Biology subjects

Bohutinska, M.

Publications and source records attributed to Bohutinska, M..

11 recordsLinked to original sources

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↗

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↗

bioRxiv2023

Repeated adaptation to whole genome duplication in outcrossing Arabidopsis is mediated by mosaic adaptive haplotypes

Polyploidy, the result of whole genome duplication (WGD), is widespread across the tree of life and is often associated with speciation or adaptability. It is thought that adaptation in autopolyploids (within-species polyploids) may be facilitated by increased access to genetic variation. This variation may be sourced from gene flow with sister diploids and new access to other tetraploid lineages, as well as from increased mutational targets provided by doubled DNA content. Here we deconstruct the origins of haplotype blocks displaying the strongest selection signals in established, successful autopolyploids, Arabidopsis lyrata and Arabidopsis arenosa. We see strong signatures of selection in 17 genes implied in meiosis, cell cycle, and transcription across all four autotetraploid lineages present in our expanded sampling of 983 sequenced genomes. Most prominent in our results is the finding that the tetraploid-characteristic haplotype blocks with the most robust signals of selection were completely absent in diploid sisters. In contrast, the fine-scaled variant mosaics in the tetraploids originated from highly diverse evolutionary sources. These include novel reassortments of trans-specific polymorphism from diploids, new mutations, and tetraploid-specific inter-species hybridization. We speculate that this broad-scale allele acquisition and re-shuffling enabled the autotetraploids to rapidly adapt to the challenges inherent to WGD, and may further promote their adaptation to environmental challenges. Lay summaryPolyploidy, the result of whole genome duplication, is associated with speciation and adaptation. To fuel their often remarkable adaptations, polyploids may access and maintain adaptive alleles more readily than diploids. Here we identify repeated signals of selection on genes that are thought to mediate adaptation to whole genome duplication in two Arabidopsis species. We found that the tetraploid-characteristic haplotype blocks, found in genes exhibiting the most robust signals of selection, were never present in their diploid relatives. Instead, these blocks were made of mosaics forged from multiple allelic sources. We hypothesize that this increased variation helped polyploids to adapt to the process that caused this increase - genome duplication - and may also help them adapt to novel environments.

evolutionary biology↗

bioRxiv2021

Parallel adaptation in autopolyploid Arabidopsis arenosa is dominated by repeated recruitment of shared alleles

Relative contributions of pre-existing vs de novo genomic variation to adaptation are poorly understood, especially in polyploid organisms, which maintain increased variation. We assess this in high resolution using autotetraploid Arabidopsis arenosa, which repeatedly adapted to toxic serpentine soils that exhibit skewed elemental profiles. Leveraging a fivefold replicated serpentine invasion, we assess selection on SNPs and structural variants (TEs) in 78 resequenced individuals and discovered substantial parallelism in candidate genes involved in ion homeostasis. We further modelled parallel selection and inferred repeated sweeps on a shared pool of variants in nearly all these loci, supporting theoretical expectations. A single, striking exception is represented by TWO PORE CHANNEL 1, which exhibits convergent evolution from independent de novo mutations at an identical, otherwise conserved site at the calcium channel selectivity gate. Taken together, this suggests that polyploid populations can rapidly adapt to environmental extremes, calling on both pre-existing variation and novel polymorphisms.

evolutionary biology↗

bioRxiv2020

Convergence and novelty in adaptation to whole genome duplication in three independent polyploids

Convergent evolution is observed broadly across the web of life, but the degree of evolutionary constraint during adaptation of core intracellular processes is not known. High constraint has been assumed for conserved processes, such as cell division and DNA repair, but reports of nimble evolutionary shifts in these processes have confounded this expectation. Whole genome duplication (WGD) necessitates the concerted adjustment of a wide range of fundamental intracellular functions but nevertheless has been repeatedly survived in all kingdoms. Given this repeated adaptation to WGD despite obvious intracellular challenges to core processes such as meiosis, we asked: how do lineages not only survive WGD, but sometimes ultimately thrive? Are the solutions employed constrained or diverse? Here we detect genes and processes under selection following WGD in the Cochlearia species complex by performing a scan for selective sweeps following WGD in a large-scale survey of 73 resequenced individuals from 23 populations across Europe. We then contrast our results from two independent WGDs in Arabidopsis arenosa and Cardamine amara. We find that while WGD does require the adaptation of particular functional processes in all three cases, the specific genes recruited to respond are highly flexible. We also observe evidence of varying degrees of convergence between different cases. Our results point to a polygenic basis for the distributed adaptive systems that control meiotic crossover number, ionomic rewiring, cell cycle control, and nuclear regulation. Given the sheer number of loci under selection post-WGD, we surmise that this polygenicity may explain the general lack of convergence between these species that are ~30 million years diverged. Based on our results, we speculate that adaptive processes themselves - such as the rate of generation of structural genomic variants--may be altered by WGD in nascent autopolyploids, contributing to the occasionally spectacular adaptability of autopolyploids observed across kingdoms.

