Tomas Fer

• PhD
• Researcher at Charles University in Prague

Societal Impact Statement The primarily neotropical plant genus Heliconia has been cultivated commercially in gardens and nurseries for hundreds of years. Many of these same species are ecological keystones in their native habitats as important resources for herbivorous insects and pollinating hummingbirds, yet they face threats of habitat loss and...

Members of the genus Heliconia L. (Heliconiaceae) have evolved complex interactions with both insect herbivores and hummingbird pollinators in tropical forests and secondary growth where they are abundant and diverse. Many of these same species have also been cultivated as ornamentals around the world for hundreds of years because of their extraord...

Understanding the proximate and ultimate causes of genome size (GS) variation is the focus of much research. However, the extent and causes of intraspecific variation in GS is debated and poorly understood. This study aims to test the large-genome constraint hypothesis through the variations of intraspecific GS. GS was measured in 53 Roscoea tibeti...

The overarching aim of the present study is to sort out the taxonomy of a group of gingers that include the useful and worldwide economically important green cardamom, Elettaria cardamomum , and its wild relatives, to highlight potentially overlooked genetic resources. These species occur naturally in India and Sri Lanka, and our study facilitates...

Genome size variation is a crucial aspect of plant evolution, influenced by a complex interplay of factors. Repetitive elements, which are fundamental components of genomic architecture, often play a role in genome expansion by selectively amplifying specific repeat motifs. This study focuses on Amomum, a genus in the ginger family (Zingiberaceae),...

European larch (Larix decidua Mill.) is an important tree species commonly used in managed forests of central Europe. However, its genetic structure, post-glacial range dynamics, and consequent nativity status are poorly understood. Here we provide the first study focusing on the genetic structure of in situ larch populations in the north-eastern C...

Plant species with large genomes tend to be excluded from climatically more extreme environments with a shorter growing season. Species that occupy such environments are assumed to be under natural selection for more rapid growth and smaller genome size (GS). However, evidence for this is available only for temperate organisms. Here, we study the e...

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 preve...

Background and Aims A targeted enrichment NGS approach was used to construct the phylogeny of Amomum Roxb. (Zingiberaceae). Phylogenies based on hundreds of nuclear genes, the whole plastome and the rDNA cistron were compared with an ITS-based phylogeny. Trends in genome size (GS) evolution were examined, chromosomes were counted and the geographic...

The monocot family Costaceae Nakai consists of seven genera but their mutual relationships have not been satisfactorily resolved in previous studies employing classical molecular markers. Phylogenomic analyses of 365 nuclear genes and nearly-complete plastome data provides almost fully resolved insights into their diversification. Paracostus is ide...

The analysis of target enrichment data in phylogenetics lacks optimization toward using paralogs for phylogenetic reconstruction. We developed a novel approach of detecting paralogs and utilizing them for phylogenetic tree inference, by retrieving both ortho‐ and paralogous copies and creating orthologous alignments, from which the gene trees are b...

A molecular systematic study of Globba section Nudae (Zingiberaceae) using ITS and matK sequences identifies three major clades, Globba subsection Nudae, G. subsection Mediocalcaratae and a new subsection, Globba subsection Pelecantherae, which is described here. The two species belonging in this subsection, Globba pelecanthera and Globba securifer...

Premise: 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 desig...

The species of Gagnepainia K.Schum. and Hemiorchis Kurz are revised throughout their ranges. These genera are shown with evidence from morphological and molecular studies to be distinct, although closely related to each other. Two species of Gagnepainia and three of Hemiorchis are recognised. A key to the genera of Globbeae and keys to the species...

Ochagavia (four species) and Fascicularia (one species) form a well-supported clade of the early-diverging Bromelioideae. The two genera are morphologically similar, but they can be easily discerned on the basis of generative characters. Besides the species distributed on the Chilean mainland, the group includes O. elegans, endemic to the Robinson...

