Jan Štěpánek

Modes of speciation and evolution of the sections inTaraxacum

Modes of evolution of species classified within different sections inTaraxacum involve diverse processes, viz. primary divergence of an ancestral sexual diploid, hybridization between a tetraploid apomict and a diploid sexual hybrid, differentiation of an advanced apomictic taxon at one ploidy level, hybridization between a sexual tetraploid and a sexual diploid, formation of a polyploid series from an apomictic ancestor of a lower polyploidy level, and remote hybridization between an autumn-flowering ancestral diploid and a spring-flowering derivative diploid or apomict. Various reproduction systems of the plants involved, different environments and different timing of the processes contribute to a very varied nature of the species groups.

Nuclear DNA content variation within the genusTaraxacum (Asteraceae)

Nuclear DNA content was estimated using flow cytometry in 13 sections represented by 18 species of the genusTaraxacum using propidium iodide as the DNA stain. Investigated plants represented diploid, triploid and tetraploid species from sections considered both primitive and advanced, i.e.,T. sect.Dioszegia, Piesis, Glacialia, Mongolica, Scariosa, Obovata, T. pyrenaicum group,T. sect.Coronata, Palustria, Taraxacum (=Crocea),Kashmirana, Ruderalia andErythrosperma. Estimated nuclear 2C DNA content ranged from 1.74 pg in diploidT. linearisquameum (T. sect.Ruderalia) to 6.91 pg in tetraploidT. albidum (T. sect.Mongolica), demonstrating 3.97-fold variation. The lowest monoploid genome size 1Cx=0.87 pg was recorded inT. linearisquameum (T. sect.Ruderalia) together withT. brachyglossum (T. sect.Erythrosperma), and the highest one (1.73 pg) was recorded inT. albidum (T. sect.Mongolica), giving a 1.99-fold difference in the genus. No significant differences in genome size were observed withinT. sect.Ruderalia, similarly no intraspecific variation was observed inT. paludosum (T. sect.Palustria) andT. serotinum (T. sect.Dioszegia). These results indicate a high intraspecific stability of the trait. Preliminary comparisons of genome size in species/sections considered to be close relatives were made. These data give tentative additional evidence for the close phylogenetic relationship between sectionsPalustria andPiesis and against the close relationship between sectionsPiesis andDioszegia.

Analysis of nrDNA polymorphism in closely related diploid sexual, tetraploid sexual and polyploid agamospermous species

Nuclear sequences of ITS1-5.8S-ITS2 region of rDNA may be an important source of phylogenetically informative data provided that nrDNA is cloned and the character of sequence variation of clones is properly analyzed. nrDNA of selected Taraxacum sections was studied to show sequence variation differences among diploid sexual, tetraploid sexual and polyploid agamospermous species. We examined nucleotide characteristics, substitution pattern, secondary structure, and the phylogenetic utility of ITS1-5.8S-ITS2 from 301 clones of 32 species representing 11 sections. The most divergent sequences of ITS1&2 differed by 17.1% and in 5.8S only by 3.7%. The ITS1-5.8S-ITS2 characteristics, integrity and also stability of secondary structures confirmed that pseudogenes are not responsible for the above variation. The within-individual polymorphism of clones implies that the concerted evolution of ITS cistron of agamospermous polyploid Taraxacum is remarkably suppressed. Sequences of ITS clones proved to be a useful tool for mapping pathways of complex reticulation (polyploid hybridity) in agamospermous Taraxacum.

Apomixis in Taraxacum paludosum (section Palustria, Asteraceae): Recombinations of apomixis elements in inter-sectional crosses

Recent studies have shown independent control of apomixis elements (restitution/diplospory, parthenogenesis and autonomous endosperm) in Taraxacum sect. Ruderalia. We studied inheritance of apomixis elements in the section Palustria using the crosses between various sections used as mother plants and apomictic T. paludosum (sect. Palustria) as pollen donor. Non-apomictic plants prevailed in F1 progeny, and a high incidence of sterility was observed. Triploid non-apomictic F1 hybrids were backcrossed with diploids (sects. Ruderalia, Palustria) and tetraploids (sects. Palustria, Piesis), and produced various types of progeny. These F1 hybrids were classified into three types depending on the occurrence of parthenogenesis along with restitution, and the occurrence of various progeny in particular crosses (i.e. within the same mother plant) was observed. The results indicate the independent genetic control of all apomixis elements in T. paludosum, and recombinations during a restitutional megasporogenesis in hybrids.

Towards a better understanding of the Taraxacum evolution (Compositae–Cichorieae) on the basis of nrDNA of sexually reproducing species