evolutionary biology↗

bioRxiv2020

Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives

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 million years 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 of 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. Significance statementRepeated evolution tends to be more predictable. The impressive spectrum of recent reports on genomic parallelism, however, revealed that the fraction of the genome that evolves in parallel largely varies, possibly reflecting different evolutionary scales investigated. Here, we demonstrate divergence-dependent parallelism using a comprehensive genome-wide dataset comprising 12 cases of parallel alpine adaptation and identify decreasing probability of adaptive re-use of genetic variation as the major underlying cause. This finding empirically demonstrates that evolutionary predictability is scale dependent and suggests that availability of pre-existing variation drives parallelism within and among populations and species. Altogether, our results inform the ongoing discussion about the (un)predictability of evolution, relevant for applications in pest control, nature conservation, or the evolution of pathogen resistance.

evolutionary biology↗

bioRxiv2020

Parallelism in gene expression between foothill and alpine ecotypes in Arabidopsis arenosa

Parallel adaptation results from independent evolution of similar traits between closely related lineages and allows testing to which extent evolution is repeatable. Parallel adaptation often involves similar gene expression changes but the identity of genes shaped by parallel selection and the causes of expression parallelism remains largely unknown. By comparing genomes and transcriptomes of four independent foothill-alpine population pairs across four treatments, we addressed genetic basis, plasticity and functional consequences of gene expression parallelism in alpine adaptation. Seeds of four population pairs of Arabidopsis arenosa from distinct mountain regions were raised under four treatments that differed in temperature and irradiance, factors varying strongly with elevation. Parallelism in gene expression was quantified by RNA-seq in leaves of young plants. By manipulating temperature and irradiance, we also tested for parallelism in plasticity (gene-by-environment interaction [GEI]). We found significant parallelism in differential gene expression across four independently recruited alpine ecotypes with an overrepresentation of genes involved in biotic stress response. In addition, we demonstrated significant parallelism in GEI indicating shared response to environmental variation in our foothill and alpine populations. Fraction of genes showing expression parallelism also encompassed genomic variants showing outlying differentiation, with greater enrichment of such variants in cis-regulatory elements. In summary, our results suggest frequent evolutionary repeatability in shaping expression difference associated with colonization of an alpine environment and support the hypothesis of an important role of genetic variation in cis-regulatory elements in gene expression parallelism.

molecular biology↗

bioRxiv2020

Parallel alpine differentiation in Arabidopsis arenosa

Parallel evolution provides powerful natural experiments for studying repeatability of evolution. Well-documented examples from plants are, however, still rare, as are inquiries of mechanisms driving convergence in some traits while divergence in others. Arabidopsis arenosa, a predominantly foothill species with scattered morphologically distinct alpine occurrences is a promising candidate. Yet, the hypothesis of parallelism remained untested. We sampled foothill and alpine populations in all regions known to harbour the alpine ecotype and used SNP genotyping to test for repeated alpine colonisation. Then, we combined field surveys and a common garden experiment to quantify phenotypic parallelism. Genetic clustering by region but not elevation and coalescent simulations demonstrated parallel origin of alpine ecotype in four mountain regions. Alpine populations exhibited parallelism in height and floral traits which persisted after two generations in cultivation. In contrast, leaf traits were distinctive only in certain region(s), reflecting a mixture of plasticity and genetically determined non-parallelism. We demonstrate varying degrees and causes of parallelism and non-parallelism across populations and traits within a plant species. Parallel divergence along a sharp elevation gradient makes A. arenosa a promising candidate for studying genomic basis of adaptation.

