Biology subjects

Agren, J.

Publications and source records attributed to Agren, J..

10 recordsLinked to original sources

bioRxiv2026

Fungal community composition links rhizosphere microbiome organization to plant phenotype in response to moderate warming

BackgroundGlobal warming increasingly challenges plant performance and ecosystem function, and plant responses to elevated temperature are shaped not only by intrinsic plasticity, but also by interactions with rhizosphere microbial communities. However, it remains unclear how warming-induced microbiome reorganization relates to plant performance, whether microbiome community composition predicts plant phenotypic responses to elevated temperature better than simple host-microbiome origin matching, and which bacterial or fungal community features contribute most strongly to this prediction. ResultsWe implemented a full factorial design manipulating plant genotype (P), microbial inoculum (M), and temperature (T) using natural Arabidopsis thaliana ecotypes and their corresponding rhizosphere microbiomes from contrasting climatic regions. By integrating high-throughput plant phenotyping, microbial community profiling, microbiome-phenotype coupling analyses, and predictive modeling, we found that elevated temperature induced a coherent thermomorphogenic shift in plant architecture, while plant phenotypic variation remained determined primarily by genotype over the 14-day vegetative growth period covered in this study. Overall, cold-origin genotypes showed larger temperature-induced trait shifts than warm-origin genotypes. Rhizosphere microbial communities were structured predominantly by inoculum origin, but were also affected by warming. Evidence for a increased thermomorphogenic growth when genotypes were combined with inoculum from their home site was limited. Instead, microbiome-phenotype associations were better captured by community composition than by matching status, with fungal community variation showing stronger and more consistent associations with plant phenotype than bacterial variation and providing more robust predictions of plant phenotypes across models. ConclusionsWarming reorganized plant-rhizosphere systems within persistent host- and inoculum-associated baselines. Plant phenotypic variation during vegetative development under elevated temperature was linked more closely to microbiome composition, especially in fungi, than to simple host-microbiome matching of origins. These findings provide a framework for identifying microbiome features associated with plant performance under climate warming.

plant biology↗

bioRxiv2025

A panel of near-isogenic lines derived from locally adapted populations of a wild plant: A powerful tool for dissecting additive and non-additive effects on ecologically important traits

Identifying and estimating the effects of loci contributing to natural variation in ecologically important traits can be hampered by quantitative inheritance, dominance, epistasis, and environmentally dependent trait expression. Here we announce the availability of germplasm and sequence data for a reciprocal panel of near-isogenic lines (NILs) derived from locally adapted natural populations of Arabidopsis thaliana, for investigating the genetic basis of ecologically important traits. We created a panel of 54 NILs and performed whole genome sequencing to precisely locate introgression segments(s) in each NIL. Deep sequencing largely confirmed prior knowledge of NIL genotypes but also identified multiple novel small introgressions and regions of residual heterozygosity. To illustrate the utility of this panel, we identified genomic regions underlying ecotypic differences in flowering time in a laboratory common garden experiment. We detected strong additive effects on flowering time in multiple NILs with segments at the top of chromosome 5 implicating the floral regulator FLC, as expected based on previous quantitative trait locus studies. We also detected novel and complex contributions to ecotypic differences in flowering time, only visible in the NILs, suggesting the possibility of epistasis. Our results highlight the utility of this panel for dissecting the genetic architecture of ecologically important traits, including the future potential for fine mapping of additive effects and testing for epistasis and linkage using NILs derived from the panel. This panel can be used by any member of the research community to investigate any of a broad suite of traits for which the parents differ.

evolutionary biology↗

bioRxiv2025

The role of secondary pollinators in the evolution of complex colour signals in a bimodal pollination system

Flower colour is recognized as a key trait influencing pollinator visitation and behaviour, evolved to match the sensory system of a particular pollinator group. However, some flowers combine colours associated with different pollinators, suggesting bimodal adaptation. The perennial herb Cyrtanthus obliquus produces red corollas with yellow tips and is pollinated by birds, but also by bees. To assess the role of the two pollinator categories in shaping selection on the bi-coloured corollas, we examined bee choices in arrays in which the colour signals of plants had been manipulated, and we quantified total as well as bird-mediated phenotypic selection on flower colour using both bird and bee visual models. Bees preferred flowers with a yellow signal over all-red flowers. The analysis of phenotypic selection indicated that both birds and bees influence net selection on flower colour, resulting in conflicting selection on the colour contrast between corolla and corolla tip. Our findings show that the optimal phenotype should depend on the relative importance of the two categories of pollinators in a given population, and are consistent with bimodal adaptation. This study fills an important gap by showing that secondary pollinators can contribute to selection on complex colour signals in angiosperm flowers.

evolutionary biology↗

bioRxiv2025

Testing a general theory for flowering time shift as a function of growing season length

