Biology subjects

Schmitz, G.

Publications and source records attributed to Schmitz, G..

10 recordsLinked to original sources

bioRxiv2026

Dozens of genetic variants sustain adaptation to urban spatial heterogeneity in Arabidopsis thaliana

Urbanization creates mosaics of microhabitats that sustain diverse plant communities and offer untapped opportunities to understand contemporary ecological and evolutionary processes. Using a city-wide colonization experiment in Cologne (Germany), we identified the environmental factors limiting establishment and persistence of the ruderal species Arabidopsis thaliana and the genetic variants enabling adaptation. We show that standing genetic variation is essential for realizing the species urban niche, enabling rapid adaptation to fine-scale gradients in disturbance, vegetation, and soil conditions. Despite originating from only two parental genotypes, populations evolved substantial adaptive differentiation within three generations, revealing a highly polygenic basis of local adaptation. More broadly, our approach establishes cities as powerful open-air laboratories for uncovering and fostering ecological and evolutionary processes that generate and sustain biodiversity in human-dominated landscapes.

evolutionary biology↗

bioRxiv2025

The complex molecular basis of enhanced stress resilience in extreme drought-tolerant Arabis grassland species

Background and AimsPlant species in competitive meadows must tolerate extreme stress, yet the mechanisms underlying resilience remain poorly understood. Arabis nemorensis, an endangered selfing species of Euro- pean floodplain grasslands, experiences both flooding and drought and hybridizes with its close relative, A. sagittata. We investigated how these species differ in drought survival and the molec- ular basis of their responses. MethodsSympatric lineages of A. nemorensis and A. sagittata were compared in a controlled dry-down experiment, complemented by transcriptome and small RNA profiling, and machine-learning anal- ysis of cis-regulatory motifs. Key ResultsBoth species wilted at 5% soil moisture, but A. sagittata recovered more effectively (90% vs. 50%). This difference was not explained by a major QTL, suggesting a polygenic basis. Transcrip- tome profiling revealed stronger induction in A. sagittata (6,359 vs. 5,571 differentially expressed genes). Small RNA analysis identified species-specific regulation of miR408, a conserved drought regulator. Machine-learning identified 307 sequence motifs predictive of stress-responsive expres- sion, with motif distributions indicating distinct regulatory networks. ConclusionsThis study reveals the polygenic and regulatory complexity underlying divergent drought resili- ence strategies in the closely related species thriving in grassland environments. Arabis nemorensis and its close relative A. sagittata co-occur in a floodplain meadow exposed to flooding and drought. In dry-down experiments, A. sagittata recovered more effectively than A. nemorensis. Transcriptome and small RNA analyses revealed stronger stress responses in A. sagittata, including regulation of miR408. These differences result from different regulatory networks and have a polygenic basis.

plant biology↗

bioRxiv2025

Contemporary hybridization among Arabis floodplain species creates opportunities for adaptation

Hybridization between closely related species is increasingly recognized as a major source of biodiversity. Yet, whether it can create advantageous trait combinations while purging harmful alleles remains unknown. We studied Arabis nemorensis and A. sagittata, two endangered species that currently hybridize in a single hotspot. We measured 22 phenotypic traits and mapped their genetic basis in an F2 population, after generating high quality genome assemblies for both species. In total, 58 QTLs were identified for 20 traits, with additive and dominance effects best fitting Gaussian and logistic distributions, respectively. Six large-effect QTLs were linked to significant hybrid fitness loss. Two genomic regions showed strong transmission bias favoring A. sagittata alleles, potentially accelerating their introgression. However, 48% of QTLs were unlinked to reduced fitness or segregation distortion and may generate genotypes exceeding parental performance. Notably, a major QTL affecting flowering time explained 23% of phenotypic variation and implicated TFL1 as a candidate gene for life history adaptation. While most QTLs lacked overlap with past selective sweeps, indicating limited recent positive selection, 5 of 7 QTLs for rosette size overlapped with sweep signatures in the parental lineages. Overall, our findings offer unique insights into incipient stages of hybridization.

evolutionary biology↗

bioRxiv2025

Heat-induced secondary dormancy contributes to local adaptation in Arabidopsis thaliana

