Biology subjects

Kolar, F.

Publications and source records attributed to Kolar, F..

At least 19 recordsLinked to original sources

bioRxiv2026

Autopolyploidization presents a transient and potential-rich window of increased transcriptional plasticity in Arabidopsis arenosa.

Whole-genome duplication (WGD, polyploidization) is a pervasive feature of Eukaryote evolution and often viewed as a source of evolutionary success and novelty, meaning a macromutation leading to higher fitness (i.e. "hopeful monsters"). Yet, the mechanisms behind the (occasional) success of nascent polyploids remain still elusive, especially from a transcriptomic point of view. Theory suggests that duplicated genetic networks are characterised by enhanced redundancy and higher output variation, promoting the exploration of the adaptive landscape during stressful times. Artificially synthesized neo-polyploid mutants provide an exciting system to test this, however, empirical studies comparing co-expression network patterns between natural and synthetic ploidies of the same species in an evolutionary context are lacking. Here we compare diploid, synthetic and naturally established autotetraploid populations of Arabidopsis arenosa to investigate short- versus long-term effects of polyploidy on gene expression complexity and plasticity under water deficiency stress. Transcriptomic profiling revealed that synthetic neo-tetraploids explored the broadest expression space and exhibited the highest number of stress-responsive genes. Co-expression network analyses demonstrated that the network of neo-tetraploids was fragmented into multiple highly connected modules, with stress-responsive genes preferentially acting as inter-modular "bridges". In contrast, diploids and established tetraploids exhibited lower expression variation, more modular architectures, with stress response genes embedded within well-defined modules. Moreover, synthetic tetraploids displayed the highest number of modules correlated with plant fitness proxy suggesting higher output variance resulting from the transcriptional shock. Together, our results indicate that WGD induces a transient phase of transcriptomic expansion and network disorganization that broadens the phenotypic landscape, followed by evolutionary stabilization and finally retention of some advantageous novelties in established polyploids. This supports the view of neo-polyploids as "hopeful monsters", in which short-term instability creates a window of enhanced variability and plasticity with long-term evolutionary potential. SignificanceSince the early concept of polyploids as "hopeful monsters," biologists have hypothesized that whole-genome duplication can generate novel phenotypes and facilitate adaptation to environmental challenges. Yet the mechanisms linking genome doubling to evolutionary innovation remain poorly understood. By comparing diploid, synthetic autotetraploid, and naturally established autotetraploid populations of Arabidopsis arenosa, we show that newly formed polyploids undergo a transient phase of expanded transcriptomic variation and extensive regulatory network rewiring. In contrast, established polyploids exhibit a more stable and modular network architecture. Our results provide empirical support for a long-standing evolutionary hypothesis, showing how genome duplication can temporarily broaden the range of possible phenotypes before subsequent stabilization through evolution.

evolutionary biology↗

bioRxiv2026

Centromeric variation is shared across ploidy barriers in Alnus glutinosa agg.

Polyploidy is often thought to cause immediate reproductive isolation due to sterility and inviability of inter-ploidy offspring. However, recent research demonstrated genome-wide introgression in natural populations of diploids and tetraploids. Yet, it still remains unknown whether introgression varies in strength along the genome and what are the forces underlying such variation. Here we analyzed whole-genome resequencing data from natural populations of the Alder tree, Alnus glutinosa agg., which includes a widespread diploid lineage found across large parts of Europe and two autotetraploid lineages with more limited ranges on the Balkan and Iberian Peninsulas. Our sampling involved mixed-ploidy populations, where diploids, triploids and tetraploids co-occur as well as ploidy pure populations. We identified genomic regions of increased admixture, which coincide with putative locations of centromeres. We hypothesize that this pattern of shared variation at pericentromeric regions involves centromere drive, which happens when centromeres increase the likelihood of being included in the oocyte during female meiosis and which has been studied in only a few plant species. While it was previously suggested that centromere drive could cause reproductive isolation and speciation, here we propose that driving centromeres could be able to lift reproductive barriers caused by ploidy differences.

evolutionary biology↗

bioRxiv2026

Transcriptomic insights into triploid seed failure in Arabidopsis arenosa natural populations

