Biology subjects

Arnold, P. A.

Publications and source records attributed to Arnold, P. A..

11 recordsLinked to original sources

bioRxiv2026

User-friendly software for high-throughput processing of chlorophyll fluorescence images to assess plant stress responses: fvfmPy and fvfmR packages

Chlorophyll fluorescence imaging is a powerful tool used to characterize abiotic and biotic stress response of photosynthesis in plants. However, extracting metrics such as Fv/Fm (maximum quantum yield of photosystem II) from chlorophyll fluorescence images remains a substantial bottleneck in large measurement campaigns, often requiring significant manual effort. To resolve this issue, we developed fvfmPy, a user-friendly program which enables rapid analysis of chlorophyll fluorescence images of arrays of leaf discs. fvfmPy uses algorithmic image segmentation to identify regions of interest and extract fluorescence metrics from tens or hundreds of leaf samples per image with little to no manual input. fvfmPy is developed in Python and includes a graphical user interface enabling intuitive parameter adjustment and real-time quality control checking. We additionally developed fvfmR, an R wrapper package for fvfmPy. Fv/Fm values extracted with fvfmPy were indistinguishable from those obtained using manual methods (r2 > 0.99) but required 94% less time to complete (13 s vs. 200 s per 100 measurements). fvfmPy and fvfmR were built to directly integrate with existing fluorescence software packages and can greatly increase throughput of fluorescence measurements to help address key challenges in agriculture and ecology.

plant biology↗

bioRxiv2026

A flexible modelling framework for estimating thermal tolerance and sensitivity

Extreme heat events are becoming more frequent, intense and prolonged, making it urgent to predict how heat intensity and exposure duration combine to threaten organisms. Thermal death time (TDT) and thermal load sensitivity (TLS) models provide this link, but conventional two-stage analyses often discard uncertainty, mishandle censored or overdispersed data and limit inference. Here, we show how the four-parameter log-logistic model can recover TDT/TLS quantities, including thermal tolerance (CTmax), sensitivity (z), critical temperature (Tcrit), heat injury and survival, from one model. Simulations show the joint model reproduces classical estimates when two-stage assumptions hold and is more reliable when they fail. We introduce these workflows as Bayesian and frequentist R packages. Case studies across plant and animal taxa demonstrate this modelling framework can estimate group contrasts and predict survival from realistic field temperature-time series. This framework provides more robust inference and flexible tools for predicting organismal responses to extreme heat events.

ecology↗

bioRxiv2026

Towards a standard approach to investigating the Thermal Load Sensitivity of photosystem II via chlorophyll fluorescence

Evaluating the drivers of variation in plant thermal tolerance limits requires a clearer understanding of how methodological matters can lead to different tolerance estimates. Chlorophyll fluorometry - to measure the temperature-dependent change in FV/FM - is a well-established approach to derive tolerance thresholds of photosystem II (PSII) in plants, but one-off, time-specific thermal exposures do not consider the fundamental dose-dependent effect of heat. The resurgent thermal death time (TDT) approach integrates both the temperature intensity and the exposure duration to derive time-based critical temperature thresholds and sensitivity parameters. We build upon this foundation to develop a protocol for evaluating thermal load sensitivity (TLS; non-lethal heat stress) of PSII in plants. Through five experiments across four diverse species, we tested the moderating effects of light, leaf sectioning, time since collection, and the temporal dynamics of FV/FM recovery. There were dramatic changes in tolerance threshold estimates based on thermal load (i.e. dose-dependent) effects on FV/FM, and strong effects of light intensity during heat and the presence of light post-heat. We offer recommendations pertaining to method implementation and discuss future empirical avenues. Appraising cumulative heat stress will enhance the utility of thermal tolerance estimates - the TLS approach outlined here moves us toward a new standard.

ecology↗

bioRxiv2026

Extreme Heat as the New Normal: A Methodological Roadmap for Behavior, Physiology, and Species Distributions

