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  • Journal article
    Smith T, Mombrikotb S, Ransome E, Kontopoulos D, Pawar S, Bell Tet al., 2022,

    Latent functional diversity may accelerate microbial community responses to temperature fluctuations

    , eLife, Vol: 11, Pages: 1-22, ISSN: 2050-084X

    How complex microbial communities respond to climatic fluctuations remains an open question. Due to their relatively short generation times and high functional diversity, microbial populations harbor great potential to respond as a community through a combination of strain-level phenotypic plasticity, adaptation, and species sorting. However, the relative importance of these mechanisms remains unclear. We conducted a laboratory experiment to investigate the degree to which bacterial communities can respond to changes in environmental temperature through a combination of phenotypic plasticity and species sorting alone. We grew replicate soil communities from a single location at six temperatures between 4°C and 50°C. We found that phylogenetically and functionally distinct communities emerge at each of these temperatures, with K-strategist taxa favored under cooler conditions and r-strategist taxa under warmer conditions. We show that this dynamic emergence of distinct communities across a wide range of temperatures (in essence, community-level adaptation) is driven by the resuscitation of latent functional diversity: the parent community harbors multiple strains pre-adapted to different temperatures that are able to ‘switch on’ at their preferred temperature without immigration or adaptation. Our findings suggest that microbial community function in nature is likely to respond rapidly to climatic temperature fluctuations through shifts in species composition by resuscitation of latent functional diversity.
  • Journal article
    Simpson EG, Fraser I, Woolf H, Pearse WDet al., 2022,

    Variation in near-surface soil temperature drives plant assemblage insurance potential

    <jats:title>Abstract</jats:title><jats:p><jats:list list-type="order"><jats:list-item><jats:p>Studying how assemblages vary across environmental gradients provides a baseline for how assemblages may respond to climate change. Per the biological insurance hypothesis, assemblages with more variation in functional diversity will maintain ecosystem functions when species are lost. In complement, environmental heterogeneity supports landscape-scale ecosystem functionality (<jats:italic>i</jats:italic>.<jats:italic>e</jats:italic>. spatial insurance), when that variation includes environments with more abundant resources.</jats:p></jats:list-item><jats:list-item><jats:p>We use the relationship between vascular plant functional diversity and microenvironment to identify where assemblages are most likely to maintain functionality in a mountainous fieldsite in northeastern Utah, USA. We assessed how life history strategies and information about phylogenetic differences affect these diversity-environment relationships.</jats:p></jats:list-item><jats:list-item><jats:p>We found less functionally dispersed assemblages, that were shorter and more resource-conservative on hotter, more variable, south-facing slopes. In contrast, we found more functionally dispersed assemblages, that were taller and more resource-acquisitive on cooler, less variable, north-facing slopes. Herbaceous and woody perennials drove these trends. Additionally, including information about phylogenetic differences in a dispersion metric indicated that phylogeny accounts for traits we did not measure.</jats:p></jats:list-item><jats:list-item><jats:p><jats:italic>Synthesis</jats:italic>. At our fieldsite, soil temperature acts as an environmental filter across aspect. If soil temperature increases and becomes more variable, the function of north- vs. south-fac
  • Journal article
    Keller A, Ankenbrand MJ, Bruelheide H, Dekeyzer S, Enquist BJ, Erfanian MB, Falster DS, Gallagher R, Hammock J, Kattge J, Leonhardt SD, Madin JS, Maitner B, Neyret M, Onstein RE, Pearse WD, Poelen JH, Salguero-Gomez R, Schneider FD, Toth AB, Penone Cet al., 2022,

    Ten (mostly) simple rules to future-proof trait data in ecological and evolutionary sciences