Until recently, Czech taxonomists often treated Betula carpatica as a distinct species. Several morphological traits for distinguishing B. carpatica from B. pubescens or other birches are described in literature; however, it has been proven impossible to reliably identify B. carpatica in the field. With the use of morphological and molecular approa...

Premise: Hybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq probe set and the outcomes of different phylogenetic analyses are investigated here. Methods: Hyb-Seq data from 112 Asteraceae samples were organized into groups at different ta...

The differential geographical distribution often observed between closely related sexuals and asexuals is termed geographical parthenogenesis (GP). The arcto-alpine Hieracium alpinum (Asteraceae) encompasses two geographically allopatric cytotypes. Diploid sexuals occur in the South-Eastern Carpathians. Triploids reproduce asexually via seeds (apom...

Many cases of rapid evolutionary radiations in plant and animal lineages are known; however phylogenetic relationships among these lineages have been difficult to resolve by systematists. Increasing amounts of genomic data have been sequentially applied in an attempt to resolve these radiations, dissecting their evolutionary patterns into a series...

The tropical ginger genus Amomum (Zingiberaceae) has always posed challenges for classification based on morphological characters. Previous molecular phylogenetic studies showed Amomum to be paraphyletic but limited sampling and absence of the data of the type Amomum subulatum made it impossible to resolve the paraphyly and make nomenclatural chang...

Hybridization-based target enrichment in combination with genome skimming (Hyb-Seq) is becoming a standard method of phylogenomics. We developed HybPhyloMaker, a bioinformatics pipeline that performs target enrichment data analysis from raw reads to supermatrix-, supertree-, and multispecies coalescent-based species tree reconstruction. HybPhyloMak...

Hybridization-based target enrichment in combination with genome skimming (Hyb-Seq) is becoming a standard method of phylogenomics. We developed HybPhyloMaker, a bioinformatics pipeline that performs target enrichment data analysis from raw reads to supermatrix-, supertree-, and multispecies coalescent-based species tree reconstruction. HybPhyloMak...

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 Senecio inhabiting montane forests and páramo represented such growth form changes. We also investigated the role of Andean geography and environment in structuring...

Groups of closely related taxa with very si­milar morphology can be found in a large number of wetland and aquatic plants. This is often caused by phenotypic plasticity in response to changing environmental factors. Determination of sterile plants is thus very difficult and sometimes even impossible. The genus Bur-reed (Sparganium) re­presents such...

Divergent natural selection is known to facilitate speciation in many taxa. The genus Bolboschoenus (Cyperaceae) is a model group for investigating ecological and homoploid hybrid speciation. Four taxa of Bolboschoenus occur in central Europe: the halophyte B. maritimus and glycophytes B.laticarpus, B. planiculmis and B. yagara. These species diffe...

Identification of postglacial migration patterns and localization of possible glacial refugia are the main tasks of phylogeographical studies. Analyses of AFLPs in the European temperate shrub Rosa pendulina L. provided an insight into this issue. Similarly to a previous study of chloroplast DNA (cpDNA) haplotype variation in this species, we detec...

The Phytophthora cactorum species complex in Europe is composed of P. cactorum, Phytophthora hedraiandra, and a hybrid species Phytophthora × serendipita. Evolutionary analyses using the amplified fragment length polymorphism (AFLP) method were carried out on 133 isolates from 19 countries. The AFLP data were complemented by sequence analysis of th...

Ve střední Evropě se vyskytují čtyři druhy kamyšníků (Bolboschoenus), které byli dříve považovány za jediný široce definovaný druh kamyšník přímořský (B. maritimus). Současná klasifikace spočívá v morfologii květenství a hlavně tvaru a anatomii nažek. Kamyšník širokoplodý (B. laticarpus) je na základě jeho přechodných znaků, chromozomového počtu a...

