Biology subjects

De Kort, H.

Publications and source records attributed to De Kort, H..

8 recordsLinked to original sources

bioRxiv2025

FvFT1-FvTFL1 epistasis drives flowering time adaptation in woodland strawberry

Floral transition and flower bud development during autumn and winter are common in plants inhabiting temperate and cold climates. However, our understanding of the natural variation and underlying molecular mechanisms of such life-history strategy remain largely limited to Brassicaceae model species. To address this gap, we investigated flowering time variation across a broad geographical and bioclimatic range in Fragaria vesca (woodland strawberry), a perennial herb from the Rosaceae family. We found that the timing of floral transition and subsequent flowering in F. vesca populations is primarily shaped by population structure, reflecting postglacial colonization patterns from distinct refugia, and is further modulated by adaptations to winter temperatures. The association of increasing expression of FvFT1, the strawberry ortholog of FLOWERING LOCUS T, with delayed flowering in accessions from diverse climatic and genetic backgrounds suggested FvFT1 as a major candidate gene regulating flowering time variation. We further demonstrated how distinct florigen and antiflorigen roles of FvFT1 are dependent on functional alleles of F. vesca TERMINAL FLOWER1 (FvTFL1) and how the epistatic relationship between FvFT1 and FvTFL1 controls adaptive flowering time variation by adjusting sensitivity to floral inductive photoperiod and vernalization. Our findings reveal a major molecular basis of how timing of floral transition has adapted to temperature in a Rosaceae model inhabiting multiple climatic zones and highlight lineage-specific adaptive mechanisms underlying convergent life-history strategy. Significance statementMolecular mechanisms underlying flowering time adaptation have been primarily investigated in annual plants that transit to flowering in spring. However, many perennial plant species in temperate climates form flower buds in autumn and winter to flower in the following spring. We uncover wide geographical and climatic patterns of flowering time adaptation in the perennial model species woodland strawberry. We report that natural variation in the expression of strawberry FLOWERING LOCUS T (FvFT1) gene originating ice ages ago and further driven by local temperature adaptations control flowering time variation in this species. Finally, we show how FvFT1 may function as both flowering promoter and repressor depending on the genetic background, thus revealing a novel mechanism of flowering time adaptation.

plant biology↗

bioRxiv2025

On the edge of extinction: Delayed plant genetic response to forest edge dynamics

Understanding genetic responses to forest dynamics is essential for predicting the long-term viability of understory plant populations and for developing effective conservation strategies. This study investigates genetic extinction debt and colonization credit in Circaea lutetiana, a clonal forest understory species, across its European range. Using pooled genotype-by-sequencing data from 40 forest edge and core populations, we examined to what extent population size, latitude and historical changes in forest configuration predict genetic diversity. Our findings reveal that the historical forest configuration profoundly shapes present-day genetic diversity. Long-established forest edge populations exhibit significantly reduced allelic richness (-9%) compared to core populations, indicating the partial pay-off of a genetic extinction debt. In contrast, populations from recently established forest edges maintain comparable allelic richness to core populations, suggesting delayed population genetic responses to land use changes. Finally, populations established in areas that were afforested during the past 250 years exhibit lower genetic diversity than historical forest core populations, indicating a delay in genetic recovery and thus a potential genetic colonization credit. Our results highlight that C. lutetiana populations are not at equilibrium with the current forest configuration, underscoring the role of lagged genetic responses across very long time scales. Connectivity and population size further moderate genetic diversity, with smaller, isolated populations particularly vulnerable to genetic erosion. Given the limited research on delayed evolution in forest understory species, our results improve the understanding of extinction risk dynamics and underscore the need for history-informed restoration efforts.

ecology↗

bioRxiv2024

Late Quaternary climatic impact on the woodland strawberry genome: a perennial herb's tale