O_LIPolyploidy is a key evolutionary force in plants; among its many consequences, hybridization between diploids and polyploids is restricted due to the "triploid block". While the molecular mechanisms of this postzygotic barrier are extensively studied in the model species Arabidopsis thaliana, our understanding of the triploid block in natural systems remains limited. C_LIO_LIHere, we investigated the transcriptome of failing triploid seeds in Arabidopsis arenosa, a close relative of A. thaliana with diploid and autotetraploid populations meeting in nature. We also identified A. arenosa imprinted genes. C_LIO_LITriploid seeds showed preferential misregulation of imprinted genes, which parallels the parent-of-origin features of the triploid block. Tissue-specific transcriptomic analyses revealed pathogen defense-like response being recurrently affected in the endosperm and seed coat. This pathway is commonly misregulated in all species with triploid seed transcriptomes studied to date. The associated genes however are likely more involved in cell-cell signaling rather than pathogen defense per se. C_LIO_LIAltogether, this study depicts a thorough molecular landscape of the triploid block for the first time in natural systems. Combining data on the understudied maternal excess transcriptome, a new imprintome, a tissue-specific focus, and a cross-species comparison, this study also advances our understanding of the triploid block and seed development. C_LI

evolutionary biology↗

bioRxiv2026

A Global Genomic Resource for Outcrossing Arabidopsis lyrata and Arabidopsis arenosa

Genetic studies leveraging natural variation in Arabidopsis species have improved our understanding of evolutionary genetic processes underlying ecologically important and adaptive traits. Integrating the thorough functional knowledge accumulated in A. thaliana with the extensive natural variation in outcrossing Arabidopsis species is a powerful approach to study the basis of adaptation in natural evolutionary and ecological contexts. Here we present an integrated genomics database of sequenced genomes from several studies in A. lyrata (1018 genomes in total) and A. arenosa (736 genomes in total), spanning the geographic ranges of these two ploidy-variable, outcrossing taxa. We provide a searchable genome browser with population data mapped to respective reference genomes, an interactive geographic map of population structure clusters, and an efficient way to subsample the full dataset of genetic variation, available at arabidopsislyrata.org. To demonstrate its utility, we perform a genome-wide association study on a latitudinal cline of A. lyrata and find strong associations of several loci with latitude, including variants in key regulators of photoperiodic growth. This resource provides access to genetic diversity data in a single repository, enabling further studies of comparative genetics and local adaptation, as well as of individual genes of interest.

evolutionary biology↗

bioRxiv2026

Flow cytometry protocols, relative genome size and ploidy levels for 1104 species of non-apomictic angiosperms from the Eastern Alps - a community resource based on the screening of 45,000 samples

Flow cytometry provides a reliable and fast method for estimating genome size and ploidy levels in plants. Until recently, most studies employed fresh tissues, which limits the use of the method with samples from remote areas or when an extremely high number of samples needs to be processed in a short time. Although there is growing evidence that silica-dried material can be used for ploidy estimation in some taxa, no flora-wide study has been available so far. Here, we provide methodological aspects of an unprecedented study exploring ploidy variation of non-apomictic angiosperms in the Eastern Alps. We have analysed ca. 45,000 silica-dried samples of 1135 species using flow cytometry with DAPI as stain. We were able to obtain ploidy level information from 1104 (97%) of species. The unsuccessful species included succulent plants of the family Crassulaceae (genera Jovibarba, Rhodiola, Sedum, Sempervivum), the achlorophyllous parasitic or mycoheterotrophic genera Orobanche and Hypopitis, and a handful of others. About 80% of samples were successfully analysed using a single universal protocol and leaf tissue, while in the remaining species the use of alternative tissues (such as petioles or flowers) and/or protocol modifications were needed (targeting composition of buffers, duration of fixation or staining time or use of alternative buffers). A total of 377 species (34%) included polyploid cytotypes and 179 (16%) species were ploidy-variable. As a community resource, we provide relative genome sizes and ploidy assignments of 1332 cytotypes retrieved from 1104 species along with methodological details (e.g. buffers, standards, analysed plant organs, histogram quality). We believe that this dataset will facilitate future research in particular species as well as in flora-wide investigations of ploidy level variation of the Central European flora in general. We are confident that novel cytotypes of many species will be discovered in other geographic areas, and we would be delighted if the present dataset could serve the botanical community for comparison.

plant biology↗

bioRxiv2025

Independent colonisations of serpentine habitats highlight species-specific evolutionary histories of lineage diversification