A defining feature of climate change is the increasing frequency, intensity, and severity of extreme weather events. Among them, extreme heat is recognized as a critical driver of ecological and evolutionary change. Intense heat episodes can exceed physiological limits, alter animal movement, restructure geographic ranges, and increase extinction risk more than gradual changes to mean temperatures. Yet links between extreme heat events and organismal biology remain limited, in part because definitions and metrics are not standardized, and user-friendly workflows and guides are lacking for many biologists. We present a methodological roadmap, with reproducible code, for integrating extreme heat into studies of behavior, physiology, biophysical ecology, species distribution models (SDMs), and population dynamics. First, we provide standardized computational approaches to define and quantify extreme heat. Second, we fit species distribution models for California quail (Callipepla californica) that include an extreme heat metric and showcase improved predictions of habitat suitability, particularly at range edges. Third, we compute biophysical simulations to quantify exposure to thermal stress in Sleepy lizards (Tiliqua rugosa) across distinct macro- and microclimates. Finally, accounting for temporal autocorrelation in temperature profiles in population simulation models, we show that clustered heat extremes--missed by averages--can increase the risk of population collapse. As extreme heat events become more common, incorporating their dynamics is essential for understanding ecological and evolutionary change, designing experiments across species geographic ranges, and supporting conservation in a rapidly warming world. Together, these case studies illustrate a reproducible, organism-informed roadmap to integrate extreme heat into predictions of ecological impacts and inference across levels of biological organization under ongoing climate change.

ecology↗

bioRxiv2025

Morphological and heat-tolerance traits are associated with progression and impact of, but not vulnerability to, tree decline

Warming and drying climate trends are driving tree dieback worldwide with broad-reaching impacts on ecosystem services. Studying decline is unavoidably a retrospective exercise in which researchers are challenged to determine whether trait values that are associated with dieback are drivers versus consquences of decline. In this study, we use the subalpine snow gum (Eucalyptus pauciflora, ssp niphophila) as a case study to illustrate how to identify whether plant traits may explain vulnerability of individual trees, assess how progression of dieback symptoms affect traits and physiological tolerance, and ask whether those changes could exacerbate decline. While the impact of drought on tree mortality has been well documented, we consider the potential role of heat which has received considerably less attention. We assessed changes in leaf and stem morphology, and stomatal anatomy across a dieback severity and an abiotic elevation gradient. We also assessed the relationship between these traits, photosystem heat tolerance and dieback progression, using results to model leaf viability under current and future climate scenarios. While severely symptomatic trees exibited trait values indicating water stress, trees with low or moderate dieback were not different from unaffected ones. Thus the differences in severely affected trees are likely responses to water stress caused by woodborer girdling and provide no evidence of underlying trait difference driving vulnerability. Severely symptomatic trees, however, had lower photosystem heat tolerance and models indicated leaves were likely to accumulate lethal damage to photosystems within a growing season, thus contributing to a feedback cycle of decline even under current thermal regimes. HighlightsO_LIAccounting for abiotic, spatial variation explains complex relationships in dieback research C_LIO_LIInsect mediated dieback induces trait variation consistent with water limitation C_LIO_LINo evidence of variation in vulnerability to dieback among snow gum individuals C_LIO_LIDieback-induced reduction in heat tolerance compounds heat load effects C_LIO_LIWarming induced heat loading will compromise carbon gain and exacerbate decline C_LI

ecology↗

bioRxiv2024

High plasticity increases phenotype-environment mismatch leading to sub-optimal performance in underutilized crop species

As climate change threatens agricultural yields, crop diversification, including the reintroduction of underutilized species, has emerged as a proposed solution for resilience. But what determines the extent of environmental change that underutilized crop species can cope with upon their reintroduction? One critical factor is maladaptive plasticity, a theoretical concept suggesting that populations may respond negatively to rapid environmental shifts, at least in the short term. To test this empirically, we conducted a repeated-measures study using historically underutilized Amaranthus species as a model. Upon reintroduction, we observed higher plasticity in vegetative and reproductive traits than in life-history traits. This suggests that while these species adapt to immediate environmental changes through adjustments in growth and reproduction, limited plasticity in life-history traits may constrain long-term adaptation. Our study aimed to (1) identify the environmental factors driving these plastic responses, (2) determine whether these responses are maladaptive, and (3) assess if maladaptive plasticity also occurs within native environments. Using machine learning models, we found that temperature was a primary driver of plastic responses. Generalized Additive Model (GAM) reaction norm analysis further revealed these temperature-induced responses to be maladaptive, suggesting a mismatch between Amaranthus traits and the new environment. Applying transfer learning to predict responses in native settings, we found similar maladaptive responses to temperature, indicating that maladaptive plasticity may not be limited to non-native environments, thereby complicating climate adaptation efforts. This study underscore the need for detailed trait plasticity assessments before crop reintroduction for agricultural resilience.

