed-ploidy populations is still low. As a model system for the study of mechanisms governing cytotype coexistence was chosen the Tripleurospermum inodorum. Research focused on natural mixed-ploidy populations and also on planted mixed-ploidy populations. Permanent plots were located in south, west, northwest and north Bohemia. Field observations were supplemented by cultivation experiments carried out in the greenhouse. Several phenomena were discovered at the level of whole populations. Cytotype distribution in the plot was random. The spatial structure of natural populations was quickly changing even within a single season. Even between single plot evaluations the cytotype ratios varied. Three percent of all plants were triploid hybrids. Most often detected cytotype in soil seed bank was diploid cytotype. The study of population dynamics shows, that tetraploids are...

Polyploidization (whole-genome duplication) is widely considered one of the most important evolutionary forces driving the diversification of flowering plants. Polyploids tend to originate recurrently and many plant species retain individuals of two or more different ploidy levels in certain parts of their distributional range of even within their populations. The main aim of this thesis was to address the understudied aspects of polyploid speciation by employing new, convenient methods and/or studying plant model systems with unique features. Difference in monoploid genome size of Tripleurospermum inodorum (Asteraceae) cytotypes provided a unique opportunity for addressing the rate of spontaneous polyploidization in natural populations by enabling the easy distinction of neopolyploid mutants from long-established polyploids in routine flow-cytometric analyses. Repeated ploidy screening in mixed-ploidy populations of annual T. inodorum have been, to our knowledge, the very first attempt to document temporal changes in cytotype composition in situ. In spite of considerable between- year oscillations in cytotype frequencies, both diploids and tetraploids usually persisted locally for several consecutive years. The common incidence of such ploidy mixtures along with a partial fertility of triploid...