Serpentine soils are characterized by high levels of heavy metals, low nutrient availability, and water scarcity, presenting significant ecological challenges for plant species. Nonetheless, some species have adapted successfully to these conditions. We investigate the population genomic structure, evolutionary history and phenotypic differentiation of three diploid generalist plant species, Lavandula stoechas L., Halimium atriplicifolium (Lam) Spach. subsp. atriplicifolium, and Phlomis purpurea L., all of which inhabit adjacent serpentine and non-serpentine soils in the Malaga region in the southern Iberian Peninsula (Spain). We explore whether populations from serpentine and non-serpentine soils represent distinct evolutionary lineages and whether there is genomic and phenotypic differentiation associated with serpentine conditions. We measured plant height and specific leaf area (SLA) to detect potential ecotypic variation associated with soil type. A ddRADseq SNP dataset was generated for each species, representing 10 populations from serpentine and 10 from non-serpentine soils. We ordinated genotype data to assess genomic variation, conducted an ADMIXTURE analysis to infer ancestral groups, and used Treemix analyses to investigate phylogenetic relationships and gene flow events between populations. Isolation by distance (IBD) analyses evaluated the role of geographic separation in observed genomic differentiation. Our results reveal species-specific patterns of genomic, and to some extent phenotypic, differentiation between serpentine and non-serpentine populations, with evidence of multiple colonisations of serpentine sites in all three species. The study highlights the role of historical differentiation and subsequent gene flow in shaping the genomic structure of plant populations, alongside observed variation in phenotypic traits across environments.

evolutionary biology↗

bioRxiv2025

Arabidopsis arenosa influences its microbiome as a serpentine soil adaptation strategy

There is growing evidence that microbes can facilitate plant growth in metal-rich soils. However, our current understanding of how plants recruit their microbiomes under abiotic stress remains incomplete. Serpentine soils are elementally skewed, with high concentrations of magnesium and nickel, often accompanied by other heavy metals, which can limit calcium availability and present unique challenges to plant growth. These soils are also nutrient-poor, prone to erosion, and have low water-holding capacity. To date, the mechanisms by which plants adapt to serpentine soils remain poorly understood and the role of plant-associated microbiomes in this process has not been described. Here, we focus on Arabidopsis arenosa populations adapted to serpentine conditions and investigate their bacterial and fungal microbiomes to better understand the role of plant-associated microbes in serpentine adaptation. We show that serpentine soils harbour distinct plant-associated microbiomes across different plant niches and that the plant genetic background plays a key role in shaping microbial community composition. Finally, we identify serpentine-specific bacterial and fungal variants that may contribute to plant adaptation under these challenging soil conditions.

ecology↗

bioRxiv2025

Autopolyploidy exacerbates dominance masking under negative frequency-dependent selection: evidence from sporophytic self-incompatibility in Arabidopsis arenosa and A. lyrata

Polyploidy is a widespread phenomenon in flowering plants, with up to 30% of extant species being recent polyploids. Whether and how polyploidy modulates the action of natural selection remains debated, and the particular case of balancing selection has been poorly explored. This study investigates the impact of autopolyploidy on sporophytic self-incompatibility in plants, a striking example of a genetic system evolving under a special form of balancing selection (strong negative frequency-dependent selection). Numerical simulations reveal that under strict codominance, the number of S-alleles maintained in tetraploid populations is expected to double as compared to diploid populations. However, under a model with strict hierarchical dominance among alleles, the number of S-alleles increases only slightly, but gene diversity and observed heterozygosity are substantially lower in tetraploids as compared to diploids, due to enhanced dominance masking effects. Empirical data on Arabidopsis arenosa and A. lyrata confirm the latter predictions, showing similar levels of allelic diversity but dramatically lower observed and expected heterozygosity at the self-incompatibility locus in tetraploids compared to diploids. The study highlights the significant impact of autopolyploidy on patterns of diversity at the self-incompatibility locus, emphasizing the increased dominance effect in tetraploids. The results also allow us to reject a scenario of strong founder effects associated with evolution of the polyploid lineages.

evolutionary biology↗

bioRxiv2025

Whole-genome duplication reshapes adaptation: autotetraploid Arabidopsis arenosa leverages its high genetic variation to compensate for selection constraints.

