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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. Of the 4 main clades identified among the diploids, 3 clades included species from the Alps, Apennine, and Balkan peninsulas, indicating close biogeographic links between these regions. We further focused on the clade distributed from the Western Alps to the Iberian Peninsula, which comprises numerous polyploids as opposed to a few diploids. Using a recently developed PhyloSD (phylogenomic subgenome detection) pipeline, we successfully tracked the ancestry of all polyploids. We inferred multiple polyploidization events that involved 2 closely related diploid progenitors, resulting into several sibling polyploids: 2 autopolyploids and 6 allopolyploids. The skewed proportions of major homeolog-types and the occurrence of some minor homeolog-types, both exhibiting geographic patterns, suggest introgression with the progenitors and other related diploids. Our study highlights a unique case of parallel polyploid speciation that was enhanced by ecological and geographic separation and provides an excellent resource for future studies of polyploid evolution., (© The Author(s) 2023. Published by Oxford University Press on behalf of The Society for the Study of Evolution (SSE). All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

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., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

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., (© 2016 Botanical Society of America.)

Premise of the Study: The Apennine Peninsula, one of the three peninsulas of the European Mediterranean, is an important hotspot of genetic and species diversity, but studies devoted to plant evolution are still very scarce in this region. We studied the diploid-polyploid complex of Alyssum montanum-A. repens, focusing on Apennine and adjacent southwestern Alpine populations from southeastern France, with the aim of examining their taxonomic position and evolutionary patterns., Methods: We employed AFLP markers and cpDNA sequences, along with cytotype determination using flow cytometry, and a multivariate morphometric approach., Key Results: The Italian and French populations formed two well-delimited groupings within the studied complex that were, in contrast to previous taxonomic treatments, clearly distinct from A. montanum. Populations from southeastern France represent A. orophilum, a previously described but abandoned species. Those from central and southern Italy correspond to A. diffusum, exhibiting high, geographically structured variation (central Apennines, Gargano, and southern Apennines/Calabria). This pattern coincides with hotspot refugial regions, in congruence with the "refugia-within-refugia" hypothesis, and is reflected here in the recognition of three subspecies within A. diffusum., Conclusions: We provide evidence for the presence of Mediterranean refugia for the studied Alyssum montanum-A. repens complex located in central and southern Italy, which, however, did not contribute to the postglacial colonization of Central Europe. Past extinctions, genetic bottlenecks, and recent expansion were inferred in Central Europe, while long-term accumulation of diversity as well as polyploidization occurred in the Apennines.

Alyssum rossetii is recorded for the first time in Spain from a single locality in the Pyrenees. After the type locality in the Valpelline valley (Pennine Alps, Italy), it is only the second known locality of this species. Morphology, diploid chromosome number (2n = 16), relative genome size, and ITS sequences confirm that the Pyrenean plants are conspecific with the Alpine ones and should be classified as A. rossetii. Phylogenetic analyses placed A. rossetii within the clade of A. sect. Gamosepalum comprising species from Turkey and demonstrated that A. rossetii is only distantly related to other Alyssum species occurring in the Pyrenees and adjacent regions: A. alyssoides, A. cacuminum, A. collinum, A. fastigiatum, A. granatense, A. montanum, and A. simplex. An identification key to all Alyssum species known from the Pyrenees is presented. Citation: Š aniel S Mártonfiová L & Zozomová-Lihová J 2024: An unex ected occurrence of Al ssum rossetii (Brassicaceae) in the Pyrenees, a new species for the Spanish flora. – Willdenowia 53: 297–307 Version of record first published online on 29 January 2024. [ABSTRACT FROM AUTHOR]