The genus Taraxacum is characterized by prevailing complex multiple hybridity, frequent polyploidy and widespread agamospermous reproduction, which makes the phylogenetic analysis difficult. On the basis of the previous analysis of the variation of nrDNA in Taraxacum taxa with different ploidy levels and modes of reproduction, to mitigate consequences of the reticulate complexity of the genus, a phylogenetic study of 52 samples of sexually reproducing dandelions of 26 sections (and another 13 agamospermous representatives of other sections known to include sexuals) was carried out. Both sexual and agamospermous samples were analysed using maximum parsimony and neighbour network. Exclusively sexual dandelions were analysed using the same approaches. In spite of the general agreement among various types of analyses, there is a limited overall congruence between results of nrDNA analyses and the established taxonomic system of the genus Taraxacum. The analyses shed light on the relationships among the most primitive groups. A stable clade is formed by representatives of the sections Primigenia, Orientalia, Sonchidium, Piesis and T. cylleneum. Another case of stable relationships is that of the members of the sect. Dioszegia. Relationships between the sects. Erythrosperma and Erythrocarpa were supported, and the relatedness of the members of sect. Australasica was confirmed. Rather unexpectedly, the agamospermous samples of the sect. Oligantha (T. minutilobum) are shown to be closely related with the sect. Macrocornuta. The latter section is generally considered to be close to sect. Ceratoidea (T. koksaghyz) on morphological grounds but this presumption is not corroborated by the results of nrDNA analyses. Analyses of 72 samples of sexual dandelions were also performed using the trnL–trnF region of the chloroplast DNA. The maximum parsimony analysis of this region reveals intraspecific variation in a number of ancestral diploid sexual species, all present in the two main branches of the cladogram. This phenomenon is attributed to the ancient gene flow and possibly to the persistence of ancestral cpDNA polymorphism. The strict consensus cpDNA tree information content and interpretability is quite low. The maximum parsimony analysis of combined nrDNA and cpDNA data sets was also performed with expectably low interpretability of the results.

Substantial Genome Size Variation in Taraxacum stenocephalum (Asteraceae, Lactuceae)

There are only a few exceptions to the rule that polyploidy in Taraxacum is associated with agamospermy. One of them is the sexual, tetraploid species Taraxacum stenocephalum. Incidentally, remarkable variation in karyology was found in this species. The present study aims to confirm this variation by an extensive screen of nuclear DNA content. Individuals from two large populations in the Lesser and Greater Caucasus, Georgia were analyzed using flow cytometry to ascertain intraspecific nuclear DNA content variation. Across the whole data set comprising all 159 individuals, a 1.223-fold difference was detected based on propidium iodide (PI) analyses. To verify this finding, we compared flow-cytometric data obtained using DAPI (4′,6-diamidino-2-phenylindole) and PI staining using a representative subset of individuals. This comparison revealed a 1.194-fold difference in DNA content for DAPI and a 1.219-fold difference for PI. Mean nuclear genome size in absolute terms (2C value ± s.d.) was estimated at 4.38u2009±u20090.21xa0pg, ranging from 4.01xa0pg to 4.89xa0pg, despite the invariable chromosome counts of 2nu2009=u200932. A regression analysis comparing the datasets for DAPI and PI staining found a strong correlation between data obtained by the DAPI and PI dyes (Ru2009=u20090.976; Pu2009=u20090.0001). Simultaneous high-resolution flow-cytometric analyses also proved the accuracy of our findings. We discuss possible sources of these large differences in DNA content within Taraxacum stenocephalum. Further research is needed to identify the source of this remarkable variation.

Post-annotation checking of prague dependency treebank 2.0 data

This paper describes methods and tools used for the post-annotation checking of Prague Dependency Treebank 2.0 data The annotation process was complicated by many factors: for example, the corpus is divided into several layers that must reflect each other; the annotation rules changed and evolved during the annotation process; some parts of the data were annotated separately and in parallel and had to be merged with the data later The conversion of the data from the old format to a new one was another source of possible problems besides omnipresent human inadvertence The checking procedures are classified according to several aspects, e.g their linguistic relevance and their role in the checking process, and prominent examples are given In the last part of the paper, the methods are compared and scored.

A revision of names in Taraxacum sect. Erythrocarpa and T. sect. Erythrosperma (Asteraceae: Cichorieae) published by C. E. Sonck from Greece, with nomenclatural comments

Abstract Štěpánek J. & Kirschner J.: A revision of names in Taraxacum sect. Erythrocarpa and T. sect. Erythrosperma (Asteraceae: Cichorieae) published by C. E. Sonck from Greece, with nomenclatural comments. — Willdenowia 44: 137–144. 20 March 2014. — Version of record published online ahead of inclusion in April 2014 issue; ISSN 1868-6397;

A monograph of Taraxacum sect. Palustria.

A Monograph of Taraxacum sect.Palustria , A Monograph of Taraxacum sect.Palustria , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی

PDTSC 2.0 - Spoken Corpus with Rich Multi-layer Structural Annotation

We present a richly annotated spoken language resource, the Prague Dependency Treebank of Spoken Czech 2.0, the primary purpose of which is to serve for speech-related NLP tasks. The treebank features several novel annotation schemas close to the audio and transcript, and the morphological, syntactic and semantic annotation corresponds to the family of Prague Dependency Treebanks; it could thus be used also for linguistic studies, including comparative studies regarding text and speech. The most unique and novel feature is our approach to syntactic annotation, which differs from other similar corpora such as Treebank-3 [8] in that it does not attempt to impose syntactic structure over input, but it includes one more layer which edits the literal transcript to fluent Czech while keeping the original transcript explicitly aligned with the edited version. This allows the morphological, syntactic and semantic annotation to be deterministically and fully mapped back to the transcript and audio. It brings new possibilities for modeling morphology, syntax and semantics in spoken language – either at the original transcript with mapped annotation, or at the new layer after (automatic) editing. The corpus is publicly and freely available.