plant biology↗

bioRxiv2024

Phenotypic plasticity in response to growth temperature far outweighs other environmental and genetic causes of variation in an alpine plant

Phenotypic plasticity and rapid evolution are fundamental processes by which organisms can maintain their function and fitness in the face of environmental changes. Here we quantified the plasticity and evolutionary potential of an alpine herb Wahlenbergia ceracea. Utilising its mixed-mating system, we generated outcrossed and self-pollinated families that were grown in either cool or warm environments, and that had parents that had also been grown in either cool or warm environments. We then analysed the contribution of environmental and genetic factors to variation in a range of phenotypic traits including phenology, leaf mass per area, photosynthetic function, thermal tolerance, and reproductive fitness. The strongest effect was that of current growth temperature, indicating strong phenotypic plasticity. All traits except thermal tolerance were plastic, whereby warm-grown plants flowered earlier, grew larger, produced more reproductive stems compared to cool-grown plants. Flowering onset and biomass were heritable and under selection, with early flowering and larger plants having higher relative fitness. There was little evidence for transgenerational plasticity, maternal effects, or genotype-by-environment interactions. Inbreeding delayed flowering and reduced reproductive fitness and biomass. Overall, we found that W. ceracea has the capacity to respond rapidly to climate warming via plasticity, and the potential for evolutionary change. HighlightWe found strong plasticity to growth environment in many phenotypic traits, but little effect of parental environment, revealing capacity to respond rapidly to climate warming, and potential for evolutionary change.

ecology↗

bioRxiv2023

Drivers of thermal tolerance breadth of plants across contrasting biomes: do mean or seasonality in climate indices matter more?

O_LIThe climate variability hypothesis (CVH) predicts that species from environments with more variable temperatures should have wider thermal tolerance breadth. This hypothesis has not yet been tested thoroughly across diverse plants. Here, we asked how local climate predictors (including precipitation, mean and extreme temperatures and thermal variability) are associated with species physiological thermal limits. C_LIO_LIMeasures of lower (Tcrit-cold) and upper (Tcrit-hot) photosystem II thermal tolerance thresholds were used to determine thermal tolerance breadth (TTB), along with ice nucleation temperature (Tnucleation, freezing tolerance) of 69 plant species sampled from the field across three contrasting biomes: alpine, desert and coastal temperate rainforest. C_LIO_LIAll measured thermal tolerance metrics (Tcrit-cold, Tnucleation, Tcrit-hot and TTB) differed among biomes. Notably, desert species had the most cold and heat tolerant leaves, and therefore the widest TTB, whereas species in alpine and temperate biomes had similar TTB. For plants in all biomes, TTB exceeded the thermal range of their local climate. C_LIO_LIOverall, two Principal Component axes of local climate drivers explained substantial variation in all tolerance metrics. Extreme hot, dry climates improved freezing and heat tolerance. High thermal variability and low minimum temperatures also improved freezing tolerance but were unrelated to heat tolerance or TTB. Species explained a significant amount of variation among all metrics, but this was not due to phylogenetic relatedness. We discuss how the remaining variation could be due to microclimate-driven plasticity, leaf traits or thermoregulatory mechanisms. C_LIO_LISynthesis. Our results provide partial support for the climate variability hypothesis in plants: photosystem thermal tolerance breadth was greatest in more thermally variable biomes. This relationship was largely driven by cold tolerance, with variation in heat tolerance explained better by mean and extreme temperatures. Therefore, we conclude that the CVH alone is not sufficient to explain variation in plant thermal tolerance, with many other aspects of climate, environment and biology being potentially important drivers. C_LI

ecology↗

bioRxiv2023

Transcriptional acclimation to warming temperatures of the Australian alpine herb Wahlenbergia ceracea