plant biology↗

bioRxiv2020

Genomic novelty versus convergence in the basis of adaptation to whole genome duplication

Whole genome duplication (WGD) occurs across kingdoms and can promote adaptation. However, a sudden increase in chromosome number, as well as changes in physiology, are traumatic to conserved processes. Previous work in Arabidopsis arenosa revealed a coordinated genomic response to WGD, involving physically interacting meiosis proteins, as well as changes related to cell cycle and ion homeostasis. Here we ask: is this coordinated shift in the same processes repeated in another species following WGD? To answer this, we resequenced and cytologically assessed replicated populations from a diploid/autotetraploid system, Cardamine amara, and test the hypothesis that gene and process-level convergence will be prevalent between these two WGDs adaptation events. Interestingly, we find that gene-level convergence is negligible, with no more in common than would be expected by chance. This was most clear at meiosis-related genes, consistent with our cytological assessment of somewhat lower meiotic stability in C. amara, despite establishment and broad occurrence of the autotetraploid in nature. In contrast, obvious convergence at the level of functional processes, including meiotic cell cycle, chromosome organisation and stress signalling was evident. This indicates that the two autotetraploids survived challenges attendant to WGD via contrasting solutions, modifying different players from similar processes. Overall, this work gives the first insight into the salient adaptations required to cope with a genome-doubled state and brings the first genomic evidence that autopolyploids can utilize multiple trajectories to achieve adaptation to WGD. We speculate that this flexibility increases the likelihood a nascent polyploid overcomes early stringent challenges to later access the spectrum of evolutionary opportunities of polyploidy. Significance statementWhole genome duplication (WGD) is a tremendous mutation and an important evolutionary force. It also presents immediate changes to meiosis and cell physiology that nascent polyploids must overcome to survive. Given the dual facts that WGD adaptation is difficult, but many lineages nevertheless survive WGD, we ask: how constrained are the evolutionary responses to a genome-doubled state? We previously identified candidate genes for WGD adaptation in Arabidopsis arenosa, which has natural diploid and tetraploid variants. Here we test for evolutionary convergence in adaptation to WGD in a species 17 million years distant, Cardamine amara. This work gives the first genomic insight into of how autopolyploids utilize multiple adaptive trajectories to manage a genome-doubled state.

evolutionary biology↗

bioRxiv2019

Interspecific introgression mediates adaptation to whole genome duplication

Adaptive gene flow is a consequential evolutionary phenomenon across all kingdoms of life. While recognition of widespread gene flow is growing, examples lack of bidirectional gene flow mediating adaptations at specific loci that cooperatively manage core cellular processes. We previously described concerted molecular changes among physically interacting members of the meiotic machinery controlling crossover number and distribution upon adaptation to whole genome duplication (WGD) in Arabidopsis arenosa. Here we conduct a population genomic study to test the hypothesis that escape from extinction following the trauma of WGD was mediated by adaptive gene flow between A. arenosa and its congener Arabidopsis lyrata. We show that A. lyrata underwent WGD more recently than A. arenosa, indicating that specific pre-adapted alleles donated by A. arenosa underwent selection and rescued the nascent A. lyrata tetraploids from early extinction. At the same time, we detect specific signals of gene flow in the opposite direction at other functionally interacting gene coding loci that display dramatic signatures of selective sweep in both tetraploid species. Cytological analysis shows that A. lyrata tetraploids exhibit similar levels of meiotic stability as A. arenosa tetraploids. Taken together, these data indicate that bidirectional gene flow allowed for an escape from extinction of the young autopolyploids, especially the rare tetraploid A. lyrata, and suggest that the merger of these species is greater than the sum of their parts.

evolutionary biology↗

bioRxiv2018

Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa

Ploidy-variable species allow direct inference of the effects of chromosome copy number on fundamental evolutionary processes. While an abundance of theoretical work suggests polyploidy should leave distinct population genomic signatures, empirical data remains sparse. We sequenced [~]300 individuals from 39 populations of Arabidopsis arenosa, a naturally diploid-autotetraploid species. We find the impacts of polyploidy on population genomic processes are subtle yet pervasive, including reduced efficiency on linked and purifying selection as well as rampant gene flow from diploids. Initial masking of deleterious mutations, faster rates of nucleotide substitution, and interploidy introgression all conspire to shape the evolutionary potential of polyploids.

evolutionary biology↗