Whole-genome duplication (WGD), a widespread macromutation across eukaryotes, is predicted to affect the tempo and modes of evolutionary processes. By theory, the additional set(s) of chromosomes present in polyploid organisms may reduce the efficiency of selection while, simultaneously, increasing heterozygosity and buffering deleterious mutations. Despite the theoretical significance of WGD, empirical genomic evidence from natural polyploid populations is scarce and a direct comparisons of selection footprints between autopolyploids and closely related diploids remains completely unexplored. We therefore combined locally sampled soil data with resequenced genomes of 76 populations of diploid-autotetraploid Arabidopsis arenosa and tested whether the genomic signatures of adaptation to distinct siliceous and calcareous soils differ between the ploidies. Leveraging multiple independent transitions between these soil types in each ploidy, we identified a set of genes associated with ion transport and homeostasis that were repeatedly selected for across the species range. Notably, polyploid populations have consistently retained greater variation at candidate loci compared to diploids, reflecting lower fixation rates. In tetraploids, positive selection predominantly acts on such a large pool of standing genetic variation, rather than targeting de novo mutations. Finally, selection in tetraploids targets genes that are more central within the protein- protein interaction network, potentially impacting a greater number of downstream fitness-related traits. In conclusion, both ploidies thrive across a broad gradient of substrate conditions, but WGD fundamentally alters the ploidies adaptive strategies: tetraploids leverage their greater genetic variation and redundancy to compensate for the predicted constraints on the efficacy of positive selection.

evolutionary biology↗

bioRxiv2025

Genomic basis of adaptation to serpentine soil in two Alyssum species shows convergence with Arabidopsis across 20 million years of divergence

Background and AimsSerpentine outcrops, characterized by low nutrient availability, high heavy metal concentrations, propensity to drought, and island-like distributions, offer valuable systems to study parallelisms in repeated adaptation to extreme environments. While shared phenotypic manifestation of adaptation to serpentine environments has been investigated in many species, it is still unclear whether there may be a common genetic basis underlying such responses. Here we assess local adaptation to serpentine soil and infer the parallel genetic signatures of local adaptation to serpentine environments in two thus far unexplored closely related species, Alyssum gmelinii and Alyssum spruneri (Brassicaceae). Then we measure gene- and function-level convergence with the previously explored Arabidopsis arenosa, to reveal candidate shared adaptive strategies within Brassicaceae. MethodsWe tested for adaptation using a reciprocal substrate-transplant experiment in A. gmelinii. Then, after assembling a reference genome, we generated population-level sequencing data of four population pairs and performed genome scans for directional selection to infer serpentine adaptive candidate genes in Alyssum. Finally, we compared candidate gene lists with those inferred in similar experiments in Arabidopsis arenosa and used protein-protein interaction networks to discern functional convergence in serpentine adaptation. Key ResultsIndependent colonization of serpentine environments by Alyssum populations is associated with footprints of selection on genes related to ion transport and homeostasis, nutrient and water uptake, and life-history traits related to germination and reproduction. Reciprocal transplant experiments demonstrated that adapted plants germinate sooner and exhibit better growth in serpentine conditions while excluding heavy metals and increasing Ca uptake in their tissues. Finally, a significant fraction of such genes and molecular pathways is shared with Arabidopsis arenosa. ConclusionsWe show that genetic adaptation to the multi-factorial challenge imposed by serpentine environments involves key pathways that are shared not only between closely related species, but also between Brassicaceae tribes of [~]20 Mya divergence.

evolutionary biology↗

bioRxiv2025

Whole-genome duplication increases genetic diversity and load in outcrossing Arabidopsis

Genetic variation underpins evolutionary change, but accumulation of slightly deleterious mutations also increases mutation load. There are multiple factors affecting the extent of load such as population size and breeding system, yet other potential determinants remain unexplored. A common macromutation, whole-genome duplication (WGD) occurs broadly across Eukaryotes, yet we lack a clear understanding of how WGD impacts neutral and selective processes within a population. Using forward simulations and empirical analysis of 632 short- and 16 long-read sequenced individuals of Arabidopsis arenosa (23 diploid and 42 natural autotetraploid populations), we test for the effects of WGD on genome-wide diversity and mutation load. Our simulations show how genetic variation gradually rises in autotetraploids due to increase of mutational target size. Moreover, mutation load increases due to relaxed purifying selection when deleterious mutations are masked by additional chromosome copies. Empirical data confirm these patterns, showing significant increase in nucleotide diversity, ratios of non-synonymous to synonymous SNPs, and number of indels and large structural variants in A. arenosa autotetraploids. However, a rather modest increase in load proxies together with a broad distribution and niche of autotetraploids suggests load accumulation has not (yet) limited their successful expansion. Overall, we demonstrate a complex interplay between neutral processes and purifying selection in shaping genetic variation following WGD and highlight ploidy as an important determinant of genetic diversity and mutation load in natural populations.

