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Journal articleZHOU B, Cai W, Zhu Z, et al., 2025,
A general model for the seasonal to decadal dynamics of leaf area
, Global Change Biology, ISSN: 1354-1013 -
Journal articleChan AHH, Putra P, Schupp H, et al., 2025,
<scp>YOLO</scp>‐Behaviour: A simple, flexible framework to automatically quantify animal behaviours from videos
, Methods in Ecology and Evolution, ISSN: 2041-210X<jats:title>Abstract</jats:title><jats:p><jats:list><jats:list-item><jats:p>Manually coding behaviours from videos is essential to study animal behaviour but it is labour‐intensive and susceptible to inter‐rater bias and reliability issues. Recent developments of computer vision tools enable the automatic quantification of behaviours, supplementing or even replacing manual annotation. However, widespread adoption of these methods is still limited, due to the lack of annotated training datasets and domain‐specific knowledge required to optimize these models for animal research.</jats:p></jats:list-item><jats:list-item><jats:p>Here, we present YOLO‐Behaviour, a flexible framework for identifying visually distinct behaviours from video recordings. The framework is robust, easy to implement, and requires minimal manual annotations as training data. We demonstrate the flexibility of the framework with case studies for event‐wise detection in house sparrow nestling provisioning, Siberian jay feeding, human eating behaviours and frame‐wise detections of various behaviours in pigeons, zebras and giraffes.</jats:p></jats:list-item><jats:list-item><jats:p>Our results show that the framework reliably detects behaviours accurately and retrieve comparable accuracy metrics to manual annotation. However, metrics extracted for event‐wise detection were less correlated with manual annotation, and potential reasons for the discrepancy between manual annotation and automatic detection are discussed. To mitigate this problem, the framework can be used as a hybrid approach of first detecting events using the pipeline and then manually confirming the detections, saving annotation time.</jats:p></jats:list-item><jats:list-item><jats:p>We provide detailed documentation and guidelines on how to implement the YOLO‐Behaviour framework, for researchers to readily train and deploy new mod
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Journal articleRen Y, Wang H, Harrison SP, et al., 2025,
Incorporating the acclimation of photosynthesis and leaf respiration in the Noah-MP land surface model: model development and evaluation
, Journal of Advances in Modeling Earth Systems, ISSN: 1942-2466 -
Journal articleWillis K, Burt A, 2025,
Engineering drive-selection balance for localized population suppression with neutral dynamics.
, Proc Natl Acad Sci U S A, Vol: 122While the release of sterile males has been highly successful in suppressing some pest populations, it is impractical for many species due to the males disappearing after a single generation, necessitating large, repeated releases to maintain sufficient impact. Synthetic gene drives promise more efficient approaches since they can increase in frequency from rare, yet this also allows them to spread across a landscape, which may not always be desired. Between these two extremes are selectively neutral genetic constructs which persist at the frequency they are released, offering the potential for efficient suppression that remains localized. One way to achieve this would be to have perfect balance, at all construct frequencies, between gene drive increasing frequency and selection decreasing it. Here, we describe a way to closely approximate this balance using a toxin-antidote genetic construct that causes recessive lethality or sterility, encodes a genomic editor that makes dominant lethal or sterile edits in the genome, and provides protection against the action or consequences of the editing. Computer modeling shows that this design can be 100-fold more efficient than sterile males, increasing to 1,000-fold when released alongside a genetic booster. We describe designs for CRISPR-based molecular construction, including options that avoid using recoded genes as antidotes.
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Journal articleGould E, Fraser HS, Parker TH, et al., 2025,
Same data, different analysts: variation in effect sizes due to analytical decisions in ecology and evolutionary biology.
