Juraj Paule

Non-coding nuclear DNA markers in phylogenetic reconstruction.

Molecular DNA based data sets are the most important resource for phylogenetic reconstruction. Among the various marker systems, which were introduced and optimized within the last decade, coding sequences played an important role, especially when molecular clock approaches and multi-gene datasets were assembled. However, non-coding DNA sequences do not only play a quantitatively dominant role, as demonstrated by the two examples nuclear ITS (Internal transcribed spacer regions of nuclear ribosomal DNA) and plastidic trnL-F region, but there is also a wide range of different marker systems that can be applied in different ways. Herein, we review the application of several non-coding nuclear DNA marker systems for phylogenetic reconstructions and summarize valuable information for future research.

A comprehensive chloroplast DNA-based phylogeny of the genus Potentilla (Rosaceae): implications for its geographic origin, phylogeography and generic circumscription.

A reconstruction of phylogenetic relationships based on three chloroplast DNA markers comprising 98 species of the genus Potentilla and 15 additional genera from the tribe Potentilleae (Rosaceae) is presented. The phylogeny supported the current generic concept of the subtribe Fragariinae and resolved major lineages within the subtribe Potentillinae. Resolved lineages corresponded to the combined genera Argentina, Piletophyllum, and Tylosperma, an European and Asian group of species approximately equivalent to the Trichocarpae Herbaceae sensu Th. Wolf, the series Tormentillae Th. Wolf, a North American clade comprising the genera Horkelia, Horkeliella, and Ivesia, the species Potentilla fragarioides and P. freyniana, and to a taxonomically highly diverse but molecularly little diverged core group of Potentilla, respectively. Age estimates of phylogenetic splits resolved in the Potentilleae using Bayesian inference, suggested a diversification of the tribe in the Eocene and radiation of two major evolutionary lineages corresponding to the Fragariinae and Potentillinae at approximately comparable times. Ancestral area reconstructions based on the recent distribution ranges of species and collection sites of cpDNA haplotypes suggested an Asian origin for Potentilla s.str., and explained the arrival of this still informal taxon in Europe and particularly North America by multiple dispersal events. In combining the phylogenetic and geographic data with molecularly inferred time estimates and taxonomy, strongly contrasting evolutionary patterns were identified. These evolutionary patterns included rapid speciation on a continental and worldwide scale accompanied by multiple intercontinental dispersals opposed to largely diverged lineages of limited taxonomic diversity and vicariant geographic distribution. The molecular-based phylogeographic hypothesis finally is discussed on the background of the fossil record of Potentilla.

The Evolutionary History of the Arabidopsis arenosa Complex: Diverse Tetraploids Mask the Western Carpathian Center of Species and Genetic Diversity

The Arabidopsis arenosa complex is closely related to the model plant Arabidopsis thaliana. Species and subspecies in the complex are mainly biennial, predominantly outcrossing, herbaceous, and with a distribution range covering most parts of latitudes and the eastern reaches of Europe. In this study we present the first comprehensive evolutionary history of the A. arenosa species complex, covering its natural range, by using chromosome counts, nuclear AFLP data, and a maternally inherited marker from the chloroplast genome [trnL intron (trnL) and trnL/F intergenic spacer (trnL/F-IGS) of tRNALeu and tRNAPhe, respectively]. We unravel the broad-scale cytogeographic and phylogeographic patterns of diploids and tetraploids. Diploid cytotypes were exclusively found on the Balkan Peninsula and in the Carpathians while tetraploid cytotypes were found throughout the remaining distribution range of the A. arenosa complex. Three centers of genetic diversity were identified: the Balkan Peninsula, the Carpathians, and the unglaciated Eastern and Southeastern Alps. All three could have served as long-term refugia during Pleistocene climate oscillations. We hypothesize that the Western Carpathians were and still are the cradle of speciation within the A. arenosa complex due to the high species number and genetic diversity and the concurrence of both cytotypes there.

Prospects and limits of the flow cytometric seed screen – insights from Potentilla sensu lato (Potentilleae, Rosaceae)

The flow cytometric seed screen allows for identification of reproductive modes of seed formation and inference of the ploidy of contributing gametes. However, the lack of a mathematical formalization to infer male/female genomic contributions, and the prerequisite of a binucleate female contribution to the endosperm limits its applicability. We evaluated this assumption combining a DNA-based progeny survey with a comparison of the cytology of reproductive pathways co-occurring within single individuals representing 14 Potentilleae species from six phylogenetic lineages. A numerical framework valid for sexual and pseudogamous taxa was developed, enabling quantification of female and male genomes contributing to embryo and endosperm independent of gametophyte origins, numbers of sperm involved and ploidy of parents. The inference strongly depended on accurate peak index estimation. The endosperm of Potentilleae species received a binucleate female contribution in five evolutionary lineages whereas endosperm formation remained uncertain in the Tormentillae. A modified flow cytometric seed screen protocol was developed to cope with low endosperm contents. Evolutionary conservation of a binucleate female contribution to the endosperm suggested wide applicability of flow cytometric seed screen – at least in the Potentilleae. However, alternative progeny surveys and precise embryo/endosperm ploidy estimates are required for a comprehensive understanding of the cytology of seed formation.

