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Parallel adaptation provides valuable insight into the predictability of evolutionary change through replicated natural experiments. A steadily increasing number of studies have demonstrated genomic parallelism, yet the magnitude of this parallelism varies depending on whether populations, species, or genera are compared. This led us to hypothesize that the magnitude of genomic parallelism scales with genetic divergence between lineages, but whether this is the case and the underlying evolutionary processes remain unknown. Here, we resequenced seven parallel lineages of two Arabidopsis species, which repeatedly adapted to challenging alpine environments. By combining genome-wide divergence scans with model-based approaches, we detected a suite of 151 genes that show parallel signatures of positive selection associated with alpine colonization, involved in response to cold, high radiation, short season, herbivores, and pathogens. We complemented these parallel candidates with published gene lists from five additional alpine Brassicaceae and tested our hypothesis on a broad scale spanning ∼0.02 to 18 My of divergence. Indeed, we found quantitatively variable genomic parallelism whose extent significantly decreased with increasing divergence between the compared lineages. We further modeled parallel evolution over the Arabidopsis candidate genes and showed that a decreasing probability of repeated selection on the same standing or introgressed alleles drives the observed pattern of divergence-dependent parallelism. We therefore conclude that genetic divergence between populations, species, and genera, affecting the pool of shared variants, is an important factor in the predictability of genome evolution.

• Premise of the study: Contact zones between polyploids and their diploid progenitors may provide important insights into the mechanisms of sympatric speciation and local adaptation. However, most published studies investigated secondary contact zones where the effects of genome duplication can be confounded by previous independent evolution of currently sympatric cytotypes. We compared genetically close diploid and autotetraploid serpentine cytotypes of Knautia arvensis (Caprifoliaceae) in a primary contact zone and evaluated the role of adaptive and nonadaptive processes for cytotype coexistence.• Methods: DNA flow cytometry was used to determine ploidy distribution at various spatial scales (from across the entire contact zone to microgeographic). Habitat preferences of diploids and polyploids were assessed by comparing vegetation composition of nearby ploidy-uniform sites and by recording plant species immediately surrounding both cytotypes in mixed-ploidy plots.• Key results: Tetraploids considerably outnumbered their diploid progenitors in the contact zone. Both cytotypes were segregated at all investigated spatial scales. This pattern was not driven by ecological shifts, because both diploids and tetraploids inhabited sites with nearly identical vegetation cover. Certain interploidy niche differentiation was indicated only at the smallest spatial scale; ecologically nonadaptive processes were most likely responsible for this difference.• Conclusions: We conclude that a shift in ecological preferences (i.e., the adaptive scenario) is not necessary for the establishment and evolutionary success of autopolyploid derivatives in primary contact zones. Spatial segregation that would support ploidy coexistence can also be achieved by ecologically nonadaptive processes, including the founder effect, limited dispersal ability, intense clonal growth, and triploid block.

Introgressive hybridization is an important evolutionary process frequently contributing to diversification and speciation of angiosperms. Its extent in other groups of land plants has only rarely been studied, however. We therefore examined the levels of introgression in the genus Diphasiastrum, a taxonomically challenging group of Lycopodiophytes, using flow cytometry and numerical and geometric morphometric analyses. Patterns of morphological and cytological variation were evaluated in an extensive dataset of 561 individuals from 57 populations of six taxa from Central Europe, the region with the largest known taxonomic complexity. In addition, genome size values of 63 individuals from Northern Europe were acquired for comparative purposes. Within Central European populations, we detected a continuous pattern in both morphological variation and genome size (strongly correlated together) suggesting extensive levels of interspecific gene flow within this region, including several large hybrid swarm populations. The secondary character of habitats of Central European hybrid swarm populations suggests that man-made landscape changes might have enhanced unnatural contact of species, resulting in extensive hybridization within this area. On the contrary, a distinct pattern of genome size variation among individuals from other parts of Europe indicates that pure populations prevail outside Central Europe. All in all, introgressive hybridization among Diphasiastrum species in Central Europe represents a unique case of extensive interspecific gene flow among spore producing vascular plants that cause serious complications of taxa delimitation.