, BMC Biol, Vol: 23Although variation in effect sizes and predicted values among studies of similar phenomena is inevitable, such variation far exceeds what might be produced by sampling error alone. One possible explanation for variation among results is differences among researchers in the decisions they make regarding statistical analyses. A growing array of studies has explored this analytical variability in different fields and has found substantial variability among results despite analysts having the same data and research question. Many of these studies have been in the social sciences, but one small "many analyst" study found similar variability in ecology. We expanded the scope of this prior work by implementing a large-scale empirical exploration of the variation in effect sizes and model predictions generated by the analytical decisions of different researchers in ecology and evolutionary biology. We used two unpublished datasets, one from evolutionary ecology (blue tit, Cyanistes caeruleus, to compare sibling number and nestling growth) and one from conservation ecology (Eucalyptus, to compare grass cover and tree seedling recruitment). The project leaders recruited 174 analyst teams, comprising 246 analysts, to investigate the answers to prespecified research questions. Analyses conducted by these teams yielded 141 usable effects (compatible with our meta-analyses and with all necessary information provided) for the blue tit dataset, and 85 usable effects for the Eucalyptus dataset. We found substantial heterogeneity among results for both datasets, although the patterns of variation differed between them. For the blue tit analyses, the average effect was convincingly negative, with less growth for nestlings living with more siblings, but there was near continuous variation in effect size from large negative effects to effects near zero, and even effects crossing the traditional threshold of statistical significance in the opposite direction. In contrast, the a
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Journal articleWoodward G, 2025,
Warming alters plankton body-size distributions in a large field experiment
, Communications Biology, ISSN: 2399-3642The threat of climate change has renewed interest in the responses of communities and ecosystems to warming, with changes insize spectra expected to signify fundamental shifts in the structure and dynamics of these multispecies systems. Whilesubstantial empirical evidence has accumulated in recent years on such changes, we still lack general insights due to a limitedcoverage of warming scenarios that span spatial and temporal scales of relevance to natural systems. We addressed this gap byconducting an extensive freshwater mesocosm experiment across 36 large field mesocosms exposed to intergenerationalwarming treatments of up to +8 °C above ambient levels. We found a nonlinear decrease in the overall mean body size ofzooplankton with warming, with a 57% reduction at +8 °C. This pattern was broadly consistent over two tested seasons andmajor taxonomic groups. We also detected some breakpoints in the community-level size-temperature relationship, indicatingthat the system’s response shifts noticeably above a certain level of warming. These results underscore the need to captureintergenerational responses to large gradients in warming at appropriate scales in time and space in order to better understandthe effects of warming on natural communities and ecosystems.
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Journal articleJiang J, Chen Y, Zhang R, et al., 2025,
New insights on the impact of light, photoperiod and temperature on the reproduction of green algae <i>Ulva prolifera</i> via transcriptomics and physiological analyses
, MARINE POLLUTION BULLETIN, Vol: 211, ISSN: 0025-326X -
Journal articlePang B, Cheng S, Huang Y, et al., 2025,
Fire-Image-DenseNet (FIDN) for predicting wildfire burnt area using remote sensing data
, Computers and Geosciences, Vol: 195, ISSN: 0098-3004Predicting the extent of massive wildfires once ignited is essential to reduce the subsequent socioeconomic losses and environmental damage, but challenging because of the complexity of fire behavior. Existing physics-based models are limited in predicting large or long-duration wildfire events. Here, we develop a deep-learning-based predictive model, Fire-Image-DenseNet (FIDN), that uses spatial features derived from both near real-time and reanalysis data on the environmental and meteorological drivers of wildfire. We trained and tested this model using more than 300 individual wildfires that occurred between 2012 and 2019 in the western US. In contrast to existing models, the performance of FIDN does not degrade with fire size or duration. Furthermore, it predicts final burnt area accurately even in very heterogeneous landscapes in terms of fuel density and flammability. The FIDN model showed higher accuracy, with a mean squared error (MSE) about 82% and 67% lower than those of the predictive models based on cellular automata (CA) and the minimum travel time (MTT) approaches, respectively. Its structural similarity index measure (SSIM) averages 97%, outperforming the CA and FlamMap MTT models by 6% and 2%, respectively. Additionally, FIDN is approximately three orders of magnitude faster than both CA and MTT models. The enhanced computational efficiency and accuracy advancements offer vital insights for strategic planning and resource allocation for firefighting operations.
