Biology subjects

Wuest, S. E.

Publications and source records attributed to Wuest, S. E..

7 recordsLinked to original sources

bioRxiv2026

Data leakage and measurement error inflate the apparent predictability of overyielding from plant traits

Predicting plant mixture overyielding from functional traits is central to understanding how biodiversity influences ecosystem functioning. Combining empirical data from a large mixture experiment (764 mixtures) and two trait-measurement experiments containing 90 soybean genotypes, with complementary simulations where trait-function relationships and noise levels were defined a priori, we show that apparent model performance depends critically on how predictive models are validated. When training and testing data share genotypes, predictive ability is strongly inflated because shared monoculture and trait measurements create data leakage. Measurement errors further propagate through these shared components, inducing spurious correlations and amplifying noise. When validation uses completely independent genotypes, the predictive power of both linear and machine-learning models declines sharply, revealing limited but genuine predictability. These results show how data structure and measurement error can produce misleading model performance and underscore the need for rigorous validation to achieve robust ecological prediction.

ecology↗

bioRxiv2025

Shade avoidance restricts soybean breeding progress and increases herbivore susceptibility

High planting densities expose field crops to competition for light, which typically induces shade avoidance responses such as stem elongation. While adaptive in natural environments, these responses can lower yield and increase susceptibility to stress in agricultural systems. We tested whether soybean breeding over the past century has altered shade avoidance and associated trade-offs. Twenty-one Canadian cultivars released between 1922 and 2018 were grown in pots under either control or shade-avoidance-inducing light conditions, achieved by altering reflected light spectrum without reducing photosynthetic radiation. Plants exposed to shade-avoidance inducing light grew taller and suffered greater thrips damage, consistent with expectations of increased stem elongation and reduced defense. More recent cultivars showed higher susceptibility to thrips than older ones. Breeding progress in seed yield was driven largely by greater biomass allocation to seeds and a reduction in branching. However, under shade-inducing light, the yield improvements were smaller, pointing to shade avoidance as a limiting factor. Our results indicate that while soybean breeding has improved yield and shifted morphology towards ideotypes suited for high-density stands, persistent shade avoidance responses constrain breeding progress and increase herbivore susceptibility. Breeding strategies that reduce sensitivity to neighbor cues may therefore improve soybean productivity and resilience.

plant biology↗

bioRxiv2025

Belowground competition increases root allocation in agreement with game-theoretical predictions, but only when plants simultaneously compete aboveground.

Competition among plants can lead to allocation strategies that favor individual competitiveness at the expense of group-level productivity. However, the role of root and shoot responses in driving these outcomes is intensely debated. Experimental approaches often have difficulty disentangling above- and belowground interactions due to the confounding effects of pot size and nutrient distribution. Here, we used physical dividers and varied inter-plant distances (3-24 cm) in soybean to isolate competitive interactions while controlling for these confounding effects. Simultaneous above- and belowground competition increased relative root allocation, but reduced total biomass. Aboveground competition alone had stronger effects, triggering shade avoidance and reducing both shoot and root biomass. This likely overrode belowground cues. These results underscore the significance of neighbor-induced responses, particularly under full competition, as pivotal drivers of allocation patterns and promising targets for breeding strategies that enhance collective crop performance.

ecology↗

bioRxiv2025

Weak evidence for heritable changes in response to selection by aphids in Arabidopsis accessions

In plants, transgenerational inheritance of certain epialleles has been observed but experimental evidence for selection of epigenetic variation independent of genetic variation is scarce. We extended an experiment simulating selection in response to herbivory in Arabidopsis thaliana to assess a potential contribution of epigenetic variation to the selected phenotypes within three accessions. To minimize maternal effects, we grew offspring from replicate populations and their ancestors for two generations in a common environment and assessed the phenotypes in the second generation. We found weak evidence for the selection of epigenetic variation: bolting time differed significantly in one accession. Significant differences between maternal lines suggested random residual or novel genetic and/or epigenetic variation. Our results are in conflict with those of a recent study reporting that environment-induced heritable variation is common in Arabidopsis. Reanalyzing the data from that study showed that the reported findings resulted from a mix-up of accessions and, thus, reflected genetic rather than epigenetic variation between accessions. To avoid future misinterpretations of studies investigating epigenetic inheritance, we provide guidelines to design experiments that clearly differentiate between epigenetic and genetic variation and distinguish standing variation from de novo variation acquired during an experiment.

