Publications by authors named "Karol Marhold"

40 Publications

MorphoTools2: an R package for multivariate morphometric analysis.

Bioinformatics 2022 05;38(10):2954-2955

Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, SK-845 23 Bratislava, Slovakia.

Summary: The package MorphoTools2 is intended for multivariate analyses of morphological data. Commonly used tools are missing or scattered across several R packages. The new package, in order to make the workflow convenient and fast, wraps available statistical and graphical tools and provides a comprehensive framework for checking and manipulating input data, core statistical analyses and a wide palette of functions designed to visualize results.

Availability And Implementation: Stable version is available from CRAN: https://cran.r-project.org/package=MorphoTools2. The development version is available from the following GitHub repository: https://github.com/MarekSlenker/MorphoTools2. The software is distributed under the GNU General Public Licence (v.3).

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btac173DOI Listing
May 2022

MorphoTools2: an R package for multivariate morphometric analysis.

Bioinformatics 2022 Mar 22. Epub 2022 Mar 22.

Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovakia.

Summary: The package MorphoTools2 is intended for multivariate analyses of morphological data. Commonly used tools are missing or scattered across several R packages. The new package, in order to make the workflow convenient and fast, wraps available statistical and graphical tools and provides a comprehensive framework for checking and manipulating input data, core statistical analyses and a wide palette of functions designed to visualize results.

Availability And Implementation: Stable version is available from CRAN: https://cran.r-project.org/package=MorphoTools2. The development version is available from the following GitHub repository: https://github.com/MarekSlenker/MorphoTools2. The software is distributed under the GNU General Public Licence (v.3).

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btac173DOI Listing
March 2022

Morphological and environmental differentiation as prezygotic reproductive barriers between parapatric and allopatric Campanula rotundifolia agg. cytotypes.

Ann Bot 2021 Sep 24. Epub 2021 Sep 24.

Charles University, Faculty of Science, Department of Botany, Benátská 2, 12843, Prague, Czech Republic.

Background And Aims: Reproductive isolation and local establishment are necessary for plant speciation. Polyploidy, possession of more than two complete chromosome sets, creates a strong postzygotic reproductive barrier between diploid and tetraploid cytotypes. However, this barrier weakens between polyploids, e.g., tetraploids and hexaploids. Reproductive isolation may be enhanced by cytotype morphological and environmental differentiation. Moreover, morphological adaptations to local conditions contribute to plant establishment. However, the relative contributions of the ploidy level and environment to morphology are generally neglected. Thus, the extent of morphological variation driven by ploidy level and the environment was modelled for diploid, tetraploid, and hexaploid cytotypes of Campanula rotundifolia agg. Cytotype distribution was updated, and morphological and environmental differentiation was tested in the presence and absence of natural contact zones.

Methods: Cytotype distribution was assessed from 231 localities in Central Europe, including 48 localities with known chromosome counts, using flow cytometry. Differentiation in environmental niche and morphology was tested for cytotype pairs using discriminant analyses. A structural equation model was used to explore the synergies between cytotype, environment and morphology.

Key Results: Tremendous discrepancies were revealed between the reported and detected cytotype distribution. Neither mixed-ploidy populations nor interploidy hybrids were detected in the contact zones. Diploids had the broadest environmental niche, while hexaploids had the smallest and specialized niche. Hexaploids and spatially isolated cytotype pairs differed morphologically, including allopatric tetraploids. While leaf and shoot morphology were influenced by environmental conditions and polyploidy, flower morphology depended exclusively on the cytotype.

Conclusions: Reproductive isolation mechanisms vary between cytotypes. While diploids and polyploids are isolated postzygotically, the environmental niche shift is essential between higher polyploids. The impact of polyploidy and the environment on plant morphology implies the adaptive potential of polyploids, while the exclusive relationship between flower morphology and cytotype accents the role of polyploidy in reproductive isolation.
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http://dx.doi.org/10.1093/aob/mcab123DOI Listing
September 2021

Editorial: Evolution and Biodiversity of Wild Polyploids.

Front Plant Sci 2021 20;12:723439. Epub 2021 Jul 20.

Department of Systematics, Biodiversity and Evolution of Plants, University of Göttingen, Göttingen, Germany.

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http://dx.doi.org/10.3389/fpls.2021.723439DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8329525PMC
July 2021

Allele Sorting as a Novel Approach to Resolving the Origin of Allotetraploids Using Hyb-Seq Data: A Case Study of the Balkan Mountain Endemic .

Front Plant Sci 2021 28;12:659275. Epub 2021 Apr 28.

Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia.