Understanding the molecular mechanisms of heat tolerance could help to predict the impacts of climate change on our native flora. However, much of our current understanding is derived from Arabidopsis thaliana and select crops exposed to short and intense periods of heat stress. Here, we characterise the transcriptomic response of Wahlenbergia ceracea, a perennial herb found in Australias subalpine regions, to sustained moderate warming. We contrasted responses between relatively heat-tolerant and heat-sensitive lines grown under cool (24/15 {o}C day/night) or warm (30/20 {o}C) temperatures. We observed that sustained warming up-regulated genes related to RNA regulation, including modification and splicing, and down-regulated genes associated with photosynthesis and plastid organization. Interestingly, heat-tolerant lines demonstrated a more pronounced repression of photosynthesis-associated genes, compared to heat-sensitive lines, suggesting that the regulation of the light-harvesting machinery may contribute to photosystem thermal tolerance. Co-expression analyses revealed only weak module-level correlations with direct measures of thermal tolerance. However, stronger associations were evident with chlorophyll content and photosynthetic efficiency, which might indirectly influence thermal tolerance. Prediction of transcription factors targeting warming-responsive genes implicated hormone signaling networks, especially ethylene, in contributing to differences in thermal tolerance. In conclusion, we present genomic resources for transcriptome analyses in W. ceracea and highlight the contrasting gene regulatory patterns between relatively heat-tolerant and heat-sensitive W. ceracea lines experiencing sustained moderate warming.

plant biology↗

bioRxiv2020

A high-throughput method for measuring critical thermal limits of leaves by chlorophyll imaging fluorescence

Plant thermal tolerance is a crucial research area as the climate warms and extreme weather events become more frequent. Leaves exposed to temperature extremes have inhibited photosynthesis and will accumulate damage to photosystem II (PSII) if tolerance thresholds are exceeded. Temperature-dependent changes in basal chlorophyll fluorescence (T-F0) can be used to identify the critical temperature at which PSII is inhibited. We developed and tested a high-throughput method for measuring the critical temperatures for PSII at low (CTMIN) and high (CTMAX) temperatures using a Maxi-Imaging fluorimeter and a thermoelectric Peltier plate heating/cooling system. We examined how experimental conditions: wet vs dry surfaces for leaves and heating/cooling rate, affect CTMIN and CTMAX across four species. CTMAX estimates were not different whether measured on wet or dry surfaces, but leaves were apparently less cold tolerant when on wet surfaces. Heating/cooling rate had a strong effect on both CTMAX and CTMIN that was species-specific. We discuss potential mechanisms for these results and recommend settings for researchers to use when measuring T-F0. The approach that we demonstrated here allows the high-throughput measurement of a valuable ecophysiological parameter that estimates the critical temperature thresholds of leaf photosynthetic performance in response to thermal extremes.

plant biology↗

bioRxiv2018

Wolbachia-infected Drosophila prefer cooler temperatures

O_LITemperature plays a fundamental role in the dynamics of host-pathogen interactions.\nC_LIO_LIWolbachia is an endosymbiotic bacteria that infects about 40% of arthropod species, which can affect host behaviour and reproduction. Yet, the effect of Wolbachia on host thermoregulatory behaviour is largely unknown, despite its use in disease vector control programs in thermally variable environments.\nC_LIO_LIHere, we used a thermal gradient to test whether Drosophila melanogaster infected with Wolbachia strain wMelCS exhibit different temperature preferences (Tp) to uninfected flies.\nC_LIO_LIWe found that Wolbachia-infected flies preferred a cooler mean temperature (Tp = 25.06{+/-}0.25{degrees}C) than uninfected flies (Tp = 25.78{+/-}0.24{degrees}C).\nC_LIO_LIThis finding suggests that Wolbachia-infected hosts might seek out cooler microclimates to reduce exposure to and lessen the consequences of high temperatures. This finding has generated hypotheses that will be fruitful in areas of research for exploring the mechanisms by which the change in Tp occurs in this complex and significant host-pathogen-environment interaction.\nC_LI

pathology↗