evolutionary biology↗

bioRxiv2024

Diploid origins, adaptation to polyploidy, and the beginning of rediploidization in allotetraploid Arabidopsis suecica

Polyploidization, followed by genome downsizing, is a recurrent evolutionary cycle that dramatically reshapes genome structure. Newly formed polyploids must quickly adjust their cell division machinery to maintain stable chromosome inheritance, while long-term stabilization involves rediploidization, returning the genome to a diploid-like state. Here, we investigate the origin and early genome evolution of Arabidopsis suecica, a hybrid polyploid derived from A. thaliana and A. arenosa Leveraging a recent genome assembly for A. suecica along with population level whole-genome resequencing of all three species, we identify the closest progenitors to A. suecica and use this knowledge to examine genes under positive selection and to assess compensatory dynamics between homeologs carrying loss-of-function mutations. Our findings show that both parental species were diploid, including the paternal A. arenosa progenitor. We identify evidence for de novo adaptation to allopolyploidy within the A. arenosa sub-genome of A. suecica, including genes involved in homolog pairing and recombination. Although relaxed purifying selection is evident, likely due to the genome-wide redundancy, we observe functional compensation between homeologous gene pairs in A. suecica: when one copy loses function, the other maintains it Together, these findings revise the origin of A. suecica and identify early genome stabilization mechanisms, including evidence for meiotic adaptation and mutational buffering through homeologous gene compensation.

genomics↗

bioRxiv2024

Overcoming ploidy barriers: the role of triploid bridges in the genetic introgression of Cardamine amara

O_LIPolyploidisation is a significant reproductive barrier, yet genetic evidence indicates that interploidy admixture is more common than previously thought. Theoretical models and controlled crosses support the triploid bridge hypothesis supposing that hybrids of intermediate ploidy facilitate gene flow. However, comprehensive evidence combining experimental and genetic data is missing. C_LIO_LIIn this study, we investigated the rates and directions of gene flow within a diploid- autotetraploid contact zone of Cardamine amara, a species with abundant natural triploids. We cytotyped over 400 wild individuals, conducted reciprocal interploidy crosses and inferred gene flow based on genome-wide sequencing of 84 individuals. C_LIO_LITriploids represent a conspicuous entity in mixed-ploidy populations (5%), yet only part of them arose through interploidy hybridisation. Despite being rarely formed, triploid hybrids can backcross with their parental cytotypes, producing viable offspring that are often euploid (in 42% of cases). In correspondence, we found a significant genome-wide signal of gene flow for sympatric, but not allopatric, diploids and tetraploids. Coalescent simulations demonstrated significant bidirectional introgression which is stronger in the direction towards the tetraploid cytotype. C_LIO_LITriploids, though rare, play a key role in overcoming polyploidy-related reproductive barriers. We present integrative evidence for bidirectional interploidy gene flow mediated by a triploid bridge in natural populations. C_LI

evolutionary biology↗

bioRxiv2024

How environment and genetic architecture of unreduced gametes shape the establishment of autopolyploids

It is broadly assumed that polyploidy success is due to an increase in fitness associated with whole genome duplication due to higher tolerance to stressful conditions. In agreement, several theoretical models found that, among other factors, a better tolerance to new environmental conditions can promote polyploidy establishment. These models, however, often made strong hypotheses, for example considering that diploids cannot adapt to new conditions, or that unreduced gametes production is not a limiting factor and that it is of a fixed quantity. In this paper, we challenged some of these hypotheses. We developed a theoretical model in which we modeled the joint evolution of a quantitative trait under selection and the production of unreduced gametes, this trait also being a quantitative trait; both traits were pleiotropically linked. We followed the adaptation of initially diploid populations to a new environment to which neo-tetraploid individuals were directly adapted. The generation of these autotetraploid individuals was enabled by the genetic production of unreduced gametes and by the environmental change modifying the average production of these gametes. We found that for realistic values of unreduced gametes production, adaptation to new environmental conditions was mainly achieved through adaptation of diploids to the new optimum rather than the fixation of newly adapted tetraploid individuals. In broader parameter sets, we found that the adaptation process led to mixed-ploidy populations, except when the populations were swamped with unreduced gametes, and that pleiotropy and environmental effects favored the co-existence of both cytotypes.

evolutionary biology↗

bioRxiv2024

Multiple polyploidizations in Arabidopsis lyrata stabilized by long-range adaptive introgression across Eurasia