Mountains of the Balkan Peninsula are significant biodiversity hotspots with great species richness and a large proportion of narrow endemics. Processes that have driven the evolution of the rich Balkan mountain flora, however, are still insufficiently explored and understood. Here we focus on a group of (Brassicaceae) perennials growing in wet, mainly mountainous habitats. It comprises several Mediterranean endemics, including those restricted to the Balkan Peninsula. We used target enrichment with genome skimming (Hyb-Seq) to infer their phylogenetic relationships, and, along with genomic hybridization (GISH), to resolve the origin of tetraploid endemic to the Southern Pindos Mts. (Greece). We also explored the challenges of phylogenomic analyses of polyploid species and developed a new approach of allele sorting into homeologs that allows identifying subgenomes inherited from different progenitors. We obtained a robust phylogenetic reconstruction for diploids based on 1,168 low-copy nuclear genes, which suggested both allopatric and ecological speciation events. In addition, cases of plastid-nuclear discordance, in agreement with divergent nuclear ribosomal DNA (nrDNA) copy variants in some species, indicated traces of interspecific gene flow. Our results also support biogeographic links between the Balkan and Anatolian-Caucasus regions and illustrate the contribution of the latter region to high Balkan biodiversity. An allopolyploid origin was inferred for , which highlights the role of mountains in the Balkan Peninsula both as refugia and melting pots favoring species contacts and polyploid evolution in response to Pleistocene climate-induced range dynamics. Overall, our study demonstrates the importance of a thorough phylogenomic approach when studying the evolution of recently diverged species complexes affected by reticulation events at both diploid and polyploid levels. We emphasize the significance of retrieving allelic and homeologous variation from nuclear genes, as well as multiple nrDNA copy variants from genome skim data.
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http://dx.doi.org/10.3389/fpls.2021.659275DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8115912PMC
April 2021

So Closely Related and Yet So Different: Strong Contrasts Between the Evolutionary Histories of Species of the Polyploid Complex in Central Europe.

Front Plant Sci 2020 18;11:588856. Epub 2020 Dec 18.

Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia.

Recurrent polyploid formation and weak reproductive barriers between independent polyploid lineages generate intricate species complexes with high diversity and reticulate evolutionary history. Uncovering the evolutionary processes that formed their present-day cytotypic and genetic structure is a challenging task. We studied the species complex of , composed of diploid endemics in the European Mediterranean and diploid-polyploid lineages more widely distributed across Europe, focusing on the poorly understood variation in Central Europe. To elucidate the evolution of Central European populations we analyzed ploidy level and genome size variation, genetic patterns inferred from microsatellite markers and target enrichment of low-copy nuclear genes (Hyb-Seq), and environmental niche differentiation. We observed almost continuous variation in chromosome numbers and genome size in s.str., which is caused by the co-occurrence of euploid and dysploid cytotypes, along with aneuploids, and is likely accompanied by inter-cytotype mating. We inferred that the polyploid cytotypes of s.str. are both of single and multiple, spatially and temporally recurrent origins. The tetraploid evolved at least twice in different regions by autopolyploidy from diploid . The extensive genome size and genetic variation of reflects differentiation induced by the geographic isolation of disjunct populations, establishment of triploids of different origins, and hybridization with sympatric . . Geographically structured genetic lineages identified in the species under study, which are also ecologically divergent, are interpreted as descendants from different source populations in multiple glacial refugia. The postglacial range expansion was accompanied by substantial genetic admixture between the lineages of . s.str., which is reflected by diffuse borders in their contact zones. In conclusion, we identified an interplay of diverse processes that have driven the evolution of the species studied, including allopatric and ecological divergence, hybridization, multiple polyploid origins, and genetic reshuffling caused by Pleistocene climate-induced range dynamics.
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http://dx.doi.org/10.3389/fpls.2020.588856DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7775393PMC
December 2020

Parallel Alpine Differentiation in .

Front Plant Sci 2020 8;11:561526. Epub 2020 Dec 8.

Department of Botany, Charles University, Prague, Czechia.

Parallel evolution provides powerful natural experiments for studying repeatability of evolution and genomic basis of adaptation. Well-documented examples from plants are, however, still rare, as are inquiries of mechanisms driving convergence in some traits while divergence in others. , a predominantly foothill species with scattered morphologically distinct alpine occurrences is a promising candidate. Yet, the hypothesis of parallelism remained untested. We sampled foothill and alpine populations in all regions known to harbor the alpine ecotype and used SNP genotyping to test for repeated alpine colonization. Then, we combined field surveys and a common garden experiment to quantify phenotypic parallelism. Genetic clustering by region but not elevation and coalescent simulations demonstrated parallel origin of alpine ecotype in four mountain regions. Alpine populations exhibited parallelism in height and floral traits which persisted after two generations in cultivation. In contrast, leaf traits were distinctive only in certain region(s), reflecting a mixture of plasticity and genetically determined non-parallelism. We demonstrate varying degrees and causes of parallelism and non-parallelism across populations and traits within a plant species. Parallel divergence along a sharp elevation gradient makes a promising candidate for studying genomic basis of adaptation.
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http://dx.doi.org/10.3389/fpls.2020.561526DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7753741PMC
December 2020

Niche similarity in diploid-autotetraploid contact zones of Arabidopsis arenosa across spatial scales.

Am J Bot 2020 10 25;107(10):1375-1388. Epub 2020 Sep 25.

Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Prague, Czech Republic.

Premise: Whole genome duplication is a major evolutionary event, but its role in ecological divergence remains equivocal. When populations of different ploidy (cytotypes) overlap in space, "contact zones" are formed, allowing the study of evolutionary mechanisms contributing toward ploidy divergence. Multiple contact zones per species' range are often described but rarely leveraged as natural replicates. We explored whether the strength of niche differentiation of diploid and autotetraploid Arabidopsis arenosa varies over distinct contact zones and if the frequency of triploids decreases from seedling to adult stage.

Methods: We characterized ploidy composition and habitat preferences in 264 populations across three contact zones using climatic niche modeling. Ecological differences of cytotypes were also assessed using local vegetation surveys at 110 populations within two contact zones, and at the finer scale within five mixed-ploidy sites. This was complemented by flow cytometry of seedlings.

