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Botanický ústav AV

By vojta, 4 Srpen, 2023

Ancient hybridization in Curcuma (Zingiberaceae)—Accelerator or brake in lineage diversifications?

Hybridization is a widespread phenomenon in the evolution of plants and exploring its role is crucial to understanding diversification processes of many taxonomic groups. Recently, more attention is focused on the role of ancient hybridization that has repeatedly been shown as triggers of evolutionary radiation, although in some cases, it can prevent further diversification. The causes, frequency, and consequences of ancient hybridization remain to be explored.

Články
Bioinformatika
Botanický ústav AV
Fylogenetika
HybSeq
Přírodovědecká fakulta UK
Věda, výzkum, biologie
By vojta, 21 Červen, 2023

Phylogenetic challenges in a recently diversified and polyploid-rich Alyssum (Brassicaceae) lineage: low divergence, reticulation, and parallel polyploid speciation

Elucidating the evolution of recently diverged and polyploid-rich plant lineages may be challenging even with high-throughput sequencing, both for biological reasons and bioinformatic difficulties. Here, we apply target enrichment with genome skimming (Hyb-Seq) to unravel the evolutionary history of the Alyssum montanum-A. repens species complex. Reconstruction of phylogenetic relationships in diploids supported recent and rapid diversification accompanied by reticulation events.

Články
Arabidopsis a Brassicaceae
Bioinformatika
Botanický ústav AV
Fylogenetika
Fylogeografie
HybSeq
Přírodovědecká fakulta UK
Taxonomie
Věda, výzkum, biologie
By vojta, 12 Říjen, 2022

The relationship between transposable elements and ecological niches in the Greater Cape Floristic Region: A study on the genus Pteronia (Asteraceae)

Non-coding repetitive DNA (repeatome) is an active part of the nuclear genome, involved in its structure, evolution and function. It is dominated by transposable elements (TEs) and satellite DNA and is prone to the most rapid changes over time. The TEs activity presumably causes the global genome reorganization and may play an adaptive or regulatory role in response to environmental challenges.

Články
Bioinformatika
Botanický ústav AV
Fylogenetika
HybSeq
Věda, výzkum, biologie
By vojta, 12 Říjen, 2022

The importance of considering the evolutionary history of polyploids when assessing climatic niche evolution

Although whole-genome duplication (WGD) is an important speciation force, we still lack a consensus on the role of niche differentiation in polyploid evolution. In addition, the role of genome doubling per se vs. later divergence on polyploid niche evolution remains obscure. One reason for this might be that the intraspecific genetic structure of polyploid complexes and interploidy gene flow is often neglected in ecological studies. Here, we aim to investigate to which extent these evolutionary processes impact our inference on niche differentiation of autopolyploids.

Články
Arabidopsis a Brassicaceae
Bioinformatika
Botanický ústav AV
Fylogeografie
Populační genetika
Přírodovědecká fakulta UK
Věda, výzkum, biologie
By vojta, 29 Září, 2021

Taraxacum assemanii represents a new section: A revision of the misinterpreted Taraxacum primigenium, and the elucidation of the enigmatic Taraxacum section Primigenia (Compositae, Crepidinae)

On the basis of new gatherings at the type locality, Taraxacum primigenium was evaluated taxonomically. Its achenes differ substantially from the protologue description that is based on achenes of T. assemanii. Taraxacum primigenium, also on the basis of an nrDNA analysis, is close to T. sect. Piesis, and represents a narrow endemic confined to the Lalezar Mts., SE Iran. Taraxacum assemanii, newly typified, is known from mountains of SE Anatolia and Lebanon, and from the Zagros in SW Iran.

Články
Botanický ústav AV
Taraxacum
Taxonomie
Věda, výzkum, biologie
By vojta, 26 Červenec, 2021

Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae

Custom probe design for target enrichment in phylogenetics is tedious and often hinders broader phylogenetic synthesis. The universal angiosperm probe set Angiosperms353 may be the solution. Here, we test the relative performance of Angiosperms353 on the Rosaceae subtribe Malinae in comparison with custom probes that we specifically designed for this clade. We then address the impact of bioinformatically altering the performance of Angiosperms353 by replacing the original probe sequences with orthologs extracted from the Malus domestica genome.

Články
Bioinformatika
Botanický ústav AV
Fylogenetika
HybSeq
Linux (a jiný software)
Přírodovědecká fakulta UK
Taxonomie
Věda, výzkum, biologie
By vojta, 15 Březen, 2021

Taraxacum mirabile, an enigmatic sexual halophilous endemic dandelion, represents a new section

Taraxacum mirabile Wagenitz (Asteraceae, Cichorieae, Crepidinae), a remarkable but taxonomically unexplored endemic species of Central Anatolia, is examined in detail. It is shown to be a sexually reproducing diploid (2n=16) species. It used to be included in Taraxacum sect. Orientalia in the literature. However, the nrDNA analysis revealed that T. mirabile is remote from that section.

Články
Botanický ústav AV
Taraxacum
Taxonomie
Věda, výzkum, biologie
By vojta, 25 Únor, 2021

STRUCTURE multi PBS Pro scripts

Set of scripts to run STRUCTURE in parallel on computing grids like MetaCentrum. Scripts are designed for grids and clusters using PBS Pro, but can be easily adopted for another queue system.

Články
Bioinformatika
Botanický ústav AV
Fylogenetika
Fylogeografie
Linux (a jiný software)
Populační genetika
Přírodovědecká fakulta UK
Taxonomie
Věda, výzkum, biologie
By vojta, 29 Prosinec, 2020

Parallel Alpine Differentiation in Arabidopsis arenosa

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. Arabidopsis arenosa, a predominantly foothill species with scattered morphologically distinct alpine occurrences is a promising candidate. Yet, the hypothesis of parallelism remained untested.

Články
Arabidopsis a Brassicaceae
Bioinformatika
Botanický ústav AV
Fylogenetika
Populační genetika
Věda, výzkum, biologie
By vojta, 13 Leden, 2020

Low genetic differentiation despite high fragmentation in the endemic serpentinophyte Minuartia smejkalii (M. verna agg., Caryophyllaceae) revealed by RADSeq SNP markers

Minuartia smejkalii is an obligate serpentinophyte plant endemic to the Czech Republic. Since the 1960s, the species’ habitat has undergone strong human-mediated fragmentation, resulting in extinction of some populations and dramatic size reduction of the remaining populations. Thus, contrary to the typically stable serpentine habitats, M. smejkalii habitats underwent a recent and severe decline, which can exacerbate the effects of fragmentation on population genetic structure. We examined the genetic structure of all known M.

Články
Botanický ústav AV
Fylogeografie
Populační genetika
Taxonomie
Věda, výzkum, biologie

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Botanický ústav AV
  • Czech Czech
  • English English

Proč používat Linux
openSUSE.org
Průvodce Linuxem
KDE - K Desktop Environment
openSUSE GNU/Linux

ORCID iD iconhttps://orcid.org/0000-0003-3481-9367

ResearchID/Publons

GitHub Logo, https://github.com/V-Z

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Licence Creative Commons
Dílo dílo, jehož autorem je Vojtěch Zeisek, podléhá licenci Creative Commons Uveďte původ-Neužívejte komerčně-Nezpracovávejte 4.0 Mezinárodní.

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