Understanding the effects of climate change on the evolution of phenological timing, such as start of flowering, is of major interest because phenology is critical for fitness of populations, and underpins many ecological dynamics. Much recent research has focused on the correlation between phenological timing and the arrival of spring. However, the evolutionarily optimal seasonal timing should depend also on the duration of the growing season, within which entire annual life cycles must unfold. Optimal energy allocation theory can explicitly address life-history scheduling in a seasonal environment, and be used to predict how scheduling should adaptively respond to seasonality shifts. Here we extend a seminal theoretical framework for perennial plant scheduling by Iwasa & Cohen (1989), and predict a specific nonlinear relationship between growing season length and optimal flowering time expressed as number of days after the start of the growing season. We tested and found strong support for this a priori prediction in two independent common-garden experiments with purple loosestrife (Lythrum salicaria) and European goldenrod (Solidago virgaurea) populations sampled along latitudinal gradients in Sweden. Climate warming is commonly associated with changes in both the start and the duration of the growing season. Considering both effects, our findings suggest that as springs start earlier and growing seasons lengthen, shifts in optimal flowering time expressed as calendar date may initially stall before accelerating, potentially explaining observed variation in phenological shifts across systems. More broadly, we show how mechanistic life history theory can advance understanding of phenological change beyond correlative conclusions. SIGNIFICANCE STATEMENTThe optimal timing for a plant to flower depends both on when spring begins and on the total length of the growing season--both shifting with climate change. However, the adaptation of flowering time to changes in growing season length is much less explored than to an advancing spring. Building on existing theory, we predict a nonlinear relationship between growing season length and optimal flowering time. Data on two species (purple loosestrife and European goldenrod) grown in common gardens strongly support this prediction. Our results demonstrate why species can vary in their observed phenological responses to climate change. More broadly, we highlight the power of mechanistic life history theory for explaining and predicting phenological shifts.

ecology↗

bioRxiv2025

Museum genomics reveals temporal genetic stasis and global genetic diversity in Arabidopsis thaliana

Global patterns of population genetic variation through time offer a window into evolutionary processes that maintain diversity. Over time, lineages may expand or contract their distribution, causing turnover in population genetic composition. At individual loci, migration, drift, and selection (among other processes) may affect allele frequencies. Museum specimens of widely distributed species offer a unique window into the genetics of understudied populations and changes over time. Here, we sequenced genomes of 130 herbarium specimens and 91 new field collections of Arabidopsis thaliana and combined these with published genomes. We sought a broader view of genomic diversity across the species, and to test if population genomic composition is changing through time. We documented extensive and previously uncharacterized diversity in a range of populations in Africa, populations that are under threat from anthropogenic climate change. Through time, we did not find dramatic changes in genomic composition of populations. Instead, we found a pattern of genetic change every 100 years of the same magnitude seen when comparing Eurasian populations that are 185 km apart, potentially due to a combination of drift and changing selection. We found only mixed signals of polygenic adaptation at phenology and physiology QTL. We did find that genes conserved across eudicots show altered levels of directional allele frequency change, potentially due to variable purifying and background selection. Our study highlights how museum specimens can reveal new dimensions of population diversity and show how wild populations are evolving in recent history.

evolutionary biology↗

bioRxiv2024

Adaptation to soil type contributes little to local adaptation in an Italian and a Swedish population of Arabidopsis thaliana growing on contrasting soils

Natural populations are subject to selection caused by a range of biotic and abiotic factors in their native habitats. Identifying these agents of selection and quantifying their effects is key to understanding how populations adapt to local conditions. We performed a fully factorial reciprocal transplant experiment using locally adapted accessions of Arabidopsis thaliana at their native sites to distinguish the contributions of adaptation to soil type and climate. Overall adaptive differentiation was strong at both sites. However, we found only very small differences in the strength of selection on local and non-local soil, and adaptation to soil type at most constituted only a few percent of overall adaptive differentiation. These results indicate that adaptation to local climatic conditions rather than soil type is the primary driver of adaptive differentiation between these ecotypes.

evolutionary biology↗

bioRxiv2023

A large effect genetic trade-off is caused by a single mutation in CBF2

Identifying the genetic basis of local adaptation and fitness trade-offs across environments is a central goal of evolutionary biology. Cold acclimation is an adaptive plastic response for surviving seasonal freezing, and costs of acclimation may be a general mechanism for fitness trade-offs across environments in temperate zone species. Starting with locally adapted ecotypes of Arabidopsis thaliana from Italy and Sweden, we examined the fitness consequences of a naturally occurring functional polymorphism in CBF2. This gene encodes a transcription factor that is a major regulator of cold-acclimated freezing tolerance, and resides within a locus responsible for a genetic trade-off for long-term mean fitness. We estimated the consequences of alternate genotypes of CBF2 on 5-year mean fitness and fitness components at the native field sites by comparing near isogenic lines with alternate genotypes of CBF2 to their genetic background ecotypes. The effects of CBF2 were validated at the nucleotide level using gene edited lines in the native genetic backgrounds grown in simulated parental environments. The foreign CBF2 genotype in the local genetic background reduced long-term mean fitness in Sweden by more than 10%, primarily via effects on survival. In Italy, fitness was reduced by more than 20%, primarily via effects on fecundity. At both sites, the effects were temporally variable and much stronger in some years. The gene edited lines confirmed that CBF2 encodes the causal variant underlying this genetic trade-off. Additionally, we demonstrated a substantial fitness cost of cold acclimation, which has broad implications for potential maladaptive responses to climate change.