Results: We found no niche differences between diploid and tetraploid populations within contact zones for either climatic or local environmental variables. Comparisons of cytotypes within mixed-ploidy sites found weak niche differences that were inconsistent in direction. Triploid individuals were virtually absent (0.14%) in the field, and they were at a similarly low frequency (0.2%) in ex situ germinated seedlings.

Conclusions: This study demonstrates the strength in investigating different spatial scales across several contact zones when addressing ecological niche differentiation between ploidies. The lack of consistent habitat differentiation of ploidies across the scales and locations supports the recently emerging picture that processes other than ecological differentiation may underlie ploidy coexistence in diploid-autopolyploid systems.
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http://dx.doi.org/10.1002/ajb2.1534DOI Listing
October 2020

Diversification and independent polyploid origins in the disjunct species Alyssum repens from the Southeastern Alps and the Carpathians.

Am J Bot 2019 11 22;106(11):1499-1518. Epub 2019 Oct 22.

Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23, Bratislava, Slovakia.

Premise: Disjunct distributions have been commonly observed in mountain plant species and have stimulated phylogeographic and phylogenetic research. Here we studied Alyssum repens, a member of the polyploid species complex A. montanum-A. repens, which exhibits SE Alpine-Carpathian disjunctions with a large elevational span and consists of diploid and tetraploid populations. We aimed to investigate the species' genetic and cytotype structure in the context of its distribution patterns, to elucidate the polyploid origins and to propose an appropriate taxonomic treatment.

Methods: We combined AFLP fingerprinting markers, sequence variation of the highly repetitive ITS region of rDNA and the low-copy DET1 nuclear gene, genome size, and morphometric data.

Results: We identified four geographically structured genetic lineages. One consisted of diploid populations from the foothills of the Southeastern Alps and neighboring regions, and the three others were allopatric montane to alpine groups comprising diploids and tetraploids growing in the Southeastern Carpathians and the Apuseni Mts. in Romania.

Conclusions: We inferred a vicariance scenario associated with Quaternary climatic oscillations, accompanied by one auto- and two allopolyploidization events most likely involving a northern Balkan relative. Whereas genetic differentiation and allopatric distribution would favor the taxonomic splitting of this species, the genetic lineages largely lack morphological distinguishability, and their ecological, cytotype and genome size divergence is only partial. Even though we probably face here a case of incipient speciation, we propose to maintain the current taxonomic treatment of Alyssum repens as a single, albeit variable, species.
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http://dx.doi.org/10.1002/ajb2.1370DOI Listing
November 2019

Role of ploidy in colonization of alpine habitats in natural populations of Arabidopsis arenosa.

Ann Bot 2019 09;124(2):255-268

Department of Botany, Charles University, Prague, Czech Republic.

Background And Aims: Polyploidy is an important driver of plant diversification and adaptation to novel environments. As a consequence of genome doubling, polyploids often exhibit greater colonizing ability or occupy a wider ecological niche than diploids. Although elevation has been traditionally considered as a key driver structuring ploidy variation, we do not know if environmental and phenotypic differentiation among ploidy cytotypes varies along an elevational gradient. Here, we tested for the consequences of genome duplication on genetic diversity, phenotypic variation and habitat preferences on closely related diploid and tetraploid populations that coexist along approx. 2300 m of varying elevation.

Methods: We sampled and phenotyped 45 natural diploid and tetraploid populations of Arabidopsis arenosa in one mountain range in Central Europe (Western Carpathians) and recorded abiotic and biotic variables at each collection site. We inferred genetic variation, population structure and demographic history in a sub-set of 29 populations genotyped for approx. 36 000 single nucleotide polymorphisms.

Key Results: We found minor effects of polyploidy on colonization of alpine stands and low genetic differentiation between the two cytotypes, mirroring recent divergence of the polyploids from the local diploid lineage and repeated reticulation events among the cytotypes. This pattern was corroborated by the absence of ecological niche differentiation between the two cytotypes and overall phenotypic similarity at a given elevation.

Conclusions: The case of A. arenosa contrasts with previous studies that frequently showed clear niche differentiation between cytotypes. Our work stresses the importance of considering genetic structure and past demographic processes when interpreting the patterns of ploidy distributions, especially in species that underwent recent polyploidization events.
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http://dx.doi.org/10.1093/aob/mcz070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6758580PMC
September 2019

The story of promiscuous crucifers: origin and genome evolution of an invasive species, Cardamine occulta (Brassicaceae), and its relatives.

Ann Bot 2019 09;124(2):209-220

Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovak Republic.

Background And Aims: Cardamine occulta (Brassicaceae) is an octoploid weedy species (2n = 8x = 64) originated in Eastern Asia. It has been introduced to other continents including Europe and considered to be an invasive species. Despite its wide distribution, the polyploid origin of C. occulta remained unexplored. The feasibility of comparative chromosome painting (CCP) in crucifers allowed us to elucidate the origin and genome evolution in Cardamine species. We aimed to investigate the genome structure of C. occulta in comparison with its tetraploid (2n = 4x = 32, C. kokaiensis and C. scutata) and octoploid (2n = 8x = 64, C. dentipetala) relatives.

Methods: Genomic in situ hybridization (GISH) and large-scale CCP were applied to uncover the parental genomes and chromosome composition of the investigated Cardamine species.

