Department of Evolutionary Plant Biology

The department was founded in 2017 as a result of fusion of two former departments with overlapping interests – Dept. of Genetic Ecology and Dept. of Flow Cytometry. Newly established research unit is targeted at numerous aspects of plant evolution at various levels: (i) investigation of individual genomes (horizontal gene transfer, DNA endoreduplication, cytogenetics), (ii) studying of micro-evolutionary processes at population level (cytotypes interaction, phylogeogpraphy, etc.), (iii) unrevealing species level interactions (evolution of diploid-polyploid complexes, hybrid speciation, molecular systematics, etc.), and (iv) detection of evolutionary forces acting at supra-generic level (e.g. causes of differential radiation at generic and higher levels). Mainly the evolutionary processes themselves and their impact on recognized biodiversity are subjected to research. The hot-spots of the research activities are geographically aimed to the Eurasia, the equatorial Andes and the Cape Floristic Region. The research combines field, experimental and laboratory work.  The integral part of the department is Laboratory of Flow Cytometry.

Main research topics

Evolution at genomic level

Foreign genetic material in Triticeae grasses

Grasses from the tribe Triticeae (Poaceae) represent fascinating examples of reticulate evolution, which is mainly caused by intratribal hybridization and polyploidization. Besides, many of Triticeae grasses capture foreign genetic material from surprisingly distant sources, that is supposed to be transferred by mechanisms other than reproduction, i.e., through horizontal gene transfer. The nature and dynamics of foreign genetic material in Triticeae grasses are studied involving molecular, bioinformatic and cytogenetic tools that allow us to capture, characterize, and physically map the foreign genetic material within the genomes of our study species.

DNA endoreplication

DNA endoreplication, i.e. intraindividual polyploidization of particular tissues or cells, is quite common process in several plant families, but its evolutionary significance is still dubious and scarcely understandable. Moreover existence of partial endoreplication in orchids, where only species specific part of genome is replicated, further tangling researchers’ heads. The investigation is aimed to find out some ecological, physiological or other traits that are associated with the process.

 

Micro-evolutionary processes in plant populations (case studies)

Pilosella echioides represents a unique polyploid complex occasionally forming mixed populations with triploid prevalence despite its sexual reproduction. Those triploids interact with other two major ploidy levels (diploids and tetraploids) and produce viable progeny. On the other hand, multiploidy populations are maintained dominantly by clonal growth that favors higher ploidy levels (triploids and tetraploids) at the expense of diploids.

Tripleurospermum inodorum is a widespread weed of man-disturbed sites with two common cytotypes, diploid and tetraploid, forming an extensive contact zone in Europe. A diffuse, mosaic-like structure of the contact zone favors common cytotype co-occurrence and formation of mixed-ploidy populations. Triploid hybrids, originating in mixed-ploidy populations, are vigorous and produce mainly aneuploid offspring that is partially-fertile. This leads to complex reproductive interactions that generate cytogenetic diversity and facilitate inter-ploidy gene flow between diploids and tetraploids. Due to predominantly annual life cycle of T. inodorum, local ploidy mixtures show a substantial between-year dynamics in both population abundance and cytotype proportions that make them unique model systems for studying the conditions allowing local cytotype coexistence.

Knautia serpentinicola is a Central-European representative of the K. arvensis group with very distinctive ecological requirements. The species is a serpentine specialist bound to four isolated serpentine outcrops of the Hercynian massif. Of the four localities inhabited by the species, three are exclusively diploid but one, in the Slavkovský les Mts. (W Bohemia, Czech Republic), is mixed-ploidy and aside from diploids is occupied by individuals of a tetraploid cytotype. Molecular-genetic and morphological evidence suggest that the tetraploids originated relatively recently from the residing diploid progenitors, which makes it one of the few well-documented cases of primary contact zones of cytotypes. The mixed-ploidy population of K. serpentinicola in Slavkovský les Mts. is a convenient “microcosm” for studying both phenotypic effects of genome doubling and the conditions enabling successful establishment of new polyploid mutants in populations of their diploid progenitors.

Phylogeography of Alnus glutinosa and A. incana.

Presently, there is a tendency to believe, that pattern of postglacial colonization of Europe was more complicated than the concept following the traditional paradigm of colonization from three southern peninsular refugia. In this project, we purpose to discover the postglacial migration routes and late glacial refugia of a boreal (Alnus incana) and temperate (A. glutinosa) tree species. We are addressing these issues by combining both chloroplast DNA and microsatellite markers, which together can provide complimentary insights at different geographical and temporal scales. Besides molecular data the hypotheses on migration routes are proposed based on paleoecological evidence and environmental niche modeling and tested using approximate bayesian computation (ABC) approach.

Hieracium subgen. Pilosella, highly complex group of partly apomictic plants is notoriously known for enormous variation (resulted in thousands of described taxa). Among sources of its intricate pattern dominate: polyploidization, combination of the sexual and apomictic breeding systems, widespread hybridization and vegetative reproduction. Our team focuses on cytogeography (flow-cytometry), reproductive pattern (experimental hybridization, FCSS) and coexistence of cytotypes in model populations (flow cytometry, SSRs).  Special attention is paid to the role of residual sexuality of facultative apomicts for the composition of populations in central Europe and the Balkan Peninsula.