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Journal articleCheaib A, Waring EF, McNellis R, et al., 2025,
Soil nitrogen supply exerts largest influence on leaf nitrogen in environments with the greatest leaf nitrogen demand
, Ecology Letters, ISSN: 1461-023X -
Journal articleNingthoujam R, Bloomfield KJ, Crawley MJ, et al., 2025,
Hyperspectral sensing of abovegroundbiomass and species diversity in a longrunninggrassland experiment
, Ecological Informatics, ISSN: 1574-9541 -
Journal articleCai W, Zhu Z, Harrison SP, et al., 2025,
A unifying principle for global greenness patterns and trends
, Nature Communications Earth and Environment, ISSN: 2662-4435 -
Journal articleMarsh CJ, Turner EC, Blonder BW, et al., 2025,
Tropical forest clearance impacts biodiversity and function, whereas logging changes structure.
, Science, Vol: 387, Pages: 171-175The impacts of degradation and deforestation on tropical forests are poorly understood, particularly at landscape scales. We present an extensive ecosystem analysis of the impacts of logging and conversion of tropical forest to oil palm from a large-scale study in Borneo, synthesizing responses from 82 variables categorized into four ecological levels spanning a broad suite of ecosystem properties: (i) structure and environment, (ii) species traits, (iii) biodiversity, and (iv) ecosystem functions. Responses were highly heterogeneous and often complex and nonlinear. Variables that were directly impacted by the physical process of timber extraction, such as soil structure, were sensitive to even moderate amounts of logging, whereas measures of biodiversity and ecosystem functioning were generally resilient to logging but more affected by conversion to oil palm plantation.
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Journal articleBridle J, Balmford A, Durant SM, et al., 2025,
Dedication: Professor Dame Georgina Mace DBE FRS (1953-2020).
, Philos Trans R Soc Lond B Biol Sci, Vol: 380 -
Journal articleBridle J, Balmford A, Durant SM, et al., 2025,
How should we bend the curve of biodiversity loss to build a just and sustainable future?
, Philos Trans R Soc Lond B Biol Sci, Vol: 380Current rates of habitat and biodiversity loss, and the threat they pose to ecological and economic productivity, would be considered a global emergency even if they were not occurring during a period of rapid anthropogenic climate change. Diversity at all levels of biological organization, both within and among species, and across genomes and communities, is critical for the resilience of the world's ecosystems in the face of such change. However, it remains an urgent scientific challenge to understand how biodiversity underpins these ecological outputs, how patterns of biodiversity are being affected by current threats, and how and where such biodiversity contributes most directly to human economies, well-being and social justice. In addition, even with such scientific understanding, there is a pressing need for societies to incorporate biodiversity protection into their economies and governance, and to stop subsidizing the loss of humanity's future prosperity for short-term private benefit. We highlight key issues and ways forward in these areas, inspired by the research and career of Dame Georgina Mace FRS, and by our discussions during the Royal Society meeting of June 2023.This article is part of the discussion meeting issue 'Bending the curve towards nature recovery: building on Georgina Mace's legacy for a biodiverse future'.
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Journal articleBezeng BS, Ameka G, Angui CMV, et al., 2025,
An African perspective to biodiversity conservation in the 21st century
, Philosophical Transactions of the Royal Society B: Biological Sciences, Vol: 380, ISSN: 0962-8436Africa boasts high biodiversity while also being home to some of the largest and fastest-growing human populations. Although the current environmental footprint of Africa is low compared to other continents, the population of Africa is estimated at around 1.5 billion inhabitants, representing nearly 18% of the world's total population. Consequently, Africa’s rich biodiversity is under threat, yet only 19% of the landscape and 17% of the seascape are under any form of protection. To effectively address this issue and align with the Convention on Biological Diversity's ambitious ‘30 by 30’ goal, which seeks to protect 30% of the world's land and oceans by 2030, substantial funding and conservation measures are urgently required. In response to this critical challenge, as scientists and conservationists working in Africa, we propose five recommendations for future directions aimed at enhancing biodiversity conservation for the betterment of African society: (i) accelerate data collection, data sharing and analytics for informed policy and decision making; (ii) innovate education and capacity building for future generations; (iii) enhance and expand protected areas, ecological networks, and foundational legal frameworks; (iv) unlock creative funding channels for cutting-edge conservation initiatives; and (v) integrate indigenous and local knowledge into forward-thinking conservation strategies. By implementing these recommendations, we believe Africa can make significant strides towards preserving its unique biodiversity, while fostering a healthier society, and contributing to global conservation efforts.