Implications of hybridisation and cytotypic differentiation in speciation assessed by AFLP and plastid haplotypes--a case study of Potentilla alpicola La Soie.

BackgroundHybridisation is presumed to be an important mechanism in plant speciation and a creative evolutionary force often accompanied by polyploidisation and in some cases by apomixis. The Potentilla collina group constitutes a particularly suitable model system to study these phenomena as it is morphologically extensively variable, exclusively polyploid and expresses apomixis. In the present study, the alpine taxon Potentilla alpicola has been chosen in order to study its presumed hybrid origin, identify underlying evolutionary processes and infer the discreteness or taxonomic value of hybrid forms.ResultsCombined analysis of AFLP, cpDNA sequences and ploidy level variation revealed a hybrid origin of the P. alpicola populations from South Tyrol (Italy) resulting from crosses between P. pusilla and two cytotypes of P. argentea. Hybrids were locally sympatric with at least one of the parental forms. Three lineages of different evolutionary origin comprising two ploidy levels were identified within P. alpicola. The lineages differed in parentage and the complexity of the evolutionary process. A geographically wide-spread lineage thus contrasted with locally distributed lineages of different origins. Populations of P. collina studied in addition, have been regarded rather as recent derivatives of the hexaploid P. argentea. The observation of clones within both P. alpicola and P. collina suggested a possible apomictic mode of reproduction.ConclusionsDifferent hybridisation scenarios taking place on geographically small scales resulted in viable progeny presumably stabilised by apomixis. The case study of P. alpicola supports that these processes played a significant role in the creation of polymorphism in the genus Potentilla. However, multiple origin of hybrids and backcrossing are considered to produce a variety of evolutionary spontaneous forms existing aside of reproductively stabilised, established lineages.

Morphology, phylogeny, and taxonomy of microthlaspi (brassicaceae: coluteocarpeae) and related genera

The genus Thlaspi has been variously subdivided since its description by Linnaeus in 1753, but due to similarities in fruit shape several segregates have still not gained broad recognition, despite the fact that they are not directly related to Thlaspi. This applies especially to segregates now considered to belong to the tribe Coluteocarpeae, which includes several well-studied taxa, e.g., Noccaea caerulescens (syn. Thlaspi caerulescens), and the widespread Microthlaspi perfoliatum (syn. Thlaspi perfoliatum). The taxonomy of this tribe is still debated, as a series of detailed monographs on Coluteocarpeae was not published in English and a lack of phylogenetic resolution within this tribe was found in previous studies. The current study presents detailed phylogenetic investigations and a critical review of morphological features, with focus on taxa previously placed in Microthlaspi. Based on one nuclear (ITS) and two chloroplast (matK, trnL-F) loci, four strongly supported major groups were recovered among the Coluteocarpeae genera included, corresponding to Ihsanalshehbazia gen. nov., Friedrichkarlmeyeria gen. nov., Microthlaspi s.str., and Noccaea s.l. In addition, two new species of Microthlaspi, M. sylvarum-cedri sp. nov. and M. mediterraneo-orientale sp. nov., were discovered, which are well supported by both morphological and molecular data. Furthermore, M. erraticum comb. nov. (diploid) and M. perfoliatum s.str. (polyploid) were shown to be distinct species, phylogenetically widely separate, but with some overlap in several morphological characters. Detailed descriptions, notes on taxonomy, geographical distribution, and line drawings for the new species and each species previously included in Microthlaspi are provided. In addition, the current taxonomic state of the tribe Coluteocarpeae is briefly discussed and it is concluded that while several annual taxa are clearly distinct from Noccaea, many perennial taxa, after thorough phylogenetic and morphological investigations, may have to be merged with this genus.