    , METHODS IN ECOLOGY AND EVOLUTION, ISSN: 2041-210X
  • Journal article
    Burton VJ, Contu S, De Palma A, Hill SLL, Albrecht H, Bone JS, Carpenter D, Corstanje R, De Smedt P, Farrell M, Ford HV, Hudson LN, Inward K, Jones DT, Kosewska A, Lo-Man-Hung NF, Magura T, Mulder C, Murvanidze M, Newbold T, Smith J, Suarez AV, Suryometaram S, Tóthmérész B, Uehara-Prado M, Vanbergen AJ, Verheyen K, Wuyts K, Scharlemann JPW, Eggleton P, Purvis Aet al., 2022,

    Land use and soil characteristics affect soil organisms differently from above-ground assemblages

    , BMC Ecology and Evolution, Vol: 22, ISSN: 2730-7182

    Background:Land-use is a major driver of changes in biodiversity worldwide, but studies have overwhelmingly focused on above-ground taxa: the effects on soil biodiversity are less well known, despite the importance of soil organisms in ecosystem functioning. We modelled data from a global biodiversity database to compare how the abundance of soil-dwelling and above-ground organisms responded to land use and soil properties.Results:We found that land use affects overall abundance differently in soil and above-ground assemblages. The abundance of soil organisms was markedly lower in cropland and plantation habitats than in primary vegetation and pasture. Soil properties influenced the abundance of soil biota in ways that differed among land uses, suggesting they shape both abundance and its response to land use.Conclusions:Our results caution against assuming models or indicators derived from above-ground data can apply to soil assemblages and highlight the potential value of incorporating soil properties into biodiversity models.
  • Journal article
    Jaureguiberry P, Titeux N, Wiemers M, Bowler DE, Coscieme L, Golden AS, Guerra CA, Jacob U, Takahashi Y, Settele J, Diaz S, Molnar Z, Purvis Aet al., 2022,

    The direct drivers of recent global anthropogenic biodiversity loss

    , SCIENCE ADVANCES, Vol: 8, ISSN: 2375-2548
  • Journal article
    Fu Z, Ciais P, Feldman A, Gentine P, Makowski D, Prentice IC, Stoy PC, Bastos A, Wigneron J-Pet al., 2022,

    Critical soil moisture thresholds of plant water stress in terrestrial cosystems

    , Science Advances, Vol: 8, Pages: 1-12, ISSN: 2375-2548

    Plant water stress occurs at the point when soil moisture (SM) limits transpiration, defining a critical SM threshold (θcrit). Knowledge of the spatial distribution of θcrit is crucial for future projections of climate and water resources. Here, we use global eddy-covariance observations to quantify θcrit and evaporative fraction (EF) regimes. Three canonical variables describe how EF is controlled by SM: the maximum EF (EFmax), θcrit, and slope (S) between EF and SM. We find systematic differences of these three variables across biomes. Variation in θcrit, S, and EFmax is mostly explained by soil texture, vapor pressure deficit and precipitation, respectively, as well as vegetation structure. Dryland ecosystems tend to operate at low θcrit and show adaptation to water deficits. The negative relationship between θcrit and S indicates that dryland ecosystems minimize θcrit through mechanisms of sustained SM extraction and transport by xylem. Our results further suggest an optimal adaptation of local EF–SM response, that maximizes growing-season evapotranspiration and photosynthesis.
  • Book chapter
    Quinlan M, Hayes KR, 2022,

    Risk analysis of transgenic insects

    , Transgenic insects: techniques and applications, Editors: Benedict, Scott, Publisher: CABI Publishing, Wallingford, United Kingdom, Pages: 552-578
  • Journal article
    Dong N, Prentice IC, Wright IJ, Wang H, Atkins OK, Bloomfield KJ, Domingues TF, Gleason SM, Maire V, Onoda Y, Poorter H, Smith NGet al., 2022,

