Biology subjects

Sramkova, G.

Publications and source records attributed to Sramkova, G..

8 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↗

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

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↗

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↗

bioRxiv2022

Niche differentiation following whole-genome duplication? The importance of considering the intricate evolutionary history of polyploids when assessing climatic niche evolution

AimAlthough whole genome duplication (WGD) is an important speciation force, we still lack a consensus on the role of niche differentiation in polyploid evolution. In addition, the role of genome doubling per se vs. later divergence on polyploids niche evolution remains obscure. One reason for this might be that the intraspecific genetic structure of polyploid complexes and interploidy gene flow is often neglected in ecological studies. Here, we aim to investigate to which extent these evolutionary processes impact our inference on niche differentiation of autopolyploids. LocationEurope TaxonArabidopsis arenosa (Brassicaceae) MethodsLeveraging a total of 352 cytotyped populations of diploid-autotetraploid A. arenosa, we examined differences among climatic niches of diploid and tetraploid lineages both globally, and independently for each tetraploid lineage with respect to the niche of its evolutionary closest relative. Then, we tested if there was an effect of additional interploidy introgression from other sympatric but more ancestral diploid lineages of A. arenosa on climatic niches of tetraploids. ResultsEcological niche shift of tetraploids is only detected when the assignment of populations to intraspecific genetic lineages is considered. We found different patterns of climatic niche evolution (i.e. niche conservatism, contraction or expansion) in each tetraploid lineage when compared to its evolutionary closest relatives. We observed an effect of interploidy gene flow in patterns of climatic niche evolution of tetraploid ruderal plants of A. arenosa. Main conclusionsThe niche shift of tetraploids in A. arenosa is not driven by WGD per se but rather reflects dynamic post-WGD evolution in the species, involving tetraploid migration out of their ancestral area and interploidy introgression with other diploid lineages. Our study supports that evolutionary processes following WGD - which usually remain undetected by studies neglecting evolutionary history of polyploids - may play a key role in the adaptation of polyploids to challenging environments.

plant 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↗

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↗