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Journal articlePurvis A, 2025,
Bending the curve of biodiversity loss requires a 'satnav' for nature.
, Philos Trans R Soc Lond B Biol Sci, Vol: 380Georgina Mace proposed bending the curve of biodiversity loss as a fitting ambition for the Convention on Biological Diversity. The new Global Biodiversity Monitoring Framework (GBMF) may increase the chances of meeting the goals and targets in the Kunming-Montreal Global Biodiversity Framework (KMGBF), which requires bending the curve. To meet the outcome goals of KMGBF, the GBMF should support adaptive policy responses to the state of biodiversity, which in turn requires a 'satnav' for nature. The twin pillars of such a satnav are (i) models to predict expected future outcomes of today's choices; and (ii) rapid feedback from monitoring to enable course corrections and model improvement. These same elements will also empower organizations to ensure that their actions are truly nature-positive, but they are not yet written into the GBMF. Without a satnav, society will effectively have to try to find its way to the outcome goals by looking in the rear-view mirror that the current headline indicators provide. Drawing contrasts and parallels with climate modelling, I discuss challenges for indicators, models, data and research culture that must be overcome if we are to bend the curve, and suggest ways forward.This article is part of the discussion meeting issue 'Bending the curve towards nature recovery: building on Georgina Mace's legacy for a biodiverse future'.
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Journal articleTolosana I, Willis K, Gribble M, et al., 2025,
A Y chromosome-linked genome editor for efficient population suppression in the malaria vector Anopheles gambiae.
, Nat Commun, Vol: 16Genetic control - the deliberate introduction of genetic traits to control a pest or vector population - offers a powerful tool to augment conventional mosquito control tools that have been successful in reducing malaria burden but that are compromised by a range of operational challenges. Self-sustaining genetic control strategies have shown great potential in laboratory settings, but hesitancy due to their invasive and persistent nature may delay their implementation. Here, instead, we describe a self-limiting strategy, designed to have geographically and temporally restricted effect, based on a Y chromosome-linked genome editor (YLE). The YLE comprises a CRISPR-Cas9 construct that is always inherited by males yet generates an autosomal dominant mutation that is transmitted to over 90% of the offspring and results in female-specific sterility. To our knowledge, our system represents a pioneering approach in the engineering of the Y chromosome to generate a genetic control strain for mosquitoes. Mathematical modelling shows that this YLE technology is up to seven times more efficient for population suppression than optimal versions of other self-limiting strategies, such as the widely used Sterile Insect Technique or the Release of Insects carrying a Dominant Lethal gene.
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Journal articleLyons-White J, Zodua PA, Yobo CM, et al., 2025,
Challenges for implementing zero deforestation commitments in a highly forested country: Perspectives from Liberia's palm oil sector
, WORLD DEVELOPMENT, Vol: 185, ISSN: 0305-750X -
Journal articleStocker B, Dong N, Perkowski EA, et al., 2025,
Empirical evidence and theoretical understanding ofecosystem carbon and nitrogen cycle interactions
, New Phytologist, Vol: 245, Pages: 49-68, ISSN: 0028-646XInteractions between carbon (C) and nitrogen (N) cycles in terrestrial ecosystems are simulated in advanced vegetation models, yet methodologies vary widely, leading to divergent simulations of past land C balance trends. This underscores the need to reassess our understanding of ecosystem processes, given recent theoretical advancements and empirical data. We review current knowledge, emphasising evidence from experiments and trait data compilations for vegetation responses to CO2 and N input, alongside theoretical and ecological principles for modelling. N fertilisation increases leaf N content but inconsistently enhances leaf-level photosynthetic capacity. Whole-plant responses include increased leaf area and biomass, with reduced root allocation and increased aboveground biomass. Elevated atmospheric CO2 also boosts leaf area and biomass but intensifies belowground allocation, depleting soil N and likely reducing N losses. Global leaf traits data confirm these findings, indicating that soil N availability influences leaf N content more than photosynthetic capacity. A demonstration model based on the functional balance hypothesis accurately predicts responses to N and CO2 fertilisation on tissue allocation, growth and biomass, offering a path to reduce uncertainty in global C cycle projections.
