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Confidence and competence in skills pertaining to data manipulation, analysis, interpretation, and presentation are increasingly sort and valued across numerous sectors but improving these competencies in students can be challenging. There is a disconnect between the steps taken to understand and analyse data and then present findings in a professional setting and students frequently struggle with this. In response to this, I have created fresh resources, introduced new teaching tools, modified assessment strategy and reinforced key concepts in data literacy across the curriculum with an aim of improving student engagement and attainment in the data sciences. This process, as with many advances in improving pedagogical practice, has largely been ad hoc and evidence for initial success and impact began as observational and qualitative. However, long-term cohort wide data sets can come into effect with consistent use of assessment and marking strategy. Here, I show how different evidence can be used to measure impact of pedagogical practice to students and then how this evidence can be applied to guide course curriculums, and more broadly, influence best practice beyond the institution.

SEB Conference Prague 2024

Scholarship in data literacy; establishing evidence of pedagogical efficacy and measuring impact and influence within and beyond the institution.

reinforcing skills

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SEB’s Annual Conference is celebrated for creating the perfect composition of research, new discoveries and collaborative connections. Be creative and innovative by exchanging ideas and knowledge with masters of biology from all over the world.

Coastal and estuary ecosystems are increasingly subjected to compound events, where multiple extreme events such as marine heatwaves (MHW) and hypoxia occur simultaneously. Given the fundamental role of temperature and oxygen in biological processes, the combined alteration of these parameters is often expected to have non-linear effects on organisms. However, the potential for an extreme temperature event to elicit a different response than gradual warming when combined with hypoxia remains understudied. Therefore, we examined the within-generational response to simultaneous hypoxia and MHW, and the transgenerational plastic responses during the recovery phase of the foundational marine copepod species, Acartia tonsa. In more detail, we measured survival, egg production rates, metabolic rates and upper thermal limits on mature males and females (F1) following a five-day exposure to the isolated and combined effects of hypoxia and a MHW, and on their offspring (F2) placed back in a control condition for their whole development, once they reached adulthood. Surprisingly, we observed only synergistic effects for F1 males’ upper thermal limits and no strong carry-over effects in the recovering F2 coming from the parental combined condition. However, MHW had a dominant effect on the physiology of A. tonsa, decreasing survival, increasing metabolic rates and causing strong carry-over effects on F2 individuals’ survival. These results indicate that potential cross-protection mechanisms between the two stressors were at play, enabling copepods to face the deletarious effects of MHW when exposed simultaneously to hypoxia. This supports the importance of looking at the impact of compound events on marine organisms.

Two extreme events are better than one? Physiological responses following simultaneous exposure to hypoxia and marine heatwave in Acartia tonsa 

The physiological response to thermal fluctuations has been a subject of investigation for decades. These studies have been fundamental in unraveling the underlying mechanisms that allow organisms to cope with temperature variations. However, when attempting to generalize organism responses to environmental changes in natural settings, we confront the inconvenient truth: the natural environment is inherently complex, characterized by diverse and variable stressors. To address this complexity, a transition from a single stressor approach to a multiple stressor scenario becomes essential. We must explore how different thermal fluctuations interact with co-variability in other environmental factors, shaping the phenotypic responses of wild organisms. While recent research has focused on predictable co-variation between stressors (e.g., heat and hypoxia), the effects of simultaneous exposure to emerging and human-driven environmental changes—such as heatwaves and toxicant releases—remain unclear. In this context, I present two case studies examining the phenotypic plasticity of thermal tolerance in adult and offspring generations of two fish species. Specifically, we investigate their responses to environmentally relevant concentrations of copper, a widely used and released metal, both independently and in conjunction with a heatwave event. Contrary to our initial hypothesis, the data revealed unexpected results: thermal plasticity was not negatively affected by copper exposure, to some extent. Instead, we observed a potential cross-tolerance effect. This suggests that exposure to one stressor may enhance an organism’s ability to cope with a second stressor. These findings offer new perspectives and inform future research directions.

One is not enough: the importance of multiple-stressor scenarios in thermal plasticity studies

The ability to perform sit-to-stand (STS) behaviours is fundamental for humans and other animals, yet the underlying high-level control goal driving the selection of a specific movement pattern for the STS transition remains elusive. Exploring the STS transition in non-human animals, particularly birds, offers an opportunity to deepen this understanding and allows for an independent assessment of how body sizes influence performance criteria. Computational biomechanical modelling and simulation, combined with optimal control methods, provide a rigorous and mechanistic approach to address these questions, offering insights that experimental limitations may hinder. Drawing inspiration from human studies, we systematically evaluate STS performance criteria (e.g., minimisation of effort and the muscle force rate) and examine how these criteria vary with body sizes, using a simplified two-link model to simulate vertical movements. We use this simplified simulation to inform fully predictive, three-dimensional, muscle-driven simulations of the STS transition in the emu (Dromaius novaehollandiae), a large bipedal bird. This study, focusing on emus, provides insights into avian species’ control strategies during the STS transition, with future investigations extending to simulate this transition in other bird species, contributing not only to our understanding of organismal morphofunctional specialisation but also to applications in robotics, prosthetics, and animal welfare, as well as aiding in the reconstruction of locomotion in extinct species.