Key Results: All investigated species descended from a common ancestral Cardamine genome (n = 8), structurally resembling the Ancestral Crucifer Karyotype (n = 8), but differentiated by a translocation between chromosomes AK6 and AK8. Allotetraploid C. scutata originated by hybridization between two diploid species, C. parviflora and C. amara (2n = 2x = 16). By contrast, C. kokaiensis has an autotetraploid origin from a parental genome related to C. parviflora. Interestingly, octoploid C. occulta probably originated through hybridization between the tetraploids C. scutata and C. kokaiensis. The octoploid genome of C. dentipetala probably originated from C. scutata via autopolyploidization. Except for five species-specific centromere repositionings and one pericentric inversion post-dating the polyploidization events, the parental subgenomes remained stable in the tetra- and octoploids.

Conclusions: Comparative genome structure, origin and evolutionary history was reconstructed in C. occulta and related species. For the first time, whole-genome cytogenomic maps were established for octoploid plants. Post-polyploid evolution in Asian Cardamine polyploids has not been associated with descending dysploidy and intergenomic rearrangements. The combination of different parental (sub)genomes adapted to distinct habitats provides an evolutionary advantage to newly formed polyploids by occupying new ecological niches.
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http://dx.doi.org/10.1093/aob/mcz019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6758578PMC
September 2019

Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa.

Nat Ecol Evol 2019 03 25;3(3):457-468. Epub 2019 Feb 25.

Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK.

Ploidy-variable species allow direct inference of the effects of chromosome copy number on fundamental evolutionary processes. While an abundance of theoretical work suggests polyploidy should leave distinct population genomic signatures, empirical data remains sparse. We sequenced ~300 individuals from 39 populations of Arabidopsis arenosa, a naturally diploid-autotetraploid species. We find that the impacts of polyploidy on population genomic processes are subtle yet pervasive, such as reduced efficiency of purifying selection, differences in linked selection and rampant gene flow from diploids. Initial masking of deleterious mutations, faster rates of nucleotide substitution and interploidy introgression likely conspire to shape the evolutionary potential of polyploids.
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http://dx.doi.org/10.1038/s41559-019-0807-4DOI Listing
March 2019

Growth form evolution and hybridization in (Asteraceae) from the high equatorial Andes.

Ecol Evol 2017 08 10;7(16):6455-6468. Epub 2017 Jul 10.

Department of Botany Faculty of Science Charles University Prague Czech Republic.

Changes in growth forms frequently accompany plant adaptive radiations, including páramo-a high-elevation treeless habitat type of the northern Andes. We tested whether diverse group of inhabiting montane forests and páramo represented such growth form changes. We also investigated the role of Andean geography and environment in structuring genetic variation of this group. We sampled 108 populations and 28 species of (focusing on species from former genera and ) and analyzed their genetic relationships and patterns of intraspecific variation using DNA fingerprinting (AFLPs) and nuclear DNA sequences (ITS). We partitioned genetic variation into environmental and geographical components. ITS-based phylogeny supported monophyly of a - clade. A grade of herbaceous alpine species subtended the - clade suggesting a change from the herbaceous to the woody growth form. Both ITS sequences and the AFLPs separated a group composed of the majority of páramo subshrubs from other group(s) comprising both forest and páramo species of various growth forms. These morphologically variable group(s) further split into clades encompassing both the páramo subshrubs and forest lianas, indicating independent switches among the growth forms and habitats. The finest AFLP genetic structure corresponded to morphologically delimited species except in two independent cases in which patterns of genetic variation instead reflected geography. Several morphologically variable species were genetically admixed, which suggests possible hybrid origins. Latitude and longitude accounted for 5%-8% of genetic variation in each of three AFLP groups, while the proportion of variation attributed to environment varied between 8% and 31% among them. A change from the herbaceous to the woody growth form is suggested for species of high-elevation Andean . Independent switches between habitats and growth forms likely occurred within the group. Hybridization likely played an important role in species diversification.
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http://dx.doi.org/10.1002/ece3.3206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5574811PMC
August 2017

Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects.

Database (Oxford) 2017 01;2017(1)

SNSB IT Center, Staatliche Naturwissenschaftliche Sammlungen Bayerns, München, Germany.

With biodiversity research activities being increasingly shifted to the web, the need for a system of persistent and stable identifiers for physical collection objects becomes increasingly pressing. The Consortium of European Taxonomic Facilities agreed on a common system of HTTP-URI-based stable identifiers which is now rolled out to its member organizations. The system follows Linked Open Data principles and implements redirection mechanisms to human-readable and machine-readable representations of specimens facilitating seamless integration into the growing semantic web. The implementation of stable identifiers across collection organizations is supported with open source provider software scripts, best practices documentations and recommendations for RDF metadata elements facilitating harmonized access to collection information in web portals.

Database Url: : http://cetaf.org/cetaf-stable-identifiers.
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http://dx.doi.org/10.1093/database/bax003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5467547PMC
January 2017

František Nábělek's Iter Turcico-Persicum 1909-1910 - database and digitized herbarium collection.

PhytoKeys 2016 1(75):69-79. Epub 2016 Dec 1.

Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovak Republic; Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-128 01 Praha 2, Czech Republic.

