Karol Marhold

The allopolyploid Arabidopsis kamchatica originated from multiple individuals of Arabidopsis lyrata and Arabidopsis halleri

Polyploidization, or genome duplication, has played a critical role in the diversification of animals, fungi and plants. Little is known about the population structure and multiple origins of polyploid species because of the difficulty in identifying multiple homeologous nuclear genes. The allotetraploid species Arabidopsis kamchatica is closely related to the model species Arabidopsis thaliana and is distributed in a broader climatic niche than its parental species. Here, we performed direct sequencing of homeologous pairs of the low‐copy nuclear genes WER and CHS by designing homeolog‐specific primers, and obtained also chloroplast and ribosomal internal transcribed spacer sequences. Phylogenetic analysis showed that 50 individuals covering the distribution range including North America are allopolyploids derived from Arabidopsis lyrata and Arabidopsis halleri. Three major clusters within A. kamchatica were detected using Bayesian clustering. One cluster has widespread distribution. The other two are restricted to the southern part of the distribution range including Japan, where the parent A. lyrata is not currently distributed. This suggests that the mountains in Central Honshu and surrounding areas in Japan served as refugia during glacial–interglacial cycles and retained this diversity. We also found that multiple haplotypes of nuclear and chloroplast sequences of A. kamchatica are identical to those of their parental species. This indicates that multiple diploid individuals contributed to the origin of A. kamchatica. The haplotypes of low‐copy nuclear genes in Japan suggest independent polyploidization events rather than introgression. Our findings suggest that self‐compatibility and gene silencing occurred independently in different origins.

Polyploidy, hybridization and reticulate evolution: lessons from the Brassicaceae

The family Brassicaceae is well known for its large variation in chromosome numbers, common occurrence of polyploids and many reports of interspecific gene flow. The present review summarizes studies from the past decades on polyploidization and hybridization events, recognizing them as important evolutionary forces in the family. Attention is drawn to the issue of the reconstruction of reticulated pattern of evolution resulting from allopolyploid and homoploid hybrid speciation. The research of various authors on several Brassicaceae genera is presented and discussed in the context of our current understanding of polyploid and hybrid evolution. Model species, Arabidopsis thaliana and Brassica taxa, are referred to only marginally, major focus is on a comprehensive survey of studies on about a dozen best explored non-model genera (e.g. Cardamine, Draba, Rorippa, Thlaspi). The increasing amount of genetic and genomic resources available for Brassicaceae model species provides excellent opportunities for comparative genetic and genomic studies. Future research directions and challenges are thus outlined, in order to obtain more detailed insights into the evolution of polyploid and hybrid genomes.

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

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.

Diploid and Tetraploid Cytotypes of Centaurea stoebe (Asteraceae) in Central Europe: Morphological Differentiation and Cytotype Distribution Patterns

The taxomically critical species Centaurea stoebe is represented in Central Europe by a diploid (2n = 18) and a tetraploid (2n = 36) cytotype. Their morphological differentiation and taxonomic treatment is still controversial. Karyological (chromosome numbers and flow cytometric measurements) and multivariate morphometric analyses were used here to address cytotype distribution patterns and their morphological differentiation. Material from 38 localities (771 individuals) in Slovakia, Hungary and Austria, including type localities of the names traditionally applied to the different cytotypes, was sampled and evaluated using both morphometric and karyological approaches. The morphological tendency towards cytotype differentiation is evident only at a population level, and is blurred at the level of individual plants. Diploid populations prevail in the area studied, as well as throughout Europe; mixed-cytotype populations were also found. The present data, namely the weak morphological distinction, largely sympatric occurrence of the cytotypes, and the existence of mixed-cytotype populations, favour taxonomic treatment as a single species, without recognition of infraspecific units.

IAPT/IOPB chromosome data 2

The new series, IAPT/IOPB Chromosome Data, presented here, is a continuation of the long-term activity of the International Organisation of Plant Biosystematists (now interest group of the International Association for Plant Taxonomy) in supporting the research and publication of data on chromosome numbers and ploidy levels. Polyploidy is a frequent phenomenon in plant evolution that produces fast and substantial changes in the genetic composition of the organisms, which seem to foster diversification. It is now widely acknowledged that most plants have undergone one or more episodes of polyploidization during their evolutionary history and thus its importance cannot be overestimated. With the rapid development of methods of molecular systematics, the knowledge of the ploidy level of the studied plant material acquires a new dimension as compared to the early days of publication of the IOPB Chromosome Number Reports in TAXON. In the 60s, 70s and 80s, chromosome numbers were used as an independent source of taxonomic (and phylogenetic) information while the last decade demands ploidy information to correctly interpret molecular data, particularly from ribosomal and lowcopy nuclear genes and from fingerprinting markers. Our intention is not only to publish available data on chromosome numbers and ploidy levels of vascular plants, which otherwise might remain unpublished, but also to encourage further research in this respect. The hundred parts of the series IOPB Chromosome Number Reports (from the 67th part on called Chromosome Number Reports), edited first by O. T. Solbrig and Á. Löve and later by Á. Löve only, were published in TAXON from 1964 to 1988. Under the editorship of C. A. Stace this activity continued in the IOPB Newsletter, where eighteen parts of the IOPB Chromosome Data were published from 1989 to 2002. The contributions published in TAXON from 1964 to 1988 can be accessed via JSTOR (www.jstor.org). The whole set of these contributions, including those published in the IOPB Newsletter will be available soon also via the IOPB web page www.iopb.org. Following the current publication policy of TAXON, the abbreviated version of the IAPT/IOPB Chromosome Data will be published in the printed version of TAXON, while its full version will appear in the electronic edition only. Electronic versions will be available from INGENTACONNECT (http://www.ingentaconnect.com/content/iapt/tax) as well as via the IOPB webpage. The printed version will include the chromosome number or ploidy level, the country of origin of the material and unequivocal reference to the voucher specimen. This will include the collector’s name and the acronym of the herbarium collection in which the specimen is deposited. In addition, either the collection number or the exact date of the collection, or the number of the specimen in the particular herbarium collection should be provided. The electronic version should include a full description of the locality (preferably including geographical coordinates) and full citation of the voucher specimen. Data based on material of unknown wild origin or not documented by herbarium specimens cannot be published in this series. Vouchers must be deposited in a public herbarium listed in Index Herbariorum (http://sciweb.nybg.org/science2/ IndexHerbariorum.asp). The potential contributors should follow the format of the most recent instalment of the series. Additional information, e.g., acknowledgements, must be included in the electronic version. The first counts for a taxon, first counts for a new number for a taxon, or data or counts from an unexplored part of the distribution area of a taxon will be given preference. The contributors are encouraged to provide photographs of mitotic or meiotic figures and comments, IOPB COLUMN