    Leaf nitrogen from the perspective of optimal plant function

    , Journal of Ecology, Vol: 110, Pages: 2585-2602, ISSN: 0022-0477

    1. Leaf dry mass per unit area (LMA), carboxylation capacity (Vcmax) and leaf nitrogen per unit area (Narea) and mass (Nmass) are key traits for plant functional ecology and ecosystem modelling. There is however no consensus about how these traits are regulated, or how they should be modelled. Here we confirm that observed leaf nitrogen across species and sites can be estimated well from observed LMA and Vcmax at 25˚C (Vcmax25). We then test the hypothesis that global variations of both quantities depend on climate variables in specific ways that are predicted by leaf-level optimality theory, thus allowing both Narea to be predicted as functions of the growth environment.2. A new global compilation of field measurements was used to quantify the empirical relationships of leaf N to Vcmax25 and LMA. Relationships of observed Vcmax25 and LMA to climate variables were estimated, and compared to independent theoretical predictions of these relationships. Soil effects were assessed by analysing biases in the theoretical predictions.3. LMA was the most important predictor of Narea (increasing) and Nmass (decreasing). About 60% of global variation across species and sites in observed Narea, and 31% in Nmass, could be explained by observed LMA and V¬cmax25. These traits in turn were quantitatively related to climate variables, with significant partial relationships similar or indistinguishable from those predicted by optimality theory. Predicted trait values explained 21% of global variation in observed site-mean Vcmax25, 43% in LMA, and 31% in Narea. Predicted Vcmax25 was biased low on clay-rich soils but predicted LMA was biased high, with compensating effects on Narea. Narea was overpredicted on organic soils.4. Synthesis. Global patterns of variation in observed site-mean Narea can be explained by climate-induced variations in optimal Vcmax25¬ and LMA. Leaf nitrogen should accordingly be modelled as a consequence (not a cause) of Vcmax25 and LMA, both being optim
  • Journal article
    Lawson J, Whitworth A, Banks-Leite C, 2022,

    Soundscapes show disruption across the diel cycle in human modified tropical landscapes

    , Ecological Indicators, Vol: 144, ISSN: 1470-160X

    1. Fluctuations in the diel cycle, especially when compared across different land-use types, can reveal key changes in acoustic activity and the biological community. Yet few studies have assessed the effects of land use change on soundscapes across the diel cycle. The emergence of passive acoustic monitoring (PAM) allows us to monitor landscapes over longer and continuous periods, providing data on temporal variability across the diel cycle.2. Using AudioMoth acoustic recorders we collected data at 120 sites on the Osa Peninsula, Costa Rica, across a gradient of land use intensity. Information was extracted from recordings using a suite of nine acoustic indices. Principal component analysis reduced the indices into two axes, the first reflecting acoustic activity in the mid frequency bands, where the majority of biotic sound is present, and the second, representing acoustic activity in the upper frequency bands and the ratio of activity between the lower and mid-frequency bands.3. In disturbed land use types we found reduced acoustic activity during the characteristic dawn and dusk peaks in the diel cycle; known as the dawn and dusk chorus. Palm oil plantations showed a complete loss of these peaks, while teak plantations retained evidence of a weaker dawn and dusk chorus. Restricting the analysis to narrower temporal windows masks these differences among habitats.4. Synthesis and applications. Evaluating acoustic diversity at specific times of the day, which is common practice in bioacoustics studies, may be misleading, as pronounced changes in acoustic activity at dawn and duskwere obscured. By assessing trends across the diel cycle, we can gain a much better representation of the changes in acoustic activity. Our results show that in disturbed ecosystems there is a deviation in acoustic activity from that seen in a healthy native forest ecosystem, suggesting that there are likely changes within the biotic community in these ecosystems.
  • Journal article
    Nainar A, Walsh RPD, Bidin K, Tanaka N, Annammala KV, Letchumanan U, Ewers RM, Reynolds Get al., 2022,

    Baseflow persistence and magnitude in oil palm, logged and primary tropical rainforest catchments in Malaysian Borneo: implications for water management under climate change