The European Alps show a high degree of endemism associated mainly with the location of glacial refugia and environmental heterogeneity. Several Alpine endemics have evolved in the genus Alyssum. Here we study perennial Alyssum populations in the Western Alps, mainly distributed in the Aosta Valley region, which hosts high species diversity, although endemics are rare. We addressed the recently described stenoendemic A. rossetii and taxonomically uncertain populations usually attributed to A. montanum s.s. to clarify their phylogenetic position and morphological differentiation. The latter entity has been shown to be distinct from A. montanum s.s. and is described as a new species, Alyssum cognense , phylogenetically placed in the A. montanum–A. repens species complex. Both morphological and genetic patterns revealed that its closest relative occurs in the central Balkans. We present detailed ecological characteristics and morphological differentiation of A. cognense sp. nov. from its relatives and geographically closest species and speculate on its biogeographic origin. Genetic patterns (reduced diversity and nestedness) suggest long-distance dispersal from the central Balkan Peninsula. The second studied species, A. rossetii , is phylogenetically distant and belongs to the mainly Asian Alyssum section Gamosepalum lineage, which includes few representatives in southern and eastern Europe. The phylogenetically closest species of A. rossetii are Anatolian endemics, so this extreme disjunction remains puzzling. The present study illustrates the need for in-depth taxonomic and phylogenetic studies, even in well-explored Alpine regions, and also shows that the processes underlying the evolution of endemics can be complex and poorly understood. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Alyssum cuneifolium has been recognized as a perennial alpine species growing in five isolated European mountain ranges: the Pyrenees, Western Alps, Apennines, Pirin Mts and Mt Smolikas. Recent molecular systematic studies revealed that the disjunct populations from distant mountains are not closely related and belong to five independent species: A. cacuminum (Spain, Pyrenees), A. cuneifolium (Italy, Apennines), A. flexicaule (France, Western Alps), A. pirinicum (Bulgaria, Pirin Mts), and A. spruneri (Greece, Mt Smolikas). The present study brings the thorough morphometric analysis of the segregated taxa. We found minor morphological differences between them. Whereas A. pirinicum can be clearly distinguished, the other taxa are recognizable only at the level of population means of investigated characters. The morphological similarity of these distantly related species is obviously the result of adaptation to similar high‐alpine scree habitats. It is not clear, however, whether this adaptation is environmentally controlled or whether it is also genetically fixed and whether it reflects parallel evolution towards similar morphotypes. The observed morphological patterns and their assumed correlation with environmental factors are discussed using examples from other Alyssum taxa. Three different ploidy levels have been reported for the species under study. In the present article, we examine variation in relative nuclear genome size. The Alpine and Pyrenean species have larger relative monoploid genome sizes than the Apennine and Balkan ones, probably reflecting the evolutionary history of the group. A nomenclatural account of the study species is presented, and lectotypes of A. cuneifolium and of two other names are selected. [ABSTRACT FROM AUTHOR]

Cardamine occulta, recently reported also as 'Asian C. flexuosa', is originally a native East Asian weed of paddy fields and other open habitats. It has been recorded throughout the world and is now also spreading widely in Europe. However, how this species differs morphologically from European C. flexuosa and its closest relatives in Asia (C. kokaiensis and C. scutata) is not fully known, particularly because it became widely recognized as a new taxon only recently. We used chromosome counting and flow cytometry to determine ploidies and genome size variation in these four species and morphometric analyses to ascertain their morphological differentiation. A uniformly octoploid level (2n = 64) is confirmed here for C. occulta and a tetraploid level for C. flexuosa and C. scutata (2n = 32). Here we formally describe C. kokaiensis, which is restricted to East Asia (Japan, Honshu; eastern China, Zhejiang Province; perhaps also the Russian Far East) and determine it to be a tetraploid. Considerable differences in monoploid genome size were revealed between these taxa, suggesting their mostly allopolyploid origins. Morphological differences between the species are demonstrated, and detailed morphological descriptions and an identification key are provided. [ABSTRACT FROM AUTHOR]

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 C. flexuosa. Apart from the informal designation "Asian C. flexuosa", this taxon has also been reported under the names C. flexuosa subsp. debilis or C. hamiltonii. Here we determine its correct species name to be C. occulta and present a nomenclatural survey of all relevant species names. A lectotype and epitype for C. occulta and a neotype for the illegitimate name C. debilis (replaced by C. flexuosa subsp. debilis and C. 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. [ABSTRACT FROM AUTHOR]

Database of published chromosome numbers and ploidy-level estimates of the tribe Alysseae is presented, together with the revised generic concept and the list of accepted names, to reflect the most recent taxonomic and phylogenetic studies in Alysseae. It is available on-line at . The tribe encompasses 24 genera and 277 species. Chromosome numbers and/or ploidy levels are known for 171 out of 297 recognized taxa. Of these, 95 (55.6 %) taxa are diploids, 43 (25.1 %) are polyploids, and 33 (19.3 %) involve both diploids and polyploids. The most common base chromosome number in the tribe is x = 8 and less frequent is x = 7. The highest variation in base chromosome numbers ( x = 7, 8, 11, 15) is found in the genus Hormathophylla. A key to all genera and descriptions of the two new genera Cuprella and Resetnikia are presented. Many new nomenclatural combinations, mainly in the re-established Odontarrhena (77), are proposed. [ABSTRACT FROM AUTHOR]

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 astriploid 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. [ABSTRACT FROM AUTHOR]