Exploring a species paleohistory is crucial for understanding its responsiveness to climatic events, identifying drivers of adaptation, and developing effective biodiversity conservation strategies in the face of ongoing climate change. We analyzed 200 genomes of the perennial herb woodland strawberry (Fragaria vesca L.) from across Europe and investigated the population structure and demographic history of the species during past geoclimatic events. We found a clear division of populations into western and eastern genetic clusters, indicative of distinct glacial refugia and adaptations to variation in temperature seasonality. The eastern core populations were several times larger (defined as effective population size, NE) than populations in other regions, showed no evidence of inbreeding, and were resilient to several glacial maxima. However, we observed decreasing NE and higher inbreeding in populations toward range edges, particularly in the north, where these individuals went through bottlenecks during glaciations. Population divergence suggested that western and eastern Europe were colonized from separate refugia in multiple waves during the Holocene, while the largest current populations from the northern Mediterranean to southern regions of the Nordic countries formed a connected population chain with gene flow between eastern core populations and western Europe, primarily occurring through Central Europe. Similar patterns of colonization and hybridization may have occurred during past interglacial periods, contributing to the present-day population structure of woodland strawberry. We suggest that the unprecedented resolution of the species climatic history across six glacial-interglacial cycles presented here holds the promise of transforming the general understanding of species paleohistory through geoclimatically tracing ancestral haplotypes.

plant biology↗

bioRxiv2023

Non-random polymorphisms near transposable elements facilitate evolution across the genome of Arabidopsis thaliana

Evolution is a key characteristic of all life on earth, and is achieved mainly through mutation and recombination. To facilitate evolutionary rates in the absence of recombination, increased mutagenesis could provide essential opportunities for evolution. Here, we harness the genomes of 973 wild accessions of Arabidopsis thaliana, a self-fertilizing species characterized by reduced recombination rates, to study the role of transposable elements (TEs) as mutagenic drivers of non-random genetic variation. We found that multiple TE superfamilies accumulate large numbers of genetic variants in gene-rich regions of the genome. Moreover, TEs were enriched in genes underpinning key molecular processes, including fertilization and mRNA cis-splicing, suggesting that TEs generate genetic variation that is fundamental to organismal functioning and reproduction. An excess of common genetic variants (maf>0.4) flanking TEs, despite the extreme degree of self-fertilization, further corroborates the notion that TEs can generate substantial evolutionary potential in the absence of outcrossing. Nevertheless, while other studies point to TE mobilization as a strategy to facilitate adaptive evolution, we find that only a fraction (4.8%) of TE families was linked to genetic variants involved in climate adaptation to a significantly larger extent than background genomic variation, possibly because the high mutation rates near TEs dilute adaptive signals. Overall, all TE superfamilies but one (Gypsy) were significantly associated with evolutionary processes through their association with genes, functional molecular processes, flanking common variants and/or climate adaptation. We conclude that non-random mutations flanking TEs provide substantial evolutionary potential in a self-fertilizing species.

evolutionary biology↗

bioRxiv2021

Standing covariation between genomic and epigenomic patterns as source for natural selection in wild strawberry plants

Adaptive evolution is generally thought to be the result of natural selection predominantly acting upon pre-existing DNA sequence polymorphisms through gene-environment interactions. Epigenetic inheritance is, however, recently considered an additional molecular force driving adaptive evolution independent of DNA sequence variation. Through comparative analyses of genome-wide genetic (SNPs) and epigenetic (DMCs) variation of wild strawberry plants raised under distinct drought settings, we demonstrate intermediate levels of genome-wide covariation between SNPs and DMCs. Cases of high SNP-DMC covariation were significantly associated with (i) applied stress, (ii) non-adaptive SNPs, and (iii) solitary DMCs (as opposed to DMC islands). We also found that DMCs, drought-responsive DMCs in particular, typically co-vary with hundreds of SNPs, indicating high genomic redundancy as a basis for polygenic adaptation. Our findings suggest that stress-responsive DMCs initially co-vary with many associated SNPs under increased environmental stress (cfr. co-gradient plasticity), and that natural selection acting upon these SNPs subsequently reduce standing covariation with stress-responsive DMCs. In addition, the degree of covariation between SNPs and DMCs appears independent of their respective genomic distance, indicating that trans-acting associations between SNPs and DMCs are as likely as cis-acting associations. Our study is in favor of DNA methylation profiles representing complex quantitative traits rather than independent evolutionary forces, but further research is required to fully rule out SNP-independence of genome-wide DMCs. We provide a conceptual framework for polygenic regulation and adaptation shaping genome-wide methylation patterns.