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 edaphic speciation on serpentine and polyploidy is widely acknowledged in plant evolution, the links between polyploid evolution and serpentine differentiation have not yet been examined. To fill this gap, we investigated the evolutionary history of the perennial herb Knautia arvensis (Dipsacaceae), a diploid-tetraploid complex that exhibits an intriguing pattern of eco-geographic differentiation. Using plastid DNA sequencing and AFLP genotyping of 336 previously cytotyped individuals from 40 populations from central Europe, we unravelled the patterns of genetic variation among the cytotypes and the edaphic types. Diploids showed the highest levels of genetic differentiation, likely as a result of long term persistence of several lineages in ecologically distinct refugia and/or independent immigration. Recurrent polyploidization, recorded in one serpentine island, seems to have opened new possibilities for the local serpentine genotype. Unlike diploids, the serpentine tetraploids were able to escape from the serpentine refugium and spread further; this was also attributable to hybridization with the neighbouring non-serpentine tetraploid lineages. The spatiotemporal history of K. arvensis allows tracing the interplay of polyploid evolution and ecological divergence on serpentine, resulting in a complex evolutionary pattern. Isolated serpentine outcrops can act as evolutionary capacitors, preserving distinct karyological and genetic diversity. The serpentine lineages, however, may not represent evolutionary 'dead-ends' but rather dynamic systems with a potential to further influence the surrounding populations, e.g., via independent polyplodization and hybridization. The complex eco-geographical pattern together with the incidence of both primary and secondary diploid-tetraploid contact zones makes K. arvensis a unique system for addressing general questions of polyploid research.

Evolutionary histories of plants from the mid-elevation (montane) zone of European mountain ranges have only rarely been documented, standing in contrast to those of well-researched inhabitants of (sub-) alpine and foothill zones. To fill this gap, we have reconstructed the phylogeography of Arabidopsis halleri, a species preferring coniferous woodlands and corresponding secondary habitats in the montane zone of the Alps, Carpathians, Hercynian massif and Dinaric Alps. Based on range-wide sampling and finer-scale analyses of multiple multilocus DNA markers, we have addressed phylogeographic patterns among the Carpathian populations and inferred their relationships to A. halleri from neighbouring mountain ranges. We also present a taxonomic re-evaluation of the species in Europe, based on the revealed genetic structure complemented by morphological data. Besides two distinct Alpine groups, we identified a major phylogeographic split between the Western and South-Eastern Carpathians. Interestingly, Western and South-Eastern Carpathian populations were genetically closer to populations from neighbouring mountain ranges (the Hercynian massif and the Dinaric Alps for the Western and South-Eastern Carpathians, respectively) than they were to each other, likely reflecting long-term isolation in different parts of the Carpathians or different (re) colonization pathways during the Holocene. In spite of the considerable environmentally correlated variation, the five major European genetic groups exhibited distinctive morphological characters, and we therefore propose treating them as separate subspecies: A. halleri subsp. halleri (Western Europe, Hercynian massif), A. halleri subsp. tatrica (Western Carpathians), A. halleri subsp. ovirensis (Eastern Alps), A. halleri subsp. occidentalis (Western Alps) and A. halleri subsp. dacica (Eastern and Southern Carpathians and Dinaric Alps).

Background and aims Serpentine soils impose limits on plant growth and survival and thus provide an ideal model for studying plant adaptation under environmental stress. Despite the increasing amount of data on serpentine ecotypic differentiation, no study has assessed the potential role of polyploidy. We tested for links between polyploidy and the response to serpentine stress in Knautia arvensis, a diploid-tetraploid, edaphically differentiated complex. Methods Variation in growth, biomass yield and tissue Mg and Ni accumulation in response to high Mg and Ni concentrations were experimentally tested using hydroponic cultivation of seedlings from eight populations of different ploidy and edaphic origin. Results Regardless of ploidy level, serpentine populations exhibited higher tolerance to both Mg and Ni stress than their non-serpentine counterparts, suggesting an adaptive character of these traits in K. arvensis. The effect of ploidy was rather weak and confined to a slightly better response of serpentine tetraploids to Mg stress and to higher biomass yields in tetraploids from both soil types. Conclusions The similar response of diploid and tetraploid serpentine populations to edaphic stress corresponded with their previously described genetic proximity. This suggests that serpentine tolerance might have been transmitted during the local autopolyploid origin of serpentine tetraploids.

Analysis of population genetic structure has become a standard approach in population genetics. In polyploid complexes, clustering analyses can elucidate the origin of polyploid populations and patterns of admixture between different cytotypes. However, combining diploid and polyploid data can theoretically lead to biased inference with (artefactual) clustering by ploidy. We used simulated mixed-ploidy (diploid-autotetraploid) data to systematically compare the performance of k-means clustering and the model-based clustering methods implemented in Structure, Admixture, FastStructure and InStruct under different scenarios of differentiation and with different marker types. Under scenarios of strong population differentiation, the tested applications performed equally well. However, when population differentiation was weak, Structure was the only method that allowed unbiased inference with markers with limited genotypic information (co-dominant markers with unknown dosage or dominant markers). Still, since Structure was comparatively slow, the much faster but less powerful FastStructure provides a reasonable alternative for large datasets. Finally, although bias makes k-means clustering unsuitable for markers with incomplete genotype information, for large numbers of loci (>1000) with known dosage k-means clustering was superior to FastStructure in terms of power and speed. We conclude that Structure is the most robust method for the analysis of genetic structure in mixed-ploidy populations, although alternative methods should be considered under some specific conditions.