    , Water, Vol: 14, Pages: 1-16, ISSN: 2073-4441

    While timber harvesting has plateaued, repeat-logging and conversion into plantations (especially oil palm) are still active in the tropics. The associated hydrological impacts especially pertaining to enhanced runoff, flood, and erosion have been well-studied, but little attention has been given to water resource availability in the humid tropics. In the light of the increasing climate extremes, this paper compared baseflow values and baseflow recession constants (K) between headwater catchments of five differing land-uses in Sabah, Malaysian Borneo, namely primary forest (PF), old growth/virgin jungle reserve (VJR), twice-logged forest with 22 years regeneration (LF2), multiple-logged forest with 8 years regeneration (LF3), and oil palm plantation (OP). Hydrological and meteorological sensors and dataloggers were established in each catchment. Daily discharge was used for computing K via four estimation methods. Catchment ranks in terms of decreasing K were VJR (0.97841), LF3 (0.96692), LF2 (0.90347), PF (0.83886), and OP (0.86756). Catchment ranks in terms of decreasing annual baseflow were PF (1877 mm), LF3 (1265 mm), LF2 (812 mm), VJR (753 mm), and OP (367 mm), corresponding to 68%, 55%, 51%, 42%, and 38% of annual streamflow, respectively. Despite the low K, PF had the highest baseflow magnitude. OP had the fastest baseflow recession and lowest baseflow magnitude. Baseflow persistence decreased with increasing degree of disturbance. K showed strong association to catchment stem density instead of basal area. For dynamic catchments in this study, the Kb3 estimator is recommended based on its lowest combination of coefficient of variation (CoV) and root mean squared error (RMSE) of prediction. For wetter catchments with even shorter recession events, the Kb4 estimator may be considered. Regarding climate change, logging and oil palm agriculture should only be conducted after considering water resource availability. Forests (even degraded ones) should be conserve
  • Journal article
    Morris OF, Loewen CJG, Woodward G, Schäfer RB, Piggott JJ, Vinebrooke RD, Jackson MCet al., 2022,

    Local stressors mask the effects of warming in freshwater ecosystems

    , Ecology Letters, Vol: 25, Pages: 2540-2551, ISSN: 1461-023X

    Climate warming is a ubiquitous stressor in freshwater ecosystems, yet its interactive effects with other stressors are poorly understood. We address this knowledge gap by testing the ability of three contrasting null models to predict the joint impacts of warming and a range of other aquatic stressors using a new database of 296 experimental combinations. Despite concerns that stressors will interact to cause synergisms, we found that net impacts were usually best explained by the effect of the stronger stressor alone (the dominance null model), especially if this stressor was a local disturbance associated with human land use. Prediction accuracy depended on stressor identity and how asymmetric stressors were in the magnitude of their effects. These findings suggest we can effectively predict the impacts of multiple stressors by focusing on the stronger stressor, as habitat alteration, nutrients and contamination often override the biological consequences of higher temperatures in freshwater ecosystems.
  • Journal article
    Matthews TJ, Wayman JP, Cardoso P, Sayol F, Hume JP, Ulrich W, Tobias JA, Soares FC, Thebaud C, Martin TE, Triantis KAet al., 2022,

    Threatened and extinct island endemic birds of the world: Distribution, threats and functional diversity

    , JOURNAL OF BIOGEOGRAPHY, Vol: 49, Pages: 1920-1940, ISSN: 0305-0270
  • Journal article
    Fernandes LD, Hintzen RE, Thompson SED, Barychka T, Tittensor D, Harfoot M, Newbold T, Rosindell Jet al., 2022,

    Species Richness and Speciation Rates for all Terrestrial Animals Emerge from a Synthesis of Ecological Theories