Predictive simulations of musculoskeletal function and sit-to-stand performance in a large bipedal bird - the emu (Dromaius novaehollandiae)

Chromosomal fusions have been hypothesized to facilitate evolutionary adaptation, but empirical evidence has been scarce. We examined patterns of genome evolution in the copepod Eurytemora affinis species complex, which are numerically dominant and highly invasive, with the extraordinary capacity to rapidly invade novel salinities. Prior studies from my laboratory (Lee Lab) revealed parallel selection acting on the same sets of ion transporter genes during independent saline to freshwater invasions by populations from genetically distinct clades. Our chromosome-level genomes of three genetically divergent clades of this species complex revealed peculiar genome architectures that might contribute to their remarkable capacity to acclimate and evolve during salinity invasions. Among the three genetically distinct clades of E. affinis complex, we discovered independent chromosomal fusions in two different clades, with the Europe clade (E. affinis proper) having 15 chromosomes, fusing independently into 7 chromosomes in the Gulf clade (E. gulfia) and 4 chromosomes in the Atlantic clade (E. carolleeae). Notably, for the highly invasive Atlantic clade (E. carolleeae), chromosomal fusion sites, especially the centromeres, were significantly enriched with signatures of selection associated with contemporary shifts from saline to freshwater habitats. These chromosomal fusions joined functionally-related ion transporter genes, forming "supergenes" at the centromeres, where recombination is low. This study uncovers novel patterns of genome architecture evolution with potentially important implications for mechanisms of adaptive evolution in response to radical environmental change.

Genome Architecture Evolution in the copepod Eurytemora affinis species complex

Large-scale comparative genomics studies offer valuable resources for understanding both functional and evolutionary rate constraints. It is suggested that constraint aligns with the topology of genomic protein-protein interaction (PPI) networks, increasing toward the center, with intermediate nodes combining relaxed constraint with higher contributions to the phenotype due to pleiotropy. However, this pattern has yet to be demonstrated in vertebrates. Here I show that constraint intensifies toward the network's center in both yeast and placental mammals. Genes with rate changes associated with emergence of mammalian hibernation cluster mostly toward intermediate positions, with higher constraint in faster-evolving genes, which is indicative of a “sweet spot” for adaptation. Network node metrics could therefore predict genomic regions favored for adaptation even in clades lacking empirical constraint data. To explore this idea, I used lacertid lizards as example for such group of species without empirical constraint data, and show that genes with signatures of selection in response to a latitudinal environmental gradient likewise cluster in more intermediate positions, which is even more pronounced in genes which have been re-used for this purpose independently multiple times across vertebrates. These particular genes further reveal a strong correlation between evolutionary rate and preference for cooler environments, affirming prior results that the diversification of lacertid lizards is predominantly driven by adaptation to cooler climates. In conclusion, genome architecture offers important clues about the co-evolution of protein-coding genes that respond to environmental stimuli, thereby enhancing our comprehension of the resilience and adaptability of organisms in the face of climate change.


Linking network topology, evolutionary constraint, and abiotic environmental adaptation

In ecological communities, body mass and species abundance create size spectra that reflect metabolic demands varying with size. These patterns are generally predictable; however, how temperature and predation alter these predictions at the community level has not been extensively explored. In this study, we recreated 24 stream ecosystems in mesocosms to test the effects of two temperatures (ambient and elevated) and two predation scenarios. After 30 days, we analyzed macroinvertebrate samples for changes in the ontogenetic scaling of their resting metabolic rates. Our study investigates the impact of temperature on the ontogenetic scaling of resting metabolic rate in freshwater macroinvertebrate communities, particularly in relation to predation regimes. We observe that rising temperatures cause a decrease in the metabolic scaling exponent in environments with predation pressure (e.g., from approximately 0.3 to 0.5, instead of the predicted 0.75 by metabolic scaling theory), resulting in steeper size spectra (e.g., from approximately -1.2 to -1.5, instead of the predicted -2 by metabolic scaling theory). These findings highlight the complex interplay between abiotic and biotic factors in shaping energy dynamics and community structure, underscoring the need to integrate individual energetics into size-based community models. This underscores the interactive influence of temperature and predation on ecophysiological processes, potentially altering the slope of size spectra and affecting energy exchange equilibrium within ecological communities. Our work paves the way for further investigation into the ecological consequences of metabolic scaling deviations in the context of global environmental changes.