Seeds should not germinate in conditions unsuitable for seedling growth. Dormancy, which allows seeds to remain inactive in an environment that would otherwise enable germination, helps optimize the timing of germination. Primary dormancy, developed during seed maturation on the parent plant, prevents immediate germination post-dispersal, regardless of external conditions. Secondary dormancy, however, is triggered post-dispersal when seeds face unfavorable conditions, enabling them to re-enter dormancy even if initially non-dormant. This mechanism allows seeds to fine-tune germination according to environmental conditions. In this study, we examined the role of heat-induced secondary dormancy in local adaptation by analyzing natural variations within 361 Arabidopsis thaliana accessions from across Europe. We discovered that secondary dormancy acquisition varies with primary dormancy levels and after-ripening. Both primary and heat-induced secondary dormancy exhibited adaptive clines along temperature and precipitation gradients, with secondary dormancy showing a steeper cline, indicating its significant role in local adaptation. Using species distribution models, we predicted that genotypes with high secondary dormancy would show greater resilience to future climate changes. Additionally, we identified specific genomic regions controlling secondary dormancy levels, including a novel candidate gene for secondary dormancy variation. Our findings show that secondary dormancy is a complex adaptive mechanism and a predominant contributor to the dormancy trait syndrome that favors plant survival in habitats exposed to harsh summers. Summary statementSecondary dormancy induced by heat exposure allows seed to adjust their germination strategies to the environment. This study shows that heat-induced secondary dormancy in Arabidopsis thaliana depends on levels of primary dormancy. Its covariance with climatic parameter indicates that it can contribute to population resilience to climate change. This study further identifies the specific genetics underlying the ability to induce dormancy after dispersal.

evolutionary biology↗

bioRxiv2022

Local adaptation of life-history traits within urban populations of Arabidopsis thaliana

O_LIThe challenges to which plants are exposed in urban environments represent, in miniature, the challenges plants face as a result of global environmental change. Hence, urban habitats provide a unique opportunity to assess whether processes of local adaptation are taking place despite the short temporal and geographical scales that characterize the Anthropocene. C_LIO_LIWe quantified the ecological diversity of urban habitats hosting A. thaliana populations. Using plant community indicators, we show that these patches differ in their levels of soil nutrient content and disturbance. Accordingly, plants in each patch displayed a range of flowering time, size and fitness. C_LIO_LIUsing a deep sampling approach coupled with reduced genome-sequencing, we demonstrate that most individuals can be assigned to a limited set of clonal lineages; the genetic diversity of these lineages is a sample of the diversity observed in western European populations of the species, indicating that established urban populations originate from a broad regional pool of lineages. C_LIO_LIWe assessed the genetic and phenotypic diversity of these lineages in a set of common garden experiments. We report marked genetic differences in life-history traits, including time of primary and secondary dormancy as well as of flowering. These genetic differences in life-history traits are not randomly distributed but sorted out by ecological differences among sites of origin. C_LIO_LISynthesis: Our study shows that the genetically diverse phenology of a regional A. thaliana gene pool is not randomly distributed but filtered by heterogeneity in the urban environment. To out knowledge, this report is the first to show a pattern indicative of environmental filtering enhancing local genetic adaptation within urban environments. We conclude that environmental filtering helps maintain functional diversity within species. C_LI

evolutionary biology↗

bioRxiv2021

Pharmacologic analysis of non-synonymous coding 5-HT2A SNPs reveals alterations psychedelic drug potencies and efficacies

Serotonin (5-Hydroxytryptamine; 5-HT) 2A receptor (5-HT2AR) signaling is essential for the actions of classical psychedelic drugs. In this study, we examined whether random sequence variations in the gene (single nucleotide polymorphisms, SNPs) encoding the 5-HT2AR affect the signaling of four commonly used psychedelic drugs. We examined the in vitro pharmacology of seven non-synonymous SNPs, which give rise to S12N, T25N, D48N, I197V, A230T, A447V, and H452Y variant 5-HT2A serotonin receptors. We found that these non-synonymous SNPs exert statistically significant, although modest, effects on the efficacy and potency of four therapeutically relevant hallucinogens. Significantly, the in vitro pharmacological effects of the SNPs drug actions at 5-HT2AR are drug specific. Table of Contents/Abstract Graphic O_FIG O_LINKSMALLFIG WIDTH=188 HEIGHT=200 SRC="FIGDIR/small/472000v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@1c1f430org.highwire.dtl.DTLVardef@86b7b6org.highwire.dtl.DTLVardef@871633org.highwire.dtl.DTLVardef@c2ae24_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2018