evolutionary biology↗

bioRxiv2022

Positive indirect effects more than balance negative direct effects of ungulate grazers on population growth of a grassland herb

O_LIHerbivores can affect plant population dynamics both directly because of the damage they inflict, and indirectly by moderating conditions for plant recruitment, competition and other biotic interactions. Still, the relative importance of indirect effects of herbivores on plant population dynamics is poorly known. C_LIO_LIWe quantified direct and indirect effects of ungulate grazers on population growth rate of the short-lived perennial herb Primula farinosa, using integral projection models based on demographic data collected over 7 years in exclosures and open control plots at nine grassland sites in southern Sweden. In addition, we explored the mechanisms behind indirect effects with simulations. C_LIO_LIGrazers had negative direct effects on P. farinosa population growth rate, but these were more than balanced by positive indirect effects. The positive indirect effects were mainly linked to improved conditions for plant recruitment. Simulations indicated that indirect effects of ungulate grazers on population growth rate via interactions with pollinators, seed predators, and small herbivores were weak in this system. C_LIO_LISynthesis. The results demonstrate that a full understanding of the effects of grazing on plant population dynamics requires that both direct and indirect effects are identified and quantified. Plant species vary considerably in their response to shifts in grazing regime. Our study sets an example for how the causes of such variation can be assessed, and thus providing a better understanding of the variable effects of herbivores on plant fitness, abundance and distribution. C_LI

ecology↗

bioRxiv2019

Root microbiota assembly and adaptive differentiation among European Arabidopsis populations

Factors that drive continental-scale variation in root microbiota and plant adaptation are poorly understood. We monitored root-associated microbial communities in Arabidopsis thaliana and co-occurring grasses at 17 European sites across three years. Analysis of 5,625 microbial community profiles demonstrated strong geographic structuring of the soil biome, but not of the root microbiota. Remarkable similarity in bacterial community composition in roots of A. thaliana and grasses was explained by the presence of a few diverse and geographically widespread taxa that disproportionately colonize roots across sites. In a reciprocal transplant between two A. thaliana populations in Sweden and Italy, we uncoupled soil from location effects and tested their respective contributions to root microbiota variation and plant adaptation. The composition of the root microbiota was affected by location and soil origin, and to a lesser degree by host genotype. The filamentous eukaryotes were particularly strongly affected by location. Strong local adaptation between the two A. thaliana populations was observed, with difference in soil properties and microbes of little importance for the observed magnitude of adaptive differentiation. Our results suggest that, across large spatial scales, climate is more important than are soil conditions for plant adaptation and variation in root-associated filamentous eukaryotic communities.

microbiology↗

bioRxiv2017

Demography And Mating System Shape The Genome-Wide Impact Of Purifying Selection In Arabis alpina

Plant mating systems have profound effects on levels and structuring of genetic variation, and can affect the impact of natural selection. While theory predicts that intermediate outcrossing rates may allow plants to prevent accumulation of deleterious alleles, few studies have empirically tested this prediction using genomic data. Here, we study the effect of mating system on purifying selection by conducting population genomic analyses on whole-genome resequencing data from 38 European individuals of the arctic-alpine crucifer Arabis alpina. We find that outcrossing and mixed-mating populations maintain genetic diversity at similar levels, whereas highly self-fertilizing Scandinavian A. alpina show a strong reduction in genetic diversity, most likely as a result of a postglacial colonization bottleneck. We further find evidence for accumulation of genetic load in highly self-fertilizing populations, whereas the genome-wide impact of purifying selection does not differ greatly between mixed-mating and outcrossing populations. Our results demonstrate that intermediate levels of outcrossing may allow efficient selection against harmful alleles whereas demographic effects can be important for relaxed purifying selection in highly selfing populations. Thus, both mating system and demography shape the impact of purifying selection on genomic variation in A. alpina. These results are important for an improved understanding of the evolutionary consequences of mating system variation and the maintenance of mixed-mating strategies.\n\nSignificanceIntermediate outcrossing rates are theoretically predicted to maintain effective selection against harmful alleles, but few studies have empirically tested this prediction using genomic data. We used whole-genome resequencing data from alpine rock-cress to study how genetic variation and purifying selection vary with mating system. We find that populations with intermediate outcrossing rates have similar levels of genetic diversity as outcrossing populations, and that purifying selection against harmful alleles is efficient in mixed-mating populations. In contrast, self-fertilizing populations from Scandinavia have strongly reduced genetic diversity, and accumulate harmful mutations, likely as a result of demographic effects of postglacial colonization. Our results suggest that mixed-mating populations can avoid the negative evolutionary consequences of high self-fertilization rates.

evolutionary biology↗