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

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.

Worldwide phylogeny and biogeography of Cardamine flexuosa (Brassicaceae) and its relatives

Phylogenetic relationships, biogeography, and taxonomy of a group of taxa putatively related to the tetraploid Cardamine flexuosa were explored using sequences of the internal transcribed spacer region of nrDNA (ITS) and the trnL-trnF region of cpDNA. Taxon sampling focused on eastern Asia, North America, and Europe, and included 19 taxa represented by 177 and 182 accessions for each data set, respectively. Our analyses provided unequivocal evidence that Asian weedy populations traditionally assigned to C. flexuosa form an independent evolutionary lineage and represent a distinct taxon from European C. flexuosa. The allopolyploid origin of this common weed in paddy fields, its origin, and/or spread associated with the establishment of suitable man-made habitats are suggested. It is also found as an introduced weed in Australia and North America. Phylogenetic relationships and the associated taxonomic implications are presented and discussed for the group as a whole. Contrasting patterns of genetic variation (particularly in cpDNA) among different species were revealed. While very little haplotype diversity was found in widespread C. hirsuta and C. flexuosa, greater variation, showing phylogeographic structure, was observed in the tetraploid C. scutata within a relatively small area of Japan.

Origin of the disjunct tetraploid Cardamine amporitana (Brassicaceae) assessed with nuclear and chloroplast DNA sequence data

Seventy-four nucleotide sequences from the ITS regions of nuclear ribosomal DNA and 76 from the trnL-trnF spacer of chloroplast DNA were used to address the origin of tetraploid Cardamine amporitana, the conspecifity of central Italian and northeastern Spanish populations, and the possible cause for such geographic disjunction. Because of the complex lineage relationships in Cardamine, the sampling included 22 taxa. In the results, both data sets are highly congruent in supporting a close relationship of C. amporitana to the widespread Eurasian C. amara. Low genetic variability in northeastern Spanish populations of C. amporitana suggests long-distance dispersal from central Italy. The interior position of the single northeastern Spanish haplotype in a statistical parsimony network of trnL-trnF haplotypes however does not support this scenario and invokes other plausible phylogeographic explanations. The disappearance of geographically intermediate populations and genetic impoverishment by migration and isolation, both probably associated with Quaternary climatic oscillations, appears as an alternative hypothesis to explain the phylogeographic pattern. A recent hybridization event is reported between C. amporitana and a diploid from the C. pratensis group in central Italy on the basis of additive polymorphisms in ITS for all the 22 distinguishing nucleotides.

The Cardamine pratensis (Brassicaceae) group in the Iberian Peninsula: Taxonomy, polyploidy and distribution

The Cardamine pratensis group is a taxonomically critical species complex with pronounced karyological and morphological variation. In the present study, representatives from the Iberian Peninsula have been investigated using karyological, morphometric and molecular (amplified fragment length polymorphism) analyses. As a result of this combined approach, three species are recognized in the area studied: C. pratensis s.str., C. crassifolia, and a herein newly described species, C. castellana. For C. pratensis s.str., consistent with the pattern known from other European regions, wide variation in chromosome numbers is revealed, consisting of diploid to heptaploid populations in northern and central parts of the Peninsula. Little morphological and genetic differentiation accompanies these cytotypes. Re-evaluation of populations up to now ascribed to C. crassifolia reveal two separate taxa: (1) populations from the Eastern Pyrenees, representing typical C. crassifolia, and (2) those from central Iberian mountains treated as C. castellana. These two diploid taxa differ in several quantitative morphological characters, as well as in morphology of rhizome and basal parts of stem, and they are also distinct in AFLP markers, indicating strong genetic differentiation.

The More the Merrier: Recent Hybridization and Polyploidy in Cardamine

Allopolyploids usually arise by hybridization of two species. This work examines the evolutionary role of a triploid bitter-cress hybrid (Cardamine × insueta) in the origin of trigenome hybrids (Cardamine × schulzii) and elucidates the 110-year history of interspecies hybridization in Cardamine, demonstrating that semifertile triploid hybrids may facilitate the origin of new trigenome allopolyploids. 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.