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Journal articleDias Fernandes L, Hintzen R, Thompson S, et al., 2024,
Species Richness and Speciation Rates for all Terrestrial Animals Emerge from a Synthesis of Ecological Theories
, Systematic Biology, ISSN: 1063-5157 -
Journal articleFlintham E, Savolainen V, Otto S, et al., 2024,
The maintenance of genetic polymorphism underlyingsexually antagonistic traits
, Evolution Letters, ISSN: 2056-3744Selection often favours different trait values in males and females, leading to genetic conflicts between the sexes when traits have a shared genetic basis. Such sexual antagonism has beenproposed to maintain genetic polymorphism. However, this notion is based on insights from population genetic models of single loci with fixed fitness effects. It is thus unclear how readily polymorphism emerges from sex-specific selection acting on continuous traits, where fitness effects arisefrom the genotype-phenotype map and the fitness landscape. Here we model the evolution of a continuous trait that has a shared genetic basis but different optima in males and females, considering a wide variety of genetic architectures and fitness landscapes. For autosomal loci, the long-termmaintenance of polymorphism requires strong conflict between males and females that generatesuncharacteristic sex-specific fitness patterns. Instead, more plausible sex-specific fitness landscapestypically generate stabilising selection leading to an evolutionarily stable state that consists of a singlehomozygous genotype. Except for sites tightly linked to the sex determining region, our results indicate that genetic variation due to sexual antagonism should arise only rarely and often be transient,making these signatures challenging to detect in genomic data.
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Journal articleSethi SS, Bick A, Chen M-Y, et al., 2024,
Reply to Araújo: Good science requires focus.
, Proc Natl Acad Sci U S A, Vol: 121 -
Journal articleParry C, Turnbull C, Gill R, 2024,
Tracking pollen tube and ovule development in vivo reveals rapid responses to pollination in Brassica napus
, AOB Plants, ISSN: 2041-2851Pollination and subsequent fertilisation in most angiosperms are precursors of seed and fruit development. Thus, understanding the developmental processes can improve management of plant reproductive success and food security. Indeed, the window between ovule fertilisation and seed development is crucial for the accumulation of metabolites which determines ultimate seed quality and yield. Establishing detailed temporal maps of development to describe pollination to early seed development is therefore extremely valuable to provide context for molecular studies, plant breeding, and to refine crop management strategies for optimal seed quality.• MethodsHere, we characterise aspects of post-pollination responses in the globally important crop plant Brassica napus (oilseed rape, canola) with a high-resolution time series of microscope images of the floral organs during the first 48 hours post pollination. • Key results We demonstrate the rapid response to pollination in B. napus (c.v. Westar), with pollen tubes germinating and traversing the style within just four hours. We also describe markers of early seed formation in response to fertilisation in the synchronous development of ovule area and stigma length. • ConclusionsOur results provide a series of temporal benchmarks for post-pollination floral morphology in B. napus, representing valuable reference points for studying and tracking pollination responses and early seed development.
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Journal articleLe Penru NP, Heath BE, Dunning J, et al., 2024,
Towards using virtual acoustics for evaluating spatial ecoacoustic monitoring technologies
, METHODS IN ECOLOGY AND EVOLUTION, ISSN: 2041-210X -
Journal articleStemkovski M, Fife A, Stuart R, et al., 2024,
Bee Phenological Distributions Predicted by Inferring Vital Rates
, AMERICAN NATURALIST, Vol: 204, Pages: E115-E127, ISSN: 0003-0147 -
Journal articleLiu J, Ryu Y, Luo X, et al., 2024,
Evidence for widespread thermal acclimation of canopy photosynthesis
, Nature Plants, Vol: 10, Pages: 1919-1927, ISSN: 2055-026XPlants acclimate to temperature by adjusting their photosynthetic capacity over weeks to months. However, most evidence for photosynthetic acclimation derives from leaf-scale experiments. Here, we address the scarcity of evidence for canopy-scale photosynthetic acclimation by examining the correlation between maximum photosynthetic rates (Amax,2000) and growth temperature ((T_air ) ̅) across a range of concurrent temperatures and canopy foliage quantity, using data from over 200 eddy covariance sites. We detect widespread thermal acclimation of canopy-scale photosynthesis, demonstrated by enhanced Amax,2000 under higher (T_air ) ̅, across flux sites with adequate water availability. A 14-day period is identified as the most relevant time scale for acclimation across all sites, with a range of 12–25 days for different plant functional types. The mean apparent thermal acclimation rate across all ecosystems is 0.41 (-0.38–1.04 for 5th–95th percentile range) µmol m-2 s-1 C-1, with croplands showing the largest and grasslands the lowest acclimation rates. Incorporating an optimality-based prediction of leaf photosynthetic capacities into a biochemical photosynthesis model is shown to improve the representation of thermal acclimation. Our results underscore the critical need for enhanced understanding and modelling of canopy-scale photosynthetic capacity to accurately predict plant responses to warmer growing seasons.
