Biology subjects

Kopp, E. B.

Publications and source records attributed to Kopp, E. B..

5 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

Fine-scale variation in pollen availability influences Bombus terrestris colony behaviour, development and fitness.

Climate change threatens the long-established synchronization of seasonal pollinator activity and flowering time. Bumble bees are particularly vulnerable to these shifts, with resource availability playing a significant role in colony establishment and success. Recently, we documented a mechanism whereby pollen-deprived bumble bees deliberately damaged plant leaves, speeding up the production of flowers in two different species. However, it is unknown whether bumble bees obtain a benefit through this behaviour, both on a spatial and temporal scale. In the current study, we evaluate the effects of pollen availability on colony development, behaviour and reproductive fitness in Bombus terrestris using semi-natural and laboratory experiments. We find that the close proximity of flowers has significant effects on reproductive investment and output of B. terrestris colonies in a small-scale rooftop experiment. Moreover, we find that small shifts in the timing of pollen availability (5 days) shape the behaviour and development of the first generation of offspring, with significant carry-over effects on reproductive fitness for B. terrestris microcolonies. This suggests that small changes in the distribution of food may have significant impacts on colony success that cannot be compensated for over the course of the season. Furthermore, our findings suggest bumble bee colonies can feasibly profit by altering the timing of pollen resources, even by a few days.

ecology↗

bioRxiv2024

Control of Inflammatory Response by Tissue Microenvironment

Inflammation is an essential defense response but operates at the cost of normal tissue functions. Whether and how the negative impact of inflammation is monitored remains largely unknown. Acidification of the tissue microenvironment is associated with inflammation. Here we investigated whether macrophages sense tissue acidification to adjust inflammatory responses. We found that acidic pH restructured the inflammatory response of macrophages in a gene-specific manner. We identified mammalian BRD4 as a novel intracellular pH sensor. Acidic pH disrupts the transcription condensates containing BRD4 and MED1, via histidine-enriched intrinsically disordered regions. Crucially, a decrease in macrophage intracellular pH is necessary and sufficient to regulate transcriptional condensates in vitro and in vivo, acting as negative feedback to regulate the inflammatory response. Collectively, these findings uncovered a pH-dependent switch in transcriptional condensates that enables environment-dependent control of inflammation, with a broader implication for calibrating the magnitude and quality of inflammation by the inflammatory cost. HighlightsO_LIAcidic pH regulates a switch-like gene-specific inflammatory response in macrophages C_LIO_LIAcidic pH impacts chromatin remodeling and transcription circuits to control inflammatory programs C_LIO_LIBRD4 transcriptional condensates are regulated by intracellular pH via the histidine-enriched intrinsically disordered region C_LIO_LITissue inflammation decreases intracellular pH and disrupts BRD4 condensates as a negative feedback C_LI

immunology↗