Floral scent and its correlation with AFLP data in Sorbus

Comparisons between floral scent-based and DNA-molecular-based taxonomies are rare, yet such comparisons indicate that scent can provide useful taxonomic information. Here, we correlate the phytochemical differentiation in floral scent to the DNA-molecular-based differentiation in the genus Sorbus. Inflorescence scent patterns of the apomictic and endemic Sorbus latifolia microspecies Sorbus franconica, Sorbus adeana, and Sorbus cordigastensis originated by hybridization as well as their parental taxa Sorbus aria agg. and Sorbus torminalis were investigated with the dynamic headspace method. The scent data (presence/absence of compounds) were used to construct an UPGMA tree, to calculate a similarity matrix, and to correlate them with the published amplified fragment length polymorphism (AFLP) data of the same individuals, populations, and taxa. Flow cytometry was used to estimate the DNA-ploidy level of the taxa. Scent analyses showed a total of 68 substances, among them aromatic compounds, terpenoids, aliphatics, and nitrogen-containing compounds. The scent patterns were taxon-specific, and the number of scent components differed among taxa. The correlations with the published AFLP data on population and individual level are highly significant, indicating that the scent and AFLP data are highly congruent in the plants studied. Scent therefore provides useful taxonomic characters in Sorbus.

Morphology, DNA-molecular variation, karyology, ecogeography, and phytosociology suggest allopatric differentiation and species rank for Potentilla rigoana (Rosaceae)

The Apennines show high floristic diversity promoted by their particular role as an ice-age refugium. However, studies on the evolution of Apennine plants are rare. Potentilla rigoana from the mainly European P. heptaphylla group is an example of a largely ignored taxon originally described from this mountain range. Its evolutionary origin and taxonomic status was studied in an interdisciplinary approach combining morphometric, karyological (flow cytometry and chromosome counting), DNA-molecular (AFLP), ecogeographic (WorldClim climatic variables), and phytosociological data. Morphometric analyses revealed 16 metric and 2 nominal characters separating P. rigoana from its close relatives P. crantzii, P. heptaphylla s.l., and P. neumanniana. Additionally, P. rigoana was intermediate with respect to temperature requirements as well as altitudinal distribution compared to P. crantzii and P. heptaphylla s.l. The species was documented from 54 populations or sampling sites located in the central and southern Apennines where it occurs in montane to subalpine dry habitats. Morphometric analysis suggested its occurrence in the Balkans. Molecular and morphometric analyses further suggested reticulate relationships of the Balkan samples of P. heptaphylla s.l. with P. rigoana. Potentilla rigoana comprises five ploidy levels with the dominant diploids and tetraploids geographically centered in the southern and central Apennines, respectively. The existence of diploids and a uniformly heptaploid population indicate the occurrence of both sexuality and apomixis. The combined datasets sug - gested species status for P. rigoana. The ecogeographic distribution indicated an allopatric differentiation of the species within the P. heptaphylla group. The latitudinal separation of diploid and polyploid cytotypes coincided with a glacial refugium in the southern Apennines and more dynamic past climatic conditions in the central Apennines.

An Annotated Draft Genome for Radix auricularia (Gastropoda, Mollusca)

Molluscs are the second most species-rich phylum in the animal kingdom, yet only 11 genomes of this group have been published so far. Here, we present the draft genome sequence of the pulmonate freshwater snail Radix auricularia. Six whole genome shotgun libraries with different layouts were sequenced. The resulting assembly comprises 4,823 scaffolds with a cumulative length of 910 Mb and an overall read coverage of 72×. The assembly contains 94.6% of a metazoan core gene collection, indicating an almost complete coverage of the coding fraction. The discrepancy of ∼690 Mb compared with the estimated genome size of R. auricularia (1.6 Gb) results from a high repeat content of 70% mainly comprising DNA transposons. The annotation of 17,338 protein coding genes was supported by the use of publicly available transcriptome data. This draft will serve as starting point for further genomic and population genetic research in this scientifically important phylum.

Chromosome numbers of the flora of Germany—a new online database of georeferenced chromosome counts and flow cytometric ploidy estimates

Abstract Chromosomal speciation processes gain increasing attention in plant systematics and evolution, and new approaches revealed a high diversity in chromosome numbers even within recognized taxa. Reliable counts linked to known accessions are thus needed yet often hardly available. We present a new online database for chromosome counts and ploidy estimates of the flora of Germany with a detailed documentation of the examined material, and its sampling locality. The chromosome database builds upon a relational database and includes standardized taxon identification, study date, georeferenced locality and additional collection as well as publication details from which the karyological information was extracted. In order to reach the best compatibility with other botanical publications of the study region, taxonomic concepts and nomenclature follow the “Rothmaler”, a widely accepted field flora of vascular plants in Germany. Our online database is available at http://chromosomes.senckenberg.de. The site consists of the main page with project information, a search tool, an interactive map display, a contact and a data submission form. The zoomable map shows the localities of the search result, allows to refine the geographic search as well as to select individual data points.