    <jats:title>A<jats:sc>bstract</jats:sc></jats:title><jats:p>The total number of species on earth and the rate at which new species are created are fundamental questions for ecology, evolution and conservation. These questions have typically been approached separately, despite their obvious interconnection. In this manuscript we approach both questions in conjunction, for all terrestrial animals, which enables a more holistic integration and generates novel emergent predictions. To do this, we combine two previously unconnected bodies of theory: general ecosystem modelling and individual based ecological neutral theory. General ecosystem models provide us with estimated numbers of individual organisms, separated by functional group and body size. Neutral theory, applied within a guild of functionally similar individuals, connects species richness, speciation rate and number of individual organisms. In combination, for terrestrial endotherms where species numbers are known, they provide us with estimates for speciation rates as a function of body size and diet class. Extrapolating the same rates to guilds of ectotherms enables us to estimate the species richness of those groups, including species yet to be described. We find that speciation rates per species per million years decrease with increasing body size. Rates are also higher for carnivores compared to omnivores or herbivores of the same body size. Our estimate for the total number of terrestrial species of animals is in the range 1.03 − 2.92 million species, a value consistent with estimates from previous studies, despite having used a fundamentally new approach. Perhaps what is most remarkable about these results is that they have been obtained using only limited data from larger endotherms and their speciation rates, with the rest of the predictive process being based on mechanistic theory. This work illustrates the potential of a new approach to classic eco-evolutionary q
  • Journal article
    Joshi J, Stocker B, Hofhansl F, Zhou S, Dieckmann U, Prentice ICet al., 2022,

    Towards a unified theory of plant photosynthesis and hydraulics

    , Nature Plants, Vol: 8, Pages: 1304-1316, ISSN: 2055-026X

    The global carbon and water cycles are governed by the coupling of CO2 and water vapour exchanges through the leaves of terrestrial plants, controlled by plant adaptations to balance carbon gains and hydraulic risks. We introduce a trait-based optimality theory that unifies the treatment of stomatal responses and biochemical acclimation of plants to environments changing on multiple timescales. Tested with experimental data from 18 species, our model successfully predicts the simultaneous decline in carbon assimilation rate, stomatal conductance and photosynthetic capacity during progressive soil drought. It also correctly predicts the dependencies of gas exchange on atmospheric vapour pressure deficit, temperature and CO2. Model predictions are also consistent with widely observed empirical patterns, such as the distribution of hydraulic strategies. Our unified theory opens new avenues for reliably modelling the interactive effects of drying soil and rising atmospheric CO2 on global photosynthesis and transpiration.
  • Journal article
    Dunn N, Savolainen V, Weber S, Andrzejaczek S, Carbone C, Curnick Det al., 2022,

    Elasmobranch diversity across a remote coral reef atoll revealed through environmental DNA metabarcoding

    , Zoological Journal of the Linnean Society, Vol: 196, Pages: 593-607, ISSN: 0024-4082

    As elasmobranchs are becoming increasingly threatened, efficient methods for monitoring the distribution and diversity of elasmobranch populations are required. Environmental DNA (eDNA) metabarcoding is an increasingly applied technique that enables mass identification of entire communities and is an effective method for the detection of rare and elusive species. We performed an eDNA metabarcoding survey for fish communities around a coral reef atoll in the Chagos Archipelago and assessed the diversity and distribution of elasmobranch species detected within these communities. Our eDNA survey detected 353 amplicon sequence variants (ASVs) attributed to fishes, 12 of which were elasmobranchs. There were no differences in fish communities based on the presence and absence of ASVs between sample depth (surface and 40m) or sampling habitat, but communities based on read abundance were significantly different between habitats. The dominant elasmobranch species were grey reef (Carcharhinus amblyrhynchos) and silvertip (C. albimarginatus) sharks, and elasmobranch communities were significantly different between sampling depth and habitat. Overall, we find that eDNA metabarcoding can be used to reveal the diversity of elasmobranchs within broader taxonomic assays, but further research and development of targeted metabarcoding primers may be required before it can be integrated into a toolkit for monitoring these species.
  • Journal article
    Mombrikotb SB, Van Agtmaal M, Johnstone E, Crawley MJ, Gweon HS, Griffiths RI, Bell Tet al., 2022,