evolutionary biology↗

bioRxiv2022

Single-gene resolution of diversity-driven community overyielding

In plant communities, diversity often increases community productivity and functioning, but the specific underlying drivers are difficult to identify. Most ecological theories attribute the positive diversity effects to complementary niches occupied by different species or genotypes. However, the type of niche complementarity often remains unclear, including how complementarity is expressed in terms of trait differences between plants. Here, we use a gene-centred approach to identify differences associated with positive diversity effects in mixtures of natural Arabidopsis thaliana genotypes. Using two orthogonal genetic mapping approaches, we found that between-plant allelic differences at the AtSUC8 locus contribute strongly to mixture overyielding. The corresponding gene encodes a proton-sucrose symporter and is expressed in root tissues. Genetic variation in AtSUC8 affected the biochemical activities of protein variants and resulted in different sensitivities of root growth to changes in substrate pH. We thus speculate that - in the particular case studied here - evolutionary divergence along an edaphic gradient resulted in the niche complementarity between genotypes that now drives overyielding in mixtures. Identifying such genes important for ecosystem functioning may ultimately allow the linking of ecological processes to evolutionary drivers, help to identify the traits underlying positive diversity effects, and facilitate the development of high-performing crop variety mixtures in agriculture.

plant biology↗

bioRxiv2019

Increasing plant group productivity through latent genetic variation for cooperation

Historic yield advances in the major crops have to a large part been achieved by selection for improved productivity of groups of plant individuals such as high-density stands. Research suggests that such improved group productivity depends on "cooperative" traits (e.g. erect leaves, short stems) that - while beneficial to the group - decrease individual fitness under competition. This poses a problem for some traditional breeding approaches, especially when selection occurs at the level of individuals, because "selfish" traits will be selected for and reduce yields in high-density monocultures. One approach therefore has been to select individuals based on ideotypes with traits expected to promote group productivity. However, this approach is limited to architectural and physiological traits whose effects on growth and competition are relatively easy to anticipate. Here, we developed a general and simple method for the discovery of alleles promoting cooperation in plant stands. Our method is based on the game-theoretical premise that alleles increasing cooperation incur a cost to the individual but benefit the monoculture group. Testing the approach using the model plant Arabidopsis thaliana, we found a major effect locus where the rarer allele was associated with increased cooperation and productivity in high-density stands. The allele likely affects a pleiotropic gene, since we find that it is also associated with reduced root competition but higher resistance against disease. Thus, even though cooperation is considered evolutionarily unstable, conflicting selective forces acting on a pleiotropic gene might maintain latent genetic variation for it in nature. Such variation, once identified in a crop, could be rapidly leveraged in modern breeding programs and provide efficient routes to increase yields.

plant biology↗

bioRxiv2018

A plant biodiversity effect resolved to a single locus

Despite extensive evidence that biodiversity promotes plant community productivity, progress towards understanding the mechanistic basis of this effect remains slow, impeding the development of predictive ecological theory and agricultural applications. Here, we analysed non-additive interactions between genetically divergent Arabidopsis accessions in experimental plant communities. By combining methods from ecology and genetics, we identified a major effect locus at which allelic differences between individuals increases above-ground productivity of communities. In experiments with near-isogenic lines, we show that this diversity effect acts independently of other genomic regions and can be resolved to a single region representing less than 0.3% of the genome. Using plant-soil-feedback experiments, we also demonstrate that allelic diversity causes genotype-specific soil legacy responses in a consecutive growing period, even after the original community has disappeared. Our work thus suggests that positive diversity effects can be linked to single Mendelian factors, and that a range of complex community properties can have a simple cause. This may pave the way to a better understanding of diversity effects, and to novel breeding strategies, focussing on phenotypic properties that manifest themselves beyond isolated individuals, i.e. at a higher level of biological organisation.

ecology↗