The role of glacial oscillations in shaping plant diversity has been only rarely addressed in endemics of formerly glaciated areas. The Galium pusillum group represents a rare example of an ecologically diverse and ploidy-variable species complex that exhibits substantial diversity in deglaciated northern Europe. Using AFLP and plastid and nuclear...

Despite the extensive use of phylogenetic methods in comparative plant biology, there is little information on how traits and their plastic responses can be affected by phylogenetic constraints (i.e. limitations in phenotypic expression resulting from the phylogenetic history of a lineage), particularly in plant radiations that may have occurred ov...

Background and Aims Plants endemic to areas covered by ice sheets during the last glaciation represent paradigmatic examples of rapid speciation in changing environments, yet very few systems outside the harsh arctic zone have been comprehensively investigated so far. The Galium pusillum aggregate (Rubiaceae) is a challenging species complex that e...

Curcuma comprises 120 species that occur throughout tropical and subtropical Asia. The taxonomy of the genus is haunted by polyploid speciation and homoploid hybridization, making it the most challenging genus in Zingibereae (Zingiberaceae). Curcuma is best known for turmeric (C. longa), but numerous species are extensively used as medicinal plants...

The molecular population structure of 20 populations of the subalpine plant Gentiana pannonica was studied by use of amplified fragment length polymorphism (AFLP) and sequencing of non-coding regions of plastid DNA. Of the populations sampled, 18 were native (11 were from the Eastern Alps, which is the distribution centre of the species, and seven...

Polyploidization is one of the leading forces in the evolution of land plants, providing opportunities for instant speciation and rapid gain of evolutionary novelties. Highly selective conditions of serpentine environments act as an important evolutionary trigger that can be involved in various speciation processes. Whereas the significance of both...

Second derivative of the inter cluster inertia of each number of groups (K) as estimated by the nonhierarchial K-means clustering. (PDF)

Summary of structure 2.2 analyses based on AFLP multilocus phenotypes of 360 plants of Knutia arvensis agg. Values of ln probability of the data for each number of groups (K) plotted against the K-values and Delta K values). (PDF)

Cluster membership of individuals estimated by STRUCTURE 2.2. A – analysis of the complete dataset. B – separate STRUCTURE analysis for the relict diploid + tetraploid subgroup (grey in the plot A) resulting in six groups. Population numbers below each plot correspond to Table 1. (PDF)

Contingency table comparing the pattern in AFLP data (results of the nonhierarchical K-means clustering; clusters K1–K7) and the distribution of chloroplast haplotypes (A-M); numbers of individuals are presented in each field. (PDF)

Primary matrix of the scored AFLP fragments. (XLS)

Geographical location of 40 analyzed populations of Knautia arvensis agg. in central Europe and their phylogeographical grouping according to the structure analysis of AFLP phenotypes. (PDF)

Principal coordinate analysis (PCoA) based on Jaccard similarity among AFLP multilocus phenotypes of Knautia arvensis agg. individuals. The different colours represent the groups identified by the structure analysis (same as in Fig. S4). (PDF)

Amplified fragment length polymorphism (AFLP) has become a standard method for investigating genetic variation in plants. Nevertheless, only a few applications in bryophytes have been published and there is still a need to optimize the method. We optimized DNA isolation and AFLP protocols for Campylopus introflexus (Hedw.) Brid. As DNA quality is c...

The phylogeographic pattern of the temperate shrub Lonicera nigra (Caprtfoliaceae) in Europe was inferred from molecular and fossil data. Population samples and pollen data from most of the contemporary natural distribution were analysed. While chloroplast DNA sequences revealed no intraspecific variation, AFLP data show a non-random geographic pat...

The relationships between genome size and the systematic and evolutionary patterns in vascular plants are equivocal, although a close relationship between genome size and evolutionary patterns has been previously reported. However, several studies have also revealed the dynamic nature of genome size evolution and its considerable ‘ups’ and ‘downs’....