    The interactions and hierarchical effects of long-term agricultural stressors on soil bacterial communities

    , ENVIRONMENTAL MICROBIOLOGY REPORTS, Vol: 14, Pages: 711-718, ISSN: 1758-2229
  • Journal article
    Morris ZS, Vliet KA, Abzhanov A, Pierce SEet al., 2022,

    Developmental origins of the crocodylian skull table and platyrostral face

    , ANATOMICAL RECORD-ADVANCES IN INTEGRATIVE ANATOMY AND EVOLUTIONARY BIOLOGY, Vol: 305, Pages: 2838-2853, ISSN: 1932-8486
  • Journal article
    Chik HYJ, Sparks AM, Schroeder J, Dugdale HLet al., 2022,

    A meta-analysis on the heritability of vertebrate telomere length

    , JOURNAL OF EVOLUTIONARY BIOLOGY, Vol: 35, Pages: 1283-1295, ISSN: 1010-061X
  • Journal article
    Liu F, Gledhill M, Tan Q-G, Zhu K, Zhang Q, Salaun P, Tagliabue A, Zhang Y, Weiss D, Achterberg EP, Korchev Yet al., 2022,

    Phycosphere pH of unicellular nano- and micro- phytoplankton cells and consequences for iron speciation

    , The ISME Journal: multidisciplinary journal of microbial ecology, Vol: 16, Pages: 2329-2336, ISSN: 1751-7362

    Surface ocean pH is declining due to anthropogenic atmospheric CO2 uptake with a global decline of ~0.3 possible by 2100. Extracellular pH influences a range of biological processes, including nutrient uptake, calcification and silicification. However, there are poor constraints on how pH levels in the extracellular microenvironment surrounding phytoplankton cells (the phycosphere) differ from bulk seawater. This adds uncertainty to biological impacts of environmental change. Furthermore, previous modelling work suggests that phycosphere pH of small cells is close to bulk seawater, and this has not been experimentally verified. Here we observe under 140 μmol photons·m−2·s−1 the phycosphere pH of Chlamydomonas concordia (5 µm diameter), Emiliania huxleyi (5 µm), Coscinodiscus radiatus (50 µm) and C. wailesii (100 µm) are 0.11 ± 0.07, 0.20 ± 0.09, 0.41 ± 0.04 and 0.15 ± 0.20 (mean ± SD) higher than bulk seawater (pH 8.00), respectively. Thickness of the pH boundary layer of C. wailesii increases from 18 ± 4 to 122 ± 17 µm when bulk seawater pH decreases from 8.00 to 7.78. Phycosphere pH is regulated by photosynthesis and extracellular enzymatic transformation of bicarbonate, as well as being influenced by light intensity and seawater pH and buffering capacity. The pH change alters Fe speciation in the phycosphere, and hence Fe availability to phytoplankton is likely better predicted by the phycosphere, rather than bulk seawater. Overall, the precise quantification of chemical conditions in the phycosphere is crucial for assessing the sensitivity of marine phytoplankton to ongoing ocean acidification and Fe limitation in surface oceans.
  • Journal article
    Pearse WD, Stemkovski M, Lee BR, Primack RB, Lee Set al., 2022,

    Consistent, linear phenological shifts across a century of observations in South Korea

    <jats:title>Abstract</jats:title><jats:p>The Korea Meteorological Agency (KMA) has monitored flowering dates over the past 100 years for seven economically important woody plant species. This unique dataset is perfect for understanding whether historical patterns of phenological plasticity are breaking down in the face of recent and rapid climate change. Here we show that a scientist armed only 50 years into this study would have been able to predict the phenological shifts of the last 50 years with a high degree of accuracy. This is despite record-breaking warm temperatures and unprecedented early flowering, suggesting consistency in phenological shifts over time.</jats:p>
  • Journal article
    Nobrega R, Prentice IC, 2022,

