Pavel Trávníček

The genus Boechera (Brassicaceae) serves as a model system for studying apomictic reproduction and ecological adaptations, with most species occurring in North America. The rare occurrence of Boechera species outside their typical range provides unique opportunities to investigate genome evolution in extralimital environments. One such species, B. calcarea, has been described from the Chandalaz Mountains in northeastern Asia (Russia). This study aimed to investigate the genome structure and evolutionary history of B. calcarea. However, our analyses reveal that the species does not belong to Boechera. Instead, an integrative approach combining cytogenetic, phylogenetic and repeatome analysis identified the species as a member of one of more ancestral clades in the tribe Arabideae. The diploid Parryodes calcarea (2n = 16) exhibits Arabideae-specific chromosomal signatures, including multiple centromere repositionings. These findings clarify the misclassification of P. calcarea as Boechera, leaving Boechera falcata and Borodinia macrophylla as the only representatives of the Boechereae in the Old World. This study highlights the importance of an integrative approach in resolving taxonomic ambiguities and provides new insights into the diversification of the largest cruciferous tribe, the Arabideae.

SUMMARY: Rapidly radiated groups are usually accompanied by unclear lineage and taxa delineation, which complicates their better understanding in terms of biodiversity, evolutionary processes, and taxonomic treatment. The most species‐rich orchid subtribe, Pleurothallidinae, exemplifies an extremely diverse group with a complex evolutionary history associated with Andean orography. Here we combined multi‐loci phylogeny reconstruction (HybSeq), genome‐wide traits (inferred by flow cytometry), spatial analyses, and biogeography to investigate the evolutionary intricacy of one clade of Pleurothallidinae orchids. To achieve deep insights, we performed multiple species tree reconstruction approaches with the implementation of custom scripts to reveal sources of topological discrepancies and alternative evolutionary scenarios. The phylogeny clearly resolves the delimitation of the main evolutionary lineages corresponding to the accepted genera, with the exception of the genus Specklinia, which is divided into three distinct monophyletic lineages whose taxonomic treatment is proposed. Genome‐wide characters (especially genome size) show an association with precipitation seasonality in a geographical context, and partial endoreplication, a unique character of orchids, is geographically restricted to the Andes, Central America, and the Caribbean. Specifically, the Andean region exemplifies the prevalence of bigger genome size and higher GC content, resulting from a higher proportion of species with partial endoreplication. The Andean origin of the clade was also revealed by biogeographic analysis. Our comprehensive approach has provided deep insights into the evolution of this clade and may be a useful tool for unraveling the intricate evolutionary history of similarly complex lineages.

Aim: Plant invasions are a global problem that requires studying plants and their environmental associations across native and introduced ranges.Location: 2000 km transects in China, Europe and North America.Time Period: June 2019–July 2020.Major Taxa Studied: Japanese knotweed (Reynoutria japonica).Methods: We surveyed 150 populations of Japanese knotweed, a noxious invader of the temperate zone, along 2000 km transects in native China and the introduced ranges of Europe and North America.Results: We found that larger plants and denser populations in the introduced ranges were associated with shifts in leaf economy and chemical defences. Introduced knotweed populations had higher SLA but reduced leaf chlorophyll, lignin, C:N ratio and leaf toughness along with altered leaf tannins, flavonoids and alkaloids. We found three distinct multivariate knotweed phenotypes primarily in the introduced ranges, and two multivariate knotweed phenotypes mainly in native populations.Main Conclusions: Decreased herbivore and pathogen impacts in introduced populations and changes in environmental associations indicate that enemy release and novel habitat conditions might have driven the emergence of novel ecological strategies in this global plant invader.

The genus Boechera (Brassicaceae) serves as a model system for studying apomictic reproduction and ecological adaptations, with most species concentrated in North America. Rare occurrences of Boechera species beyond their typical range offers unique opportunities to investigate genome evolution in extralimital environments. One such species, B. calcarea , was described from the Chandalaz Range in northeastern Asia (Russia). This study aimed to investigate the genome structure and evolutionary history of B. calcarea . However, our analyses reveal that the species does not belong to Boechera . Instead, an integrative approach combining cytogenetic, phylogenetic and repeatome analyses identified the species as a member of an ancestral clades within the tribe Arabideae. The diploid Parryodes calcarea (Dudkin) D.A.German & Lysak (2 n = 16) exhibits Arabideae-specific chromosomal signatures, including multiple centromere repositionings. These findings clarify the misattribution of P. calcarea to Boechera , leaving Boechera falcata and Borodinia macrophylla as the only Old World representatives of the Boechereae. This study highlights the importance of integrative methodologies in resolving taxonomic ambiguities and provides new insights into the diversification of the largest cruciferous tribe, Arabideae.