The Czech botanist František Nábělek (1884-1965) explored the Middle East in 1909-1910, visiting what are now Israel, Palestine, Jordan, Syria, Lebanon, Iraq, Bahrain, Iran and Turkey. He described four new genera, 78 species, 69 varieties and 38 forms of vascular plants, most of these in his work (1923-1929). The main herbarium collection of Iter Turcico-Persicum comprises 4163 collection numbers (some with duplicates), altogether 6465 specimens. It is currently deposited in the herbarium SAV. In addition, some fragments and duplicates are found in B, E, W and WU. The whole collection at SAV was recently digitized and both images and metadata are available via web portal www.nabelek.sav.sk, and through JSTOR Global Plants and the Biological Collection Access Service. Most localities were georeferenced and the web portal provides a mapping facility. Annotation of specimens is available via the AnnoSys facility. For each specimen a CETAF stable identifier is provided enabling the correct reference to the image and metadata.
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http://dx.doi.org/10.3897/phytokeys.75.9780DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5234538PMC
December 2016

On the origins of Balkan endemics: the complex evolutionary history of the Cyanus napulifer group (Asteraceae).

Ann Bot 2016 11 21;118(6):1071-1088. Epub 2016 Jul 21.

Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84523 Bratislava, Slovakia.

Background And Aims: The Balkan Peninsula is one of the most important centres of plant diversity in Europe. Here we aim to fill the gap in the current knowledge of the evolutionary processes and factors modelling this astonishing biological richness by applying multiple approaches to the Cyanus napulifer group.

Methods: To reconstruct the mode of diversification within the C. napulifer group and to uncover its relationships with potential relatives with x = 10 from Europe and Northern Africa, we examined variation in genetic markers (amplified fragment length polymorphisms [AFLPs]; 460 individuals), relative DNA content (4',6-diamidino-2-phenylindole [DAPI] flow cytometry, 330 individuals) and morphology (multivariate morphometrics, 40 morphological characters, 710 individuals). To elucidate its evolutionary history, we analysed chloroplast DNA (cpDNA) sequences of the genus Cyanus deposited in the GenBank database.

Key Results: The AFLPs revealed a suite of closely related entities with variable levels of differentiation. The C. napulifer group formed a genetically well-defined unit. Samples outside the group formed strongly diversified and mostly species-specific genetic lineages with no further geographical patterns, often characterized also by a different DNA content. AFLP analysis of the C. napulifer group revealed extensive radiation and split it into nine allopatric (sub)lineages with varying degrees of congruence among genetic, DNA-content and morphological patterns. Genetic admixture was usually detected in contact zones between genetic lineages. Plastid data indicated extensive maintenance of ancestral variation across Cyanus perennials.

Conclusion: The C. napulifer group is an example of a rapidly and recently diversified plant group whose genetic lineages have evolved in spatio-temporal isolation on the topographically complex Balkan Peninsula. Adaptive radiation, accompanied in some cases by long-term isolation and hybridization, has contributed to the formation of this species complex and its mosaic pattern.
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http://dx.doi.org/10.1093/aob/mcw142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5091721PMC
November 2016

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism.

Nat Genet 2016 09 18;48(9):1077-82. Epub 2016 Jul 18.

Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.

The notion of species as reproductively isolated units related through a bifurcating tree implies that gene trees should generally agree with the species tree and that sister taxa should not share polymorphisms unless they diverged recently and should be equally closely related to outgroups. It is now possible to evaluate this model systematically. We sequenced multiple individuals from 27 described taxa representing the entire Arabidopsis genus. Cluster analysis identified seven groups, corresponding to described species that capture the structure of the genus. However, at the level of gene trees, only the separation of Arabidopsis thaliana from the remaining species was universally supported, and, overall, the amount of shared polymorphism demonstrated that reproductive isolation was considerably more recent than the estimated divergence times. We uncovered multiple cases of past gene flow that contradict a bifurcating species tree. Finally, we showed that the pattern of divergence differs between gene ontologies, suggesting a role for selection.
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http://dx.doi.org/10.1038/ng.3617DOI Listing
September 2016

Northern glacial refugia and altitudinal niche divergence shape genome-wide differentiation in the emerging plant model Arabidopsis arenosa.

Mol Ecol 2016 08 29;25(16):3929-49. Epub 2016 Jul 29.

Department of Botany, Faculty of Science, Charles University in Prague, Prague, CZ-128 01, Czech Republic.

Quaternary climatic oscillations profoundly impacted temperate biodiversity. For many diverse yet undersampled areas, however, the consequences of this impact are still poorly known. In Europe, particular uncertainty surrounds the role of Balkans, a major hotspot of European diversity, in postglacial recolonization of more northerly areas, and the Carpathians, a debatable candidate for a northern 'cryptic' glacial refugium. Using genome-wide SNPs and microsatellites, we examined how the interplay of historical processes and niche shifts structured genetic diversity of diploid Arabidopsis arenosa, a little-known member of the plant model genus that occupies a wide niche range from sea level to alpine peaks across eastern temperate Europe. While the northern Balkans hosted one isolated endemic lineage, most of the genetic diversity was concentrated further north in the Pannonian Basin and the Carpathians, where it likely survived the last glaciation in northern refugia. Finally, a distinct postglacial environment in northern Europe was colonized by populations of admixed origin from the two Carpathian lineages. Niche differentiation along altitude-related bioclimatic gradients was the main trend in the phylogeny of A. arenosa. The most prominent niche shifts, however, characterized genetically only slightly divergent populations that expanded into narrowly defined alpine and northern coastal postglacial environments. Our study highlights the role of eastern central European mountains not only as refugia for unique temperate diversity but also sources for postglacial expansion into novel high-altitude and high-latitude niches. Knowledge of distinct genetic substructure of diploid A. arenosa also opens new opportunities for follow-up studies of this emerging model of evolutionary biology.
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http://dx.doi.org/10.1111/mec.13721DOI Listing
August 2016

Cardamine occulta, the correct species name for invasive Asian plants previously classified as C. flexuosa, and its occurrence in Europe.