• Recently formed allopolyploids represent an excellent system to study the impacts of hybridization and genomic duplication on genome structure and evolution. Here we explored the 35SrRNA genes (rDNA) in the Cardamine × schulzii allohexaploid that was formed by two subsequent hybridization events within the past c. 150 yr. • The rDNA loci were analyzed by cloning, next generation sequencing (NGS), RT-PCR and FISH methods. • The primary C. × insueta triploid hybrid derived from C. rivularis (♀) and C. amara (♂) had gene ratios highly skewed towards maternal sequences. Similarly, C. × schulzii, originating from the secondary hybridization event involving C. × insueta (♀) and C. pratensis (♂), showed a reduction in paternal rDNA homeologs despite an excess of chromosomes inherited from C. pratensis. We also identified novel rDNA loci in C. × schulzii, suggesting that lost loci might be slowly reinstalled by translocation (but not recombination) of genes from partner genomes. • Prevalent clonal propagation of allopolyploids, C. × insueta and C. × schulzii, indicates that concerted evolution of rDNA may occur in the absence of extensive meiotic cycles. Adoption of NGS in rDNA variant analysis is highly informative for deciphering the evolutionary histories of allopolyploid species with ongoing homogenization processes. [ABSTRACT FROM AUTHOR]

Background and Aims Recently formed allopolyploid species represent excellent subjects for exploring early stages of polyploid evolution. The hexaploid Cardamine schulzii was regarded as one of the few nascent allopolyploid species formed within the past ∼150 years that presumably arose by autopolyploidization of a triploid hybrid, C. × insueta; however, the most recent investigations have shown that it is a trigenomic hybrid. The aims of this study were to explore the efficiency of progenitor-specific microsatellite markers in detecting the hybrid origins and genome composition of these two allopolyploids, to estimate the frequency of polyploid formation events, and to outline their evolutionary potential for long-term persistence and speciation. Methods Flow-cytometric ploidy-level screening and genotyping by progenitor-specific microsatellite markers (20 microsatellite loci) were carried out on samples focused on hybridizing populations at Urnerboden, Switzerland, but also including comparative material of the parental species from other sites in the Alps and more distant areas. Key Results It was confirmed that hybridization between the diploids C. amara and C. rivularis auct. gave rise to triploid C. × insueta, and it is inferred that this has occurred repeatedly. Evidence is provided that C. schulzii comprises three parental genomes and supports its origin from hybridization events between C. × insueta and the locally co-occurring hypotetraploid C. pratensis, leading to two cytotypes of C. schulzii: hypopentaploid and hypohexaploid. Each cytotype of C. schulzii is genetically uniform, suggesting their single origins. Conclusions Persistence of C. schulzii has presumably been achieved only by perennial growth and clonal reproduction. This contrasts with C. × insueta, in which multiple origins and occasional sexual reproduction have generated sufficient genetic variation for long-term survival and evolutionary success. This study illustrates a complex case of recurrent hybridization and polyploidization events, and highlights the role of triploids that promoted the origin of trigenomic hybrids. [ABSTRACT FROM PUBLISHER]

Recent studies of the Alyssum montanum-A. repens complex in Europe showed that populations from central and southern Italy are, in contrast to previous taxonomic treatments, clearly distinct from A. montanum and should be classified as A. diffusum. Based on the high, geographically structured genetic variation (central Apennines, Gargano, and southern Apennines/Calabria) of A. diffusum, three subspecies were recently recognised. Here, we present a detailed morphometric study of A. diffusum in Italy, exploring its differentiation from A. montanum and differentiation among the three subspecies (A. diffusum subsp. diffusum, subsp. garganicum and subsp. calabricum). We report that A. diffusum differs from A. montanum subsp. gmelinii particularly by having (on average) larger flower parts and from subsp. montanum by a different density and morphology of trichomes and narrower petals. The subspecies of A. diffusum can be distinguished by the number of trichome rays, by trichome density on the lower leaf surface and by the leaf length. In this study, we present an identification key that includes the subspecies of A. diffusum, those of A. montanum and the related A. cuneifolium. We also provide detailed morphological descriptions of all three subspecies of A. diffusum and a nomenclatural account, including the designation of the lectotype of the name A. diffusum. [ABSTRACT FROM AUTHOR]

Alyssum montanum ssp. montanum and A. montanum ssp. gmelinii have been treated as two largely sympatric taxa that occur throughout the European continent, the former growing on calcareous and serpentine rocks and in dry grasslands, and the latter mostly on sand dunes. In this study, we demonstrate that the traditional delimitation of these two subspecies is not substantiated and should be considerably revised. Focusing on Central Europe (encompassing the type localities of both names) and inferring from genetic (plastid DNA sequences and amplified fragment length polymorphism markers) and morphological data, we provide here a new circumscription of these two subspecies of A. montanum. The name A. montanum ssp. montanum is applicable to populations in south-western Germany, Switzerland and eastern France, characterized by wider petals and denser leaf indumentum. Alyssum montanum ssp. gmelinii includes diploid and tetraploid populations that are widespread in the rest of Central Europe. Habitat specificity was not confirmed by our studies. The subspecies are allopatric in Central Europe, but their overall distribution ranges in Europe need to be explored further. Genetic patterns suggest different evolutionary histories for the two subspecies. An identification key and a nomenclatural survey are also presented. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169, 378-402. [ABSTRACT FROM AUTHOR]