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Journal articleEwers RM, Cook J, Daniel OZ, et al., 2024,
New insights to be gained from a Virtual Ecosystem
, ECOLOGICAL MODELLING, Vol: 498, ISSN: 0304-3800 -
Journal articleParry C, Turnbull C, Barter L, et al., 2024,
Shedding light on pollination deficits: cueing into plant spectral reflectance signatures to monitor pollination delivery across landscapes
, Journal of Applied Ecology, Vol: 61, Pages: 2873-2883, ISSN: 0021-8901Pollination underlies plant yield, health and reproductive success in agricultural and natural systems worldwide. It is therefore concerning that declining animal pollinator populations compounded by growing demands for food are leading to rising pollination deficits, with globally significant economic and environmental implications.Despite this urgent issue, accurate and scalable tools to quantify and track pollination across useful spatiotemporal scales are lacking. Here, we propose to shed new light on pollination deficits, looking to remote sensing platforms as a transformative mapping and monitoring tool and a solution for pollinator conservation and crop management.Providing a synthesis of our current understanding of pollination-triggered floral senescence and underlying ultrastructural and metabolic changes, we propose how spectral reflectance technologies could be applied to accurately detect pollination events in real-time and at the landscape scale.Synthesis and applications: We highlight where research efforts can be targeted to produce scalable methods for identifying field-relevant bioindicators of pollination. We provide guidance on how spectral imaging accompanied by machine learning and coupled with autonomous operation technologies will enable applications to detect pollination delivery across complex landscapes. Ultimately, such an ecological application will transform our quantitative understanding of pollination services and, by directly linking plant yields and health, will reveal pollination deficits at high resolution to help mitigate risks to food security and ecosystem functioning.
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Journal articleSayol F, Wayman JP, Dufour P, et al., 2024,
AVOTREX: A Global Dataset of Extinct Birds and Their Traits
, GLOBAL ECOLOGY AND BIOGEOGRAPHY, Vol: 33, ISSN: 1466-822X -
Journal articleClegg T, Pawar S, 2024,
Variation in thermal physiology can drive the temperature-dependence of microbial community richness
, eLife, ISSN: 2050-084XPredicting how species diversity changes along environmental gradients is an enduring problem in ecology. In microbes current theories tend to invoke energy availability and enzyme kinetics as the main drivers of temperature-richness relationships. Here we derive a general empirically-grounded theory that can explain this phenomenon by linking microbial species richness in competitive communities to variation in the temperature-dependence of their interaction and growth rates. Specifically, the shape of the microbial community temperature-richness relationship depends on how rapidly the strength of effective competition between species pairs changes with temperature relative to the variance of their growth rates. Furthermore, it predicts that a thermal specialist-generalist tradeoff in growth rates alters coexistence by shifting this balance, causing richness to peak at relatively higher temperatures. Finally, we show that the observed patterns of variation in thermal performance curves of metabolic traits across extant bacterial taxa is indeed sufficient to generate the variety of community-level temperature-richness responses observed in the real world. Our results provide a new and general mechanism that can help explain temperature-diversity gradients in microbial communities, and provide a quantitative framework for interlinking variation in the thermal physiology of microbial species to their community-level diversity.
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