PhytoKeys 2016 25(62):57-72. Epub 2016 Mar 25.

Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovakia.

The nomenclature of Eastern Asian populations traditionally assigned to Cardamine flexuosa has remained unresolved since 2006, when they were found to be distinct from the European species Cardamine flexuosa. Apart from the informal designation "Asian Cardamine flexuosa", this taxon has also been reported under the names Cardamine flexuosa subsp. debilis or Cardamine hamiltonii. Here we determine its correct species name to be Cardamine occulta and present a nomenclatural survey of all relevant species names. A lectotype and epitype for Cardamine occulta and a neotype for the illegitimate name Cardamine debilis (replaced by Cardamine flexuosa subsp. debilis and Cardamine hamiltonii) are designated here. Cardamine occulta is a polyploid weed that most likely originated in Eastern Asia, but it has also been introduced to other continents, including Europe. Here data is presented on the first records of this invasive species in European countries. The first known record for Europe was made in Spain in 1993, and since then its occurrence has been reported from a number of European countries and regions as growing in irrigated anthropogenic habitats, such as paddy fields or flower beds, and exceptionally also in natural communities such as lake shores.
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http://dx.doi.org/10.3897/phytokeys.62.7865DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856903PMC
May 2016

Is hybridization driving the evolution of climatic niche in Alyssum montanum.

Am J Bot 2016 07 14;103(7):1348-57. Epub 2016 Apr 14.

Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland.

Premise Of The Study: After decades of interest, the contribution of hybridization to ecological diversification remains unclear. Hybridization is a potent source of novelty, but nascent hybrid lineages must overcome reproductive and ecological competition from their parental species. Here, we assess whether hybrid speciation is advantageous over alternative modes of speciation, by comparing the geographical and ecological ranges and climatic niche evolutionary rates of stabilized allopolyploid vs. autopolyploids in the Alyssum montanum species complex.

Methods: We combined an extensive review of studies addressing the systematics and genetic diversity of A. montanum s.l., with flow cytometry and cloning of nuclear markers, to establish the ploidy level and putative hybrid nature of 205 populations. The respective geographic distribution and climatic niche evolution dynamics of the allo- and autopolyploids were investigated using multivariate analyses and comparative phylogenetic approaches.

Key Results: As expected by theory, allopolyploids occur mainly along contact zones and are generally spatially overlapping with their diploid counterparts. However, they demonstrate higher rates of niche evolution and expand into different climatic conditions than those of their diploid congeners. In contrast, autopolyploids show lower rates of niche evolution, occupy ecological niches similar to their ancestors and are restricted to less competitive and peripheral geographic areas.

Conclusions: Hybridization thus seems advantageous by promoting ecological niche evolution and more readily allowing escape from competitive exclusion.
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http://dx.doi.org/10.3732/ajb.1500368DOI Listing
July 2016

Hybridization among distantly related species: Examples from the polyploid genus Curcuma (Zingiberaceae).

Mol Phylogenet Evol 2016 07 28;100:303-321. Epub 2016 Apr 28.

The Herbarium, Singapore Botanic Gardens, Singapore.

Discerning relationships among species evolved by reticulate and/or polyploid evolution is not an easy task, although it is widely discussed. The economically important genus Curcuma (ca. 120 spp.; Zingiberaceae), broadly distributed in tropical SE Asia, is a particularly interesting example of a group of palaeopolyploid origin whose evolution is driven mainly by hybridization and polyploidization. Although a phylogeny and a new infrageneric classification of Curcuma, based on commonly used molecular markers (ITS and cpDNA), have recently been proposed, significant evolutionary questions remain unresolved. We applied a multilocus approach and a combination of modern analytical methods to this genus to distinguish causes of gene tree incongruence and to identify hybrids and their parental species. Five independent regions of nuclear DNA (DCS, GAPDH, GLOBOSA3, LEAFY, ITS) and four non-coding cpDNA regions (trnL-trnF, trnT-trnL, psbA-trnH and matK), analysed as a single locus, were employed to construct a species tree and hybrid species trees using (*)BEAST and STEM-hy. Detection of hybridogenous species in the dataset was also conducted using the posterior predictive checking approach as implemented in JML. The resulting species tree outlines the relationships among major evolutionary lineages within Curcuma, which were previously unresolved or which conflicted depending upon whether they were based on ITS or cpDNA markers. Moreover, by using the additional markers in tests of plausible topologies of hybrid species trees for C. vamana, C. candida, C. roscoeana and C. myanmarensis suggested by previous molecular and morphological evidence, we found strong evidence that all the species except C. candida are of subgeneric hybrid origin.
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http://dx.doi.org/10.1016/j.ympev.2016.04.017DOI Listing
July 2016

PESI - a taxonomic backbone for Europe.

Biodivers Data J 2015 28(3):e5848. Epub 2015 Sep 28.