SUMMARY: The Greater Cape Floristic Region (GCFR) is renowned for its exceptional biodiversity, accommodating over 11 000 plant species, notable degree of endemism, and substantial diversification within limited plant lineages, a phenomenon ascribed to historical radiation events. While both abiotic and biotic factors contribute to this diversification, comprehensive genomic alterations, recognized as pivotal in the diversification of angiosperms, are perceived as uncommon. This investigation focuses on the genus Pteronia, a prominent representative of the Asteraceae family in the GCFR. Employing NGS‐based HybSeq and RADSeq methodologies, flow cytometry, karyology, and ecological modeling, we scrutinize the intricacies of its polyploid evolution. Phylogenetic reconstructions using 951 low‐copy nuclear genes confirm Pteronia as a well‐supported, distinct clade within the tribe Astereae. The ingroup displays a structure indicative of rapid radiation likely antedating polyploid establishment, with the two main groups demarcated by their presence or absence in the fynbos biome. Genome size analysis encompasses 1293 individuals across 347 populations, elucidating significant variation ranging from 6.1 to 34.2 pg (2C‐value). Pteronia demonstrates substantially large genome sizes within Astereae and phanerophytes. Polyploidy is identified in 31% of the studied species, with four discerned ploidy levels (2x, 4x, 6x, 8x). Cytotypes exhibit marked distinctions in environmental traits, influencing their distribution across biomes and augmenting their niche differentiation. These revelations challenge the presumed scarcity of polyploidy in the Cape flora, underscoring the imperative need for detailed population studies. The intricate evolutionary history of Pteronia, characterized by recent polyploidy and genome size variation, contributes substantially to the comprehension of diversification patterns within the GCFR biodiversity hotspot.

SUMMARY: 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 evolution of GS in two subfamilies of the tropical family Zingiberaceae to find out whether species with larger genomes are confined to environments where the vegetative season is longer. We tested our hypothesis on 337 ginger species from regions with contrasting climates by correlating their GS with an array of plant traits and environmental variables. We revealed 16‐fold variation in GS which was tightly related to shoot seasonality. Negative correlations of GS with latitude, temperature and precipitation emerged in the subfamily Zingiberoidae, demonstrating that species with larger GS are excluded from areas with a shorter growing season. In the subfamily Alpinioideae, GS turned out to be correlated with the type of stem and light requirements and its members cope with seasonality mainly by adaptation to shady and moist habitats. The Ornstein–Uhlenbeck models suggested that evolution in regions with humid climates favoured larger GS than in drier regions. Our results indicate that climate seasonality exerts an upper constraint on GS not only in temperate regions but also in the tropics, unless species with large genomes find alternative ways to escape from that constraint.

The Greater Cape Floristic Region is one of the world's biodiversity hotspots and is considered poor in polyploids. To test this assumption, ploidy variation was investigated in a widespread Cape shrub Dicerothamnus rhinocerotis (renosterbos, Asteraceae). The aim is to elucidate the cytotype distribution and population composition across the species range, and to assess differences in morphology, environmental niches, and genetics. Ploidy level and genome size were determined via flow cytometry, cytotype assignment was confirmed by chromosome counting. RADseq analyses were used to infer genetic relationships. Cytotype climatic and environmental niches were compared using a range of environmental layers and a soil model, while morphological differences were examined using multivariate methods. The survey of 171 populations and 2370 individuals showed that the species comprises diploid and tetraploid cytotypes, no intermediates and only 16.8 % of mixed populations. Mean 2C-values are 1.80–2.06 pg for diploids and 3.48–3.80 pg for tetraploids, with very similar monoploid genome sizes. Intra-cytotype variation showed a significant positive correlation with altitude and longitude in both cytotypes and with latitude in diploids. Although niches of both cytotypes are highly equivalent and similar, their optima and breadth are shifted due to differences mainly in isothermality and available water capacity. Morphometric analyses showed significant differences in the leaves and corolla traits, in the number of florets per capitulum, and cypsela dimensions between the two cytotypes. Genetic analyses revealed four groups, three of them including both cytotypes. Dicerothamnus rhinocerotis includes two distinct cytotypes that are genetically similar. While tetraploids arise several times independently within different genetic groups, morphological and ecological differences are evident between cytotypes. Our results open up new avenues for questions regarding the importance of ploidy in the megadiverse Cape flora, and exemplify the need for population-based studies focused on ploidy variation.

Madisonia has been delimited recently based on DNA analyses and morphological characters. In this article, we focus on Specklinia ordinata (Pleurothallidinae), a poorly known species. We obtained DNA data for this taxon and demonstrated that it is clearly a member of Madisonia. This species also shares morphological characters with Madisonia, in which we propose to include it.

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. This assumption is applied here for the first time to plants from the Cape Floristic hotspot to determine whether changes in repetitive DNA are related to responses to a harsh, but extremely species-rich environment. The genus Pteronia (Asteraceae) serves as a suitable model group because it shows considerable variation in genome size at the diploid level and has high and nearly equal levels of endemism in the two main Cape biomes, Fynbos and Succulent Karoo. First, we constructed a phylogeny based on multiple low-copy genes that served as a phylogenetic framework for detecting quantitative and qualitative changes in the repeatome. Second, we performed a comparative analysis of the environments of two groups of Pteronia differing in their TEs bursts. Our results suggest that the environmental transition from the Succulent Karoo to the Fynbos is accompanied by TEs burst, which is likely also driving phylogenetic divergence. We thus hypothesize that analysis of rapidly evolving repeatome could serve as an important proxy for determining the molecular basis of lineage divergence in rapidly radiating groups.