The phylogeographical structure of the European forest grass Hordelymus europaeus (Poaceae) was studied by sequencing three non-coding regions of chloroplast DNA. Forty-three populations within the entire natural distribution area were analysed. The greatest haplotype variation and divergence were revealed on Balkan and Apennine Peninsula, suggesti...

Unlabelled: Premise: Studies of hybridizing species are facilitated by the availability of species-specific molecular markers for identifying early- and later-generation hybrids. Cattails are a dominant feature of wetland communities, and a better understanding of the prevalence of hybrids is needed to assess the ecological and evolutionary effe...

The use of flow cytometry in research on genus Betula L. Over the last decade there has been a huge increase in the use of flow cytometry (FCM) in studies on the biosystematics, ecology and population biology of vascular plant. In the present study, this method was used for research on genus Betula L. in the area of the Czech Republic. FCM was used...

Variation in genome size in a particular taxonomic group can reflect different evolutionary processes including polyploidy, hybridization and natural selection but also neutral evolution. Using flow cytometry, karyology, ITS sequencing and field surveys, the causes of variation in genome size in the ecologically and morphologically diverse high-And...

Gentiana pannonica SCOP. (Gentianaceae) is a long-lived perennial mountain species. It is a typical east-Alpine element. The centre of its distribution is situated in the eastern Alps, where the species occurs in alpine and subalpine areas. Besides the Alps, G. pannonica occurs also in the Bohemian Forest, Czech Republic. The reproduction strategy...

Even though the reed. Phragmites australis, is an extensively studied wetland species, little is known about reproduction and dispersal modes within and among reed populations at the scale of small river systems. Using microsatellite analysis of 189 individuals from three adjacent river catchments in the Czech Republic, we elucidated the role of th...

The phylogeographical structure amongst 39 populations of the temperate forest plant Carex pilosa in Europe was studied using amplified fragment length polymorphism (AFLP), polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and sequencing of non-coding regions of plastid DNA. No plastid DNA polymorphisms were found withi...

1. River corridors are well-known for their role in plant dispersal. The buoyancy of seeds, the possibility of dispersal by vegetative fragments, and the frequency and efficiency of dispersal among different river catchments determine linear distribution patterns. Little is known about the relative importance of these factors to observed patterns o...

The phylogeographical structure of the temperate shrub Rosa pendulina at 45 locations in Europe was studied using sequencing of a non-coding cpDNA region (trnL-trnF). Our study revealed a clear geographic structure of cpDNA haplotypes. Three main haplotypes were geographically widespread, but showed little overlap in their distributions, suggesting...

Genome size and chromosome numbers are important cytological characters that significantly influence various organismal traits. However, geographical representation of these data is seriously unbalanced, with tropical and subtropical regions being largely neglected. In the present study, an investigation was made of chromosomal and genome size vari...

Aim Plants in islands have often evolved through adaptive radiation, providing the classical model of evolution of closely related species each with strikingly different morphological and ecological features and with low levels of genetic divergence. We emphasize the importance of an alternative (anagenetic) model of evolution, whereby a single isl...

Aim Plants in islands have often evolved through adaptive radiation, providing the classical model of evolution of closely related species each with strikingly different morphological and ecological features and with low levels of genetic divergence. We emphasize the importance of an alternative (anagenetic) model of evolution, whereby a single isl...

Dystaenia (Apiaceae) consists of two species, one distributed in Japan (D. ibukiensis), and the other endemic to Ullung Island, Korea (D. takesimana). In comparison with representative outgroup taxa in Ligusticum, Seseli, Angelica, and Osmorhiza, Dystaenia is shown to be monophyletic based on sequences from chloroplast trnL-F intron and spacer regi...

Rivers represent linear corridors in landscape. All possible suitable sites for water plants are connected by the stream flow and species can migrate along the linear structure downstream. Transport of both vegetative and generative diasporas is possible. But it is still the question how numerous and how far diasporas can be dispersed. We use...