Temperature and predation affect metabolic scaling: Do individual metabolic constraints shape community size spectra?

Fishes are fantastically plastic creatures, capable of altering their morphology, physiology, life-history, and even offspring responses to changes in the environment. A key question in freshwater ecology is how fishes will respond through plasticity to continued changes in climate - especially to predicted increases in the variability of temperature. Here, we describe lessons learned from long-term, multi-generational experiments examining thermal variability's plastic effects in a model organism, zebrafish (Danio rerio). We found that long-term exposure to thermal variability confers relative benefits in a number of fitness-related traits, but these benefits were not without costs. We highlight the advantages of using thermally variable regimes in experiments and discuss important knowledge gaps that remain in the study of thermal variability and plasticity.

Plasticity to thermal variability within and across generations

Core body temperature (Tc) is increasingly used as a biomarker of the fitness of an animal to its environment. Periodogram and cosinor analysis can be used to estimate the characteristics of the circadian rhythm of Tc. The sampling interval can be manipulated to maximise the recording period of loggers, but the impact of interval on the output of periodogram or cosinor analysis is unknown. Basic guidelines are available from signal analysis theory, but have never been tested on Tc data. We obtained data at 1-, 5-, or 10-minute intervals from nine avian or mammalian species, and re-sampled those data to simulate logging at up to 240-minute interval. The period of the rhythm was first analysed using the Lomb-Scargle periodogram, and the mesor, amplitude, acrophase, and adjusted coefficient of determination (R2) from the original and the re-sampled data were obtained using cosinor analysis. Sampling intervals longer than 60 minutes did not affect the average mesor, amplitude, acrophase, or adjusted R2, but did impact the period of the rhythm. In most species, the period was not detectable when intervals longer than 120 minutes were used. In all individual profiles, a 30-minute sampling interval modified the values of the mesor and amplitude by less than 0.1°C, and the adjusted R2 by less than 0.1. At a 30-minute interval, the acrophase was accurate to within 15 minutes for all species except mice. In most cases, a 30-minute sampling interval provides a reliable balance between parameter accuracy and logger longevity.

Optimal sampling interval for characterisation of the circadian rhythm of body temperature in homeothermic animals using periodogram and cosinor analysis

In West Africa, cereals production per capita is declining due to the fast growth in population outpacing the increase in food production. Moreover, models predict that global changes will reduce cereals yield in this region. Improve crop productivity and resilience is therefore a major challenge. Pearl millet is a key cereal for food security in sub-Saharan Africa, mostly grown in areas with limited agronomic potential characterized by low rainfall and low-fertility soils. 
Root traits represent potential new targets for breeding pearl millet varieties more adapted to future climate scenarios. The aim of this work was to characterize the main water stress pattern faced by pearl millet in West Africa and to identify root traits that contribute to tolerance to this stress. 
Crop modelling revealed that vegetative drought stress is a major constraint in the Sahel. Subsequently, a panel of 160 newly re-sequenced inbred lines was grown under irrigated and vegetative drought stress over two years in field conditions in Senegal and was phenotyped for root anatomical traits, as well as yield components traits. We observed a large diversity of response to drought stress for root traits and yield stress tolerance indexes. We found that some root vasculature traits were associated with tolerance to vegetative drought stress. Further physiological studies suggest a link between metaxylem traits and transpiration efficiency and suggest an overall strategy to deal with vegetative stress. QTLs controlling these traits were identified by association genetics. Our results could provide new avenues to improve drought tolerance in pearl millet.


Targeting root traits to improve tolerance to vegetative drought episodes in pearl millet (Pennisetum glaucum L.) 

Reproductive senescence is increasingly reported to occur in vertebrate populations in the wild but how the onset and rate of reproductive senescence vary in response to environmental fluctuations remains poorly understood. Taking benefit on a long-term detailed individual monitoring of reproductive performance of known-aged females for over 35 years in a forest roe deer population in western France, we first provide firm evidence that both pregnancy rates and litter size display senescence, with different age at onset and different rate of senescence. Then, we show that cohort quality markedly influences reproductive senescence patterns. Moreover, condition-dependence of reproductive performance differs both across female ages and among cohorts of different quality.

Scholarship in data literacy; establishing evidence of pedagogical efficacy and measuring impact and influence within and beyond the institution.

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Two extreme events are better than one? Physiological responses following simultaneous exposure to hypoxia and marine heatwave in Acartia tonsa

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Scholarship in data literacy; establishing evidence of pedagogical efficacy and measuring impact and influence within and beyond the institution.

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Next from SEB Conference Prague 2024

Two extreme events are better than one? Physiological responses following simultaneous exposure to hypoxia and marine heatwave in Acartia tonsa

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