Muséum national d'Histoire naturelle, Département Systématique & Evolution, UMR 7205 MNHN-CNRS-UPMC-EPHE, (ISyEB), Paris, France.

Background: Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information.

New Information: This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs.
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http://dx.doi.org/10.3897/BDJ.3.e5848DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609752PMC
October 2015

Microsatellite markers for the Pilosella alpicola group (Hieraciinae, Asteraceae) and their cross-amplification in other Hieraciinae genera.

Appl Plant Sci 2015 Aug 17;3(8). Epub 2015 Aug 17.

Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, CZ-252 43 Průhonice, Czech Republic ; Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Prague CZ-165 21, Czech Republic.

Premise Of The Study: Microsatellite markers were developed for the Pilosella alpicola group (Asteraceae), comprising four closely related species distributed in subalpine areas of Europe. These species are believed to have diverged recently, but display contrasting cytogeographic patterns and variation in breeding systems, representing a promising model system for studying plant speciation, adaptation, and recent polyploidization.

Methods And Results: We developed 17 microsatellite markers for the P. alpicola group using 454 sequencing. Sixteen markers were polymorphic, with the number of alleles per locus ranging from seven to 16 and observed and expected heterozygosity ranging from 0.45 to 0.84 and 0.72 to 0.92, respectively. Ten and five loci amplified in the related species, P. echioides and P. officinarum, respectively, but only two in Andryala and one in Hieracium s. str.

Conclusions: The developed microsatellite markers have high potential to become useful tools to study microevolutionary processes in the P. alpicola group and related Pilosella species.
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http://dx.doi.org/10.3732/apps.1500048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542946PMC
August 2015

Cytotype distribution patterns, ecological differentiation, and genetic structure in a diploid-tetraploid contact zone of Cardamine amara.

Am J Bot 2015 Aug 12;102(8):1380-95. Epub 2015 Aug 12.

Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovak Republic Department of Botany, Faculty of Sciences, Charles University, Benátská 2, CZ-128 01 Praha, Czech Republic.

Unlabelled: •

Premise Of The Study: Contact zones between diploids and their autopolyploid descendants represent a unique evolutionary venue for studying polyploid establishment, cytotype coexistence, and interactions. Here, we examine cytotype coexistence in a diploid-tetraploid contact zone of a perennial herb, Cardamine amara, located north of the Alps by assessing cytotype spatial patterns, ecological divergence, and genetic variation and structure.•

Methods: Flow cytometry was applied to screen DNA ploidy levels in 302 populations (3296 individuals) and the genetic variation of a selection of 25 populations was examined using microsatellite and AFLP markers. Environmental (landscape and climatic) data were analyzed to assess ecological differentiation between the cytotypes.•

Key Results: A parapatric distribution of the cytotypes with a relatively wide (over 100 km in some regions) secondary contact zone was identified. Mixed-ploidy populations, documented for the first time in this species, as well as triploid individuals were found along the diploid-tetraploid borderline. Different climatic requirements of the two main cytotypes were revealed, mirrored in their altitudinal separation. The tetraploids were genetically differentiated from both the diploids and the modeled, in silico autotetraploid genotypes, in accordance with the assumed polyploid origin and spread linked to past glaciations, and largely independent evolution in allopatry.•

Conclusions: The observed spatial and genetic patterns likely reflect the evolutionary and colonization history of the two cytotypes and have been maintained by multiple factors such as ecological divergence, limited gene flow between the cytotypes, and the restricted dispersal capacity.
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http://dx.doi.org/10.3732/ajb.1500052DOI Listing
August 2015

Lectotypification of names of Himalayan Brassicaceae taxa currently placed in the genus Cardamine.

PhytoKeys 2015 13(50):9-23. Epub 2015 May 13.

Missouri Botanical Garden, P.O. Box 299, St. Louis, Missouri, 63166-0299, U.S.A.

Lectotypes of twenty-eight names of taxa currently recognized or synonymized in Cardamine are designated as part of the work on the account of the genus for the Pan-Himalayan Flora. Among them, the previous first-step lectotypification of the name Cardaminecalthifolia is finalized. In cases when specimen images are available online, stable identifiers for specimens, other permanent links, or links via JSTOR Global Plants are provided.
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http://dx.doi.org/10.3897/phytokeys.50.5080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489080PMC
July 2015

Taming the wild: resolving the gene pools of non-model Arabidopsis lineages.

BMC Evol Biol 2014 Oct 27;14:224. Epub 2014 Oct 27.

Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, 69120, Germany.

Background: Wild relatives in the genus Arabidopsis are recognized as useful model systems to study traits and evolutionary processes in outcrossing species, which are often difficult or even impossible to investigate in the selfing and annual Arabidopsis thaliana. However, Arabidopsis as a genus is littered with sub-species and ecotypes which make realizing the potential of these non-model Arabidopsis lineages problematic. There are relatively few evolutionary studies which comprehensively characterize the gene pools across all of the Arabidopsis supra-groups and hypothesized evolutionary lineages and none include sampling at a world-wide scale. Here we explore the gene pools of these various taxa using various molecular markers and cytological analyses.