Abundance of polyploidy varies across lineages, evolutionary time and geography, suggesting both genetics and environment play a role in polyploid persistence. Arabidopsis lyrata appears to be the most polyploidy-rich species-complex in the Arabidopsis genus, with multiple origins of autotetraploidy. This is revealed by genomic data from over 400 samples across Eurasia. We found over 30 previously undescribed autotetraploid populations in Siberia with a minimum of two separate origins, independent of those previously reported in Central Europe. The establishment of Siberian tetraploids is mediated by meiotic adaptation at the same genes as in European tetraploid A. lyrata and Arabidopsis arenosa, despite high divergence and geographical separation. Haplotype analysis based on synthetic long-read assemblies supports the long-range introgression of adaptive alleles from the tetraploid interspecific pool of European A. lyrata and A. arenosa to tetraploid Siberian A. lyrata. Once evolved, adaptation to polyploidy promotes the establishment of new polyploid lineages through adaptive inter- and intraspecific introgression.

genomics↗

bioRxiv2024

Varying importance of postzygotic isolation in polyploid speciation? A survey of the triploid block strength, its causal mechanisms, and evolutionary consequences

The triploid block, primarily caused by endosperm developmental issues, is known as a significant barrier to interploidy hybridization among flowering plants and thereby, polyploid speciation. However, its strength varies across taxa, with some instances of leakiness, questioning its universal role as a barrier. We conducted a literature survey to explore the causes of the variation in the strength of triploid block across angiosperms. We particularly assessed the impact of interploidy cross direction, types of endosperm development, endosperm persistence at seed maturity, and ploidy divergence. None of these factors had a significant impact on triploid seed viability, likely due to limited data and inconsistencies in estimation methods across the literature. In addition, triploid seed viability in experimental crosses was sometimes correlated to the occurrence of triploid hybrids in nature, sometimes not, suggesting a mixed role of the triploid block in shaping interspecies gene flow. Altogether, our study highlights the need for unified approaches in future studies on the triploid block to advance our understanding of its variation and evolutionary implications.

evolutionary biology↗

bioRxiv2024

Different resource partitioning explains plant species richness patterns in tropical alpine ecosystems

Species co-existence based on resource partitioning modulates biodiversity patterns across latitudes and altitudes. Resource partitioning can occur via specialisation or separation in the geographic range or niche. Here, we compare two tropical alpine ecosystems with similar climates to test for geographic range and climatic niche partitioning strategies in explaining species richness difference. We compare the species-rich tropical alpine ecosystem in the South American Andes with the more species-poor one in the eastern African mountains. We combine phylogenomic data for three locally diversified plant lineages in each region with occurrence records and estimate climatic niche and geographic range metrics (size and overlap). We found that the Andean species have overall larger niches than the African species, thus smaller niches indicating specialisation is not the explanation for the higher species richness in the Andes. Instead, for species with overlapping geographic ranges, we found that the Andean species tend to show less niche overlap than the African species, indicating more effective niche separation. Taken together, we propose that different degrees of niche separation in geographically overlapping species, and hence, a different pattern of resource partitioning, explain the differences in species richness between the two tropical alpine ecosystems.

ecology↗

bioRxiv2023

Impact of whole-genome duplications on structural variant evolution in the plant genus Cochlearia

Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. All angiosperms have undergone ancient WGDs, and today stable polyploids account for a substantial portion of both wild and domesticated plant species. Despite its centrality in evolution, WGD is a hugely disruptive mutation, and we still lack a clear understanding of its fitness consequences. Here, we study whether WGD results in greater diversity of genomic structural variants (SVs) and how this influences evolutionary dynamics in nature. Using a set of long-read sequenced samples from the plant genus Cochlearia (Brassicaceae), which contains diploids and a recent ploidy series up to octoploid, we show that masking of recessive mutations due to WGD has led to a substantial and progressive accumulation of genic SVs across four ploidy levels. Such SVs likely constitute a genetic load and thus reduce the adaptive potential of polyploid populations. However, this SV accumulation also provides a rich pool of standing genetic variation upon which selection may act in novel environments. By constructing a graph-based pangenome for Cochlearia, we identify SVs in hundreds of samples and study the genomic basis of environmental adaptation. We find putatively beneficial SVs involved in pathogen resistance, root development, and salt tolerance, many of which are unique to polyploids. Finally, we explore the adaptive landscapes of SVs and SNPs, identify geographical regions where SVs make novel contributions to adaptive variation, and predict that the role of SVs in environmental adaptation increases due to rapid climate change.

evolutionary biology↗