evolutionary biology↗

bioRxiv2019

Ecological divergence of DNA methylation patterns at distinct spatial scales

Adaptive trait divergence between populations is regulated by genetic and non-genetic processes. Compared to genetic change, epigenetic change is unstable and short-lived, questioning its contribution to long-term adaptive potential. However, epigenetic change can accumulate over time, and may result in beneficial epigenetic memories where environments are heterogeneous. Diverging epigenetic memories have been observed across large spatial scales, and can persist through multiple generations even in the absence of the causative environmental stressor. It is unknown, however, how and to what extent epigenetic memories contribute to fine-scale population structure and evolution. Here, we performed whole genome bisulfite sequencing on 30 Fragaria vesca F1 plants originating from distinct ecological settings and grown in a controlled environment. Specifically, we compared methylation patterns between a steep, altitudinal gradient (<2 km) and a wide spatial gradient (>500 km). If epigenetic variation is random, arising from errors during replication and without evolutionary implications, one would expect similar amounts of epigenetic variation across populations and no spatial scale-effect. Here, we find that epigenetic memories arise even at fine spatial scale, and that both parallel and non-parallel biological processes underpin epigenetic divergence at distinct spatial scales. For example, demethylation of transposable elements consistently occurred at the large but not the small spatial scale, while methylation differentiation for most biological processes were shared between spatial scales. Acute drought stress did not result in significant epigenetic differentiation, indicating that repeated historical stress levels associated with heterogeneous environmental conditions are required for acquiring a stable epigenetic memory and for coping with future environmental change.

ecology↗

bioRxiv2019

Pre-adaptation to climate change through topography-driven evolution of traits and their plasticity

Climate change is expected to increase the level of drought stress experienced by many plant populations, yet the spatial distribution of changes in dryness remains highly uncertain. Species can, to some extent, adapt to climate uncertainty through evolving increased trait plasticity. Biodiversity conservation could capitalize on such natural variation in the ability of populations to cope with climate variability. Yet, disentangling evolution of trait means vs. trait plasticity is challenging, as it requires a sampling design with genetic replicates grown under distinct environmental conditions. Here, we applied different soil moisture treatments to clones of Fragaria vesca plants that were raised from seeds that were sampled in distinct mountainous topographical settings, to study adaptive trait and plasticity divergence in response to drought. We demonstrate that various fitness traits evolved along topographical gradients, including increased specific leaf area (SLA) with increasing slope, and increased growth plasticity with increasing altitude. Our results indicate that traits and their plasticity can evolve independently in response to distinct topographical stressors. We further show that trait heritability varies considerably among traits and topographical settings. Heritability of phenotypic plasticity tended to increase with altitude for all traits, with populations from high altitudes harboring more than twice the heritability for growth and SLA plasticity compared to populations from low altitudes. We conclude that (i) low altitudinal populations, which are expected to be least vulnerable to climate change, may only withstand limited increases in drought stress, while (ii) populations that evolved to thrive under more heterogeneous mountain conditions are pre-adapted to climate change through high plasticity and heritability. Highly heterogeneous landscapes may thus represent invaluable sources of quantitative genetic variation that could support conservation under climate change across the globe.

ecology↗

bioRxiv2017

Habitat Fragmentation Causes Coevolutionary Burning Spots

Habitat fragmentation increasingly threatens the services provided by natural communities and ecosystem worldwide. An understanding of the underlying eco-evolutionary processes in natural settings is lacking, yet critical to realistic and sustainable conservation. Through integrating the multivariate genetic, biotic and abiotic facets of a natural community network experiencing various degrees of habitat fragmentation, we provide unique insights into the processes underlying community functioning in real, natural conditions. The focal community network comprises a parasitic butterfly of conservation concern, and its two obligatory host species, a plant and an ant. We show that fragmentation of butterfly habitat has the potential to impair the balance between dispersal and coevolution. This process can cause coevolutionary burning spots of decreased genetic diversity and therefore of increased extinction risk. We stress that ignoring such eco-evolutionary feed-backs inherent to the very functioning of natural communities can strongly impact their persistence.\n\nOne Sentence SummaryCommunities under threat of habitat fragmentation suffer increased extinction risk through coevolutionary overheating.

evolutionary biology↗