Results: Based on ITS, microsatellite, chloroplast and nuclear DNA content data we demonstrate the presence of three major evolutionary groups broadly characterized as A. lyrata group, A. halleri group and A. arenosa group. All are composed of further species and sub-species forming larger aggregates. Depending on the resolution of the marker, a few closely related taxa such as A. pedemontana, A. cebennensis and A. croatica are also clearly distinct evolutionary lineages. ITS sequences and a population-based screen based on microsatellites were highly concordant. The major gene pools identified by ITS sequences were also significantly differentiated by their homoploid nuclear DNA content estimated by flow cytometry. The chloroplast genome provided less resolution than the nuclear data, and it remains unclear whether the extensive haplotype sharing apparent between taxa results from gene flow or incomplete lineage sorting in this relatively young group of species with Pleistocene origins.

Conclusions: Our study provides a comprehensive overview of the genetic variation within and among the various taxa of the genus Arabidopsis. The resolved gene pools and evolutionary lineages will set the framework for future comparative studies on genetic diversity. Extensive population-based phylogeographic studies will also be required, however, in particular for A. arenosa and their affiliated taxa and cytotypes.
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http://dx.doi.org/10.1186/s12862-014-0224-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4216345PMC
October 2014

The widespread crucifer species Cardamine flexuosa is an allotetraploid with a conserved subgenomic structure.

New Phytol 2014 Feb 30;201(3):982-992. Epub 2013 Oct 30.

Plant Cytogenomics research group, Central European Institute of Technology (CEITEC), Masaryk University, CZ-62500, Brno, Czech Republic.

The origin of Cardamine flexuosa (Wavy Bittercress) has been a conundrum for more than six decades. Here we identify its parental species, analyse its genome structure in comparison to parental genomes and describe intergenomic structural variations in C. flexuosa. Genomic in situ hybridization (GISH) and comparative chromosome painting (CCP) uncovered the parental genomes and the chromosome composition of C. flexuosa and its presumed diploid progenitors. Cardamine flexuosa is an allotetraploid (2n = 4x = 32), originating from two diploid species, Cardamine amara and Cardamine hirsuta (2n = 2x = 16). The two parental species display almost perfectly conserved chromosomal collinearity for seven out of the eight chromosomes. A 13 Mb pericentric inversion distinguishes chromosome CA1 from CH1. A comparative cytomolecular map was established for C. flexuosa by CCP/GISH. Whereas conserved chromosome collinearity between the C. amara and C. hirsuta subgenomes might have promoted intergenomic rearrangements through homeologous recombination, only one reciprocal translocation between two homeologues has occurred since the origin of C. flexuosa. The genome of C. flexuosa demonstrates that allopolyploids can maintain remarkably stable subgenomes over 10(4) -10(5)  yr throughout a wide distribution range. By contrast, the rRNA genes underwent genome-specific elimination towards a diploid-like number of loci.
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http://dx.doi.org/10.1111/nph.12567DOI Listing
February 2014

The more the merrier: recent hybridization and polyploidy in cardamine.

Plant Cell 2013 Sep 30;25(9):3280-95. Epub 2013 Sep 30.

Research Group Plant Cytogenomics, Central European Institute of Technology (CEITEC), Masaryk University, CZ-62500 Brno, Czech Republic.

This article describes the use of cytogenomic and molecular approaches to explore the origin and evolution of Cardamine schulzii, a textbook example of a recent allopolyploid, in its ~110-year history of human-induced hybridization and allopolyploidy in the Swiss Alps. Triploids are typically viewed as bridges between diploids and tetraploids but rarely as parental genomes of high-level hybrids and polyploids. The genome of the triploid semifertile hybrid Cardamine × insueta (2n = 24, RRA) was shown to combine the parental genomes of two diploid (2n = 2x = 16) species, Cardamine amara (AA) and Cardamine rivularis (RR). These parental genomes have remained structurally stable within the triploid genome over the >100 years since its origin. Furthermore, we provide compelling evidence that the alleged recent polyploid C. schulzii is not an autohexaploid derivative of C. × insueta. Instead, at least two hybridization events involving C. × insueta and the hypotetraploid Cardamine pratensis (PPPP, 2n = 4x-2 = 30) have resulted in the origin of the trigenomic hypopentaploid (2n = 5x-2 = 38, PPRRA) and hypohexaploid (2n = 6x-2 = 46, PPPPRA). These data show that the semifertile triploid hybrid can promote a merger of three different genomes and demonstrate how important it is to reexamine the routinely repeated textbook examples using modern techniques.
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http://dx.doi.org/10.1105/tpc.113.114405DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3809532PMC
September 2013

Genetic diversity in widespread species is not congruent with species richness in alpine plant communities.

Ecol Lett 2012 Dec 25;15(12):1439-48. Epub 2012 Sep 25.

Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, Grenoble Cedex, France.

The Convention on Biological Diversity (CBD) aims at the conservation of all three levels of biodiversity, that is, ecosystems, species and genes. Genetic diversity represents evolutionary potential and is important for ecosystem functioning. Unfortunately, genetic diversity in natural populations is hardly considered in conservation strategies because it is difficult to measure and has been hypothesised to co-vary with species richness. This means that species richness is taken as a surrogate of genetic diversity in conservation planning, though their relationship has not been properly evaluated. We tested whether the genetic and species levels of biodiversity co-vary, using a large-scale and multi-species approach. We chose the high-mountain flora of the Alps and the Carpathians as study systems and demonstrate that species richness and genetic diversity are not correlated. Species richness thus cannot act as a surrogate for genetic diversity. Our results have important consequences for implementing the CBD when designing conservation strategies.
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http://dx.doi.org/10.1111/ele.12004DOI Listing
December 2012
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