Arabidopsis species deploy distinct strategies to cope with drought stress

O_LIBackground and Aims Water limitation is an important determinant of the distribution, abundance and diversity of plant species. Yet, little is known about how the response to limiting water supply changes among closely related plant species with distinct ecological preferences. Comparison of the model annual species A. thaliana to its close perennial relatives A. lyrata and A. halleri, can help disentangle the molecular and physiological changes contributing to tolerance and avoidance mechanisms, because these species must maintain tolerance and avoidance mechanisms to increase long-term survival, but they are exposed to different levels of water stress and competition in their natural habitat.\nC_LIO_LIMethods We conducted a dry-down experiment that mimics a period of missing precipitation. We quantified the covariation of progressive decrease in soil water content (SWC) with various physiological and morphological plant traits across a set of representative genotypes in Arabidopsis thaliana, A. lyrata and A. halleri. To quantify the degree of plant stress, transcriptome changes were also monitored.\nC_LIO_LIKey Results The analysis of trait co-variation demonstrates that the three species differ in the strategies they deploy to respond to drought stress. A. thaliana showed drought avoidance reaction but failed to survive wilting. A. lyrata efficiently combined avoidance and tolerance mechanisms. By contrast, A. halleri showed some degree of tolerance to wilting but it did not seem to protect itself from the stress imposed by drought. Transcriptome data collected just before plant wilting and after recovery corroborated the phenotypic analysis, with A. lyrata and A. halleri showing a stronger activation of recovery- and stress-related genes, respectively.\nC_LIO_LIConclusions We conclude that these three Arabidopsis species have evolved distinct strategies to face drought stress, and discuss the extent to which these strategic differences reflect their respective ecological priorities.\nC_LI

plant biology↗

bioRxiv2018

Robustness of Transposable Element regulation but no genomic shock observed in interspecific Arabidopsis hybrids

The merging of two divergent genomes in a hybrid is believed to trigger a \"genomic shock\", disrupting gene regulation and transposable element (TE) silencing. Here, we tested this expectation by comparing the pattern of expression of transposable elements in their native and hybrid genomic context. For this, we sequenced the transcriptome of the Arabidopsis thaliana genotype Col-0, the A. lyrata genotype MN47 and their F1 hybrid. Contrary to expectations, we observe that the level of TE expression in the hybrid is strongly correlated to levels in the parental species. We detect that at most 1.1% of expressed transposable elements belonging to two specific subfamilies change their expression level upon hybridization. Most of these changes, however, are of small magnitude. We observe that the few hybrid-specific modifications in TE expression are more likely to occur when TE insertions are close to genes. In addition, changes in epigenetic histone marks H3K9me2 and H3K27me3 following hybridization do not coincide with TEs with changed expression. Finally, we further examined TE expression in parents and hybrids exposed to severe dehydration stress. Despite the major reorganization of gene and TE expression by stress, we observe that hybridization does not lead to increased disorganization of TE expression in the hybrid. We conclude that TE expression is globally robust to hybridization and that the term \"genomic shock\" is no longerappropriate to describe the anticipated consequences of merging divergent genomes in a hybrid.

genomics↗

bioRxiv2017

Super-Resolution Ultrasound Bubble Tracking for Preclinical and Clinical Multiparametric Tumor Characterization

Super-resolution imaging methods promote tissue characterization beyond the spatial resolution limits of the devices and bridge the gap between histopathological analysis and non-invasive imaging. Here, we introduce Ultrasound Bubble Tracking (UBT) as an easily applicable and robust new tool to morphologically and functionally characterize fine vascular networks in tumors at super-resolution. In tumor-bearing mice and for the first time in patients, we demonstrate that within less than one minute scan time UBT can be realized using conventional preclinical and clinical ultrasound devices. In this context, next to highly detailed images of tumor microvascularization and the reliable quantification of relative blood volume and perfusion, UBT provides access to multiple new functional and morphological parameters that showed superior performance in discriminating tumors with different vascular phenotypes. Furthermore, our initial clinical results indicate that UBT is a highly translational technology with strong potential for the multiparametric characterization of tumors and the assessment of therapy response.

cancer biology↗

bioRxiv2017

Signature Of Co-Evolution Between Defense And Vegetative Lifespan Strategies In Arabidopsis thaliana

The selective impact of pathogen epidemics on host defenses can be strong but remains transient. By contrast, life-history shifts can durably and continuously modify the balance between costs and benefits of immunity, which arbitrates the evolution of host defenses. Their impact on the evolutionary dynamics of host immunity, however, has seldom been documented. Optimal investment into immunity is expected to decrease with shortening lifespan, because a shorter life decreases the probability to encounter pathogens or enemies. Here, we document that in natural populations of Arabidopsis thaliana, the expression levels of immunity genes correlate positively with flowering time, which in annual species is a proxy for lifespan. Using a novel genetic strategy based on bulk-segregants, we partitioned flowering time-dependent from - independent immunity genes and could demonstrate that this positive co-variation can be genetically separated. It is therefore not explained by the pleiotropic action of some major regulatory genes controlling both immunity and lifespan. Moreover, we find that immunity genes containing variants reported to impact fitness in natural field conditions are among the genes whose expression co-varies most strongly with flowering time. Taken together, these analyses reveal that natural selection has likely assorted alleles promoting lower expression of immunity genes with alleles that decrease the duration of vegetative lifespan in A. thaliana and vice versa. This is the first study documenting a pattern of variation consistent with the impact that selection on flowering time is predicted to have on diversity in host immunity.

evolutionary biology↗