 

Evolution at species level (case studies)

Alnus polyploids

Recently the existence of two tetraploid Alnus species, A. lusitanica and A. rohlenae, endemics to Iberian peninsula and the Dinaric Alps, respectively, were recognized. Their origin, postglacial history and interactions to closely relative diploid A. glutinosa are investigated using flow-cytometric, cpDNA and nuclear microsatellite data in combination with environmental niche and ABC modeling.

Anthoxanthum odoratum agg. is formed by several diploids, occupying namely the Mediterranean area, Macaronesia and the mountains of Eurasia, and polyploids that are distributed widely (e. g. worldwide A. odoratum s. str.) or locally (e.g. Iberian endemic A. amarum). The evidence that the Mediterranean area is the place of origin of the European Anthoxanthum (sect. Anthoxanthum) was assembled and that climatic changes starting in the Miocene were the main factors promoting taxa differentiation. The later divergence probably took place in the Pleistocene and started polyploid evolution that has further shaped the genus. It seems, however, that speciation of a substantial part of the diploid taxa is still an ongoing process which makes difficult the understanding of origin of polyploids.

Bolboschoenus

The study is focused on wetland plant species of genus Bolboschoenus, in which the same morphological pattern repeats across continents. These morphotypes occurring in Eurasia, Australia and North America are usually known under different names. This may either represents parallel evolution of species within one morphotype and/or be a consequence of migration of plants between continents in the past. The investigation of European species refers that inter-specific ecological differentiation may be stronger than morphological differentiation, and distinguishing the closely related species may lead to an explanation for the relatively wide ecological range of original species complex. The ecological properties represent crucial features influencing geographic distribution of the species, their frequency of occurrence and coexistence that may result in (homoploid) hybridization.

Chenopodium album agg.

Many species of diploid-polyploid complex of C. album aggregate evolved through hybridization and polyploidization events. However, different studies brought contradictory results most likely due to incomplete sampling design. We apply a set of various approaches (classical caryology, flow-cytometry, genomic in situ hybridization and sequencing of cpDNA and both rDNA and low-copy nuclear markers) on so far the most comprehensive collection of taxa, to estimate the ploidy level and genome size variation, reconstruct the basic evolutionary relationships within this group and infer the origin of polyploid taxa.

 

Adaptive radiation

Evolution of the most diverse orchid group – Pleurothallidinae

The project aims at investigating the role of genome-wide processes (whole genome duplication, genome size upsizing/downsizing) and ecological speciation (potential shifts in environmental niche space) in the most diverse subtribe of the orchid family, Pleurothallidinae. Using a combination of state-of-the-art methodological approaches (Hyb-Seq, cytogenomics, flow cytometry, niche modelling) we will build a robust phylogeny, assess variation in nuclear genome size and the processes behind it, identify frequency of polyploids, and characterize ecological niches of a representative set of species. Cross-disciplinary data integration will provide a new level of understanding of evolutionary drivers generating the biological diversity in the largest angiosperm family.

Evolution of Oxalis

The research aims to test if and, if so, to what extent polyploidization and hybridization played a role in the radiation of Oxalis L., a genus of high cytotype variation of its species. Our focus lies on Oxalis species of the Greater Cape Floristic Region. We combine phylogenetics (Hyb-Seq) with cytogenetic methods (flow cytometry, chromosome counts, Fluorescence In Situ Hybridization) in order to address the role of polyploidization and hybridization in Oxalis differentiation both on a phylogenetic and population scale.

 

 

Further extra projects and activities:

Genome size database of the Greater Cape Flora

The ambitious aim of the project is to gather genome size data and GC content of majority of plant species forming world’s biodiversity hot-spot – the Greater Cape Flora. This task is provided in cooperation with South African scientific institutions (Stellenbosch University, Kirstenbosch National Botanical Garden) as well as local botanic enthusiasts. Up-to-date more than 10 % of known plant species is analyzed and will be subjected to publication in near future.

 

Laboratory of Flow Cytometry

The mission of the laboratory, established in September 2000, is to provide accurate and timely estimates of genome size (both in absolute units and in relative terms as an indication of ploidy level) to meet demands of different research groups. The data obtained are widely used in plant population and evolutionary biology, ecology, and biosystematics to address questions of phenotypic manifestation, spatial distribution, and evolutionary significance of genome duplication (polyploidy) and chromosomal variation (aneuploidy). The high speed and reliability of flow cytometry paves the way for large-scale surveys at the landscape, population, individual, and tissue levels. Combination with other, namely molecular, techniques is emphasized as it promises qualitative advances in our understanding of genome multiplication in the population biology of vascular plants.

The laboratory is equipped with two Partec PA II instruments (with argon-ion 488-nm laser and mercury arc lamp) and one Partec CyFlow Space instrument (equipped with UV-chip) used mainly for ploidy level estimation, and Partec CyFlow SL and Partec CyFlow Space instruments (both equipped with solid state 532-nm laser) used mainly to determine nuclear genome size.