In this study, we aimed to systematically assess the frequency at which potentially deleterious phenotypes appear in natural populations of the outcrossing model plant Arabidopsis arenosa, and to establish their underlying genetics. For this purpose, we collected seeds from wild A. arenosa populations and screened over 2,500 plants for unusual phenotypes in the greenhouse. We repeatedly found plants with obvious phenotypic defects, such as small stature and necrotic or chlorotic leaves, among first-generation progeny of wild A. arenosa plants. Such abnormal plants were present in about 10% of maternal sibships, with multiple plants with similar phenotypes in each of these sibships, pointing to a genetic basis of the observed defects. A combination of transcriptome profiling, linkage mapping and genome-wide runs of homozygosity patterns using a newly assembled reference genome indicated a range of underlying genetic architectures associated with phenotypic abnormalities. This included evidence for homozygosity of certain genomic regions, consistent with alleles that are identical by descent being responsible for these defects. Our observations suggest that deleterious alleles with different genetic architectures are segregating at appreciable frequencies in wild A. arenosa populations.

Despite the recent wealth of studies targeted at contact zones of cytotypes in various species, some aspects of polyploid evolution are still poorly understood. This is especially the case for the frequency and success rate of spontaneous neopolyploidization or the temporal dynamics of ploidy coexistence, requiring massive ploidy screening and repeated observations, respectively. To fill this gap, an extensive study of spatio-temporal patterns of ploidy coexistence was initiated in the widespread annual weed Tripleurospermum inodorum (Asteraceae). DNA flow cytometry along with confirmatory chromosome counts was employed to assess ploidy levels of 11 018 adult individuals and 1263 ex situ germinated seedlings from 1209 Central European populations. The ploidy screening was conducted across three spatial scales and supplemented with observations of temporal development of 37 mixed-ploidy populations. The contact zone between the diploid and tetraploid cytotypes has a diffuse, mosaic-like structure enabling common cytotype coexistence from the within-population to the landscape level. A marked difference in monoploid genome size between the two cytotypes enabled the easy distinction of neotetraploid mutants from long-established tetraploids. Neotetraploids were extremely rare (0·03 %) and occurred solitarily. Altogether five ploidy levels (2 x -6 x ) and several aneuploids were discovered; the diversity in nuclear DNA content was highest in early ontogenetic stages (seedlings) and among individuals from mixed-ploidy populations. In spite of profound temporal oscillations in cytotype frequencies in mixed-ploidy populations, both diploids and tetraploids usually persisted up to the last census. Diploids and tetraploids commonly coexist at all spatial scales and exhibit considerable temporal stability in local ploidy mixtures. Mixed-ploidy populations containing fertile triploid hybrids probaby act as effective generators of cytogenetic novelty and may facilitate inter-ploidy gene flow. Neopolyploid mutants were incapable of local establishment.

Plants able to resprout from roots have a potential bud bank that gets initiated after injury to overcome meristem limitation after loss of all stem parts and to facilitate regeneration. Knautia arvensis is reportedly able to sprout from its roots on arable land, but information is missing regarding such ability in serpentine populations or how it might differ between diploids and tetraploids. We hypothesized that (1) 'ruderal' non-serpentine populations better tolerate severe disturbance than relic, serpentine ones; (2) tetraploid populations resprout more readily than diploids due to enhanced growth of higher ploidy levels; and (3) plants of different ploidy levels from serpentine soils are, for evolutionary reasons, more similar in their response to disturbances than plants from non-serpentine soils. To test these hypotheses, we conducted a pot experiment. Its results do not support our hypothesis that the ability to sprout from roots is a factor driving the spread of new weedy taxa into central Europe or the hypothesis that it is related to polyploidization in the genus Knautia. Both tetraploids and plants from non-serpentine populations regenerated less vigorously than diploids and plants from serpentine populations. However, the genetically closer populations of serpentine origin were more similar in their response to experimental manipulations than their genetically distinct non-serpentine counterparts. The success of non-serpentine taxa in disturbed habitats of central Europe might be related to traits other than the ability to resprout.