    Holistic analysis of the carbon and water cycles to quantify the human footprint in basin-wide hydrological processes in the Amazon

    <jats:p>&amp;lt;p&amp;gt;While land-cover clearing (LCC) immediately reduces evapotranspiration (ET), its effects on other water fluxes, such as river discharge and terrestrial water storage, exhibit contrasting responses depending on location and scale. One explanation for this is that LCC triggers a series of asynchronous disruptions in the equilibrium of hydrological processes that was established upon the long-term balance with regional climatological, edaphic, and geological characteristics. Water fluxes under these circumstances are not well represented by hydrological models that have Budyko-like approaches or rely on the stationarity of the hydrological responses. The complexity of such analysis is incremented once LCC is followed by the conversion to pastures and crops established over random spatial and temporal patterns throughout river basins. Here, we propose an analysis of river discharge and root zone storage capacity (RZSC) to unveil underlying relationships between stream dynamics and water consumption by plants. We use a time-series segmentation and residual trend analysis on streamflow and precipitation of high-order tributaries of the Tapaj&amp;amp;#243;s River in the Amazon whose catchments underwent an intense land-use change over the past decades. We estimate the RZSC using the mass-curve balance method by considering the annual land-cover changes over a &amp;gt;30-year period. Despite the common belief that increases in river discharge are primarily caused by reduced ET when precipitation trends are not significant, we show that this might not be the main trigger of streamflow change in these major Amazon catchments. Instead, the reduction in the RZSC caused by changes in the water consumption by plants over the dry season is tightly associated with the increased baseflow contribution to rivers. Finally, we analysed gross primary productivity (GPP) and ET estimates generated by a model based on eco-evolutionary optimalit
  • Journal article
    Chen JM, Wang R, Liu Y, He L, Croft H, Luo X, Wang H, Smith NG, Keenan TF, Prentice IC, Zhang Y, Ju W, Dong Net al., 2022,

    Global datasets of leaf photosynthetic capacity for ecological and earth system research

    , Earth System Science Data, Vol: 14, Pages: 4077-4093, ISSN: 1866-3508

    The maximum rate of Rubisco carboxylation (Vcmax) determines leaf photosynthetic capacity and is a keyparameter for estimating the terrestrial carbon cycle, but its spatial information is lacking, hindering global ecologicalresearch. Here, we convert leaf chlorophyll content (LCC) retrieved from satellite data to Vcmax, based on plants’ optimaldistribution of nitrogen between light harvesting and carboxylation pathways. We also derive Vcmax from satellite (GOME-2)observations of sun-induced chlorophyll fluorescence (SIF) as a proxy of leaf photosynthesis using a data assimilationtechnique. These two independent global Vcmax products agree well (r2=0.79, RMSE=15.46 μmol m-2s-1 25 , P<0.001) andcompare well with 3672 ground-based measurements (r2=0.68, RMSE=13.55 μmol m-2s-1and P<0.001 for SIF; r2=0.55,RMSE=17.55 μmol m-2s-1 and P<0.001 for LCC). The LCC-derived Vcmax product is also used to constrain the retrieval ofVcmax from TROPOMI SIF data to produce an optimized Vcmax product using both SIF and LCC information. The globaldistributions of these products are compatible with Vcmax computed from an ecological optimality theory using meteorological variables, but importantly reveal additional information on the influence of land cover, irrigation, soil pH andleaf nitrogen on leaf photosynthetic capacity. These satellite-based approaches and spatial Vcmax products are primed to play amajor role in global ecosystem research. The three remote sensing Vcmax products based on SIF, LCC and SIF+LCC areavailable at https://doi.org/10.5281/zenodo.6466968 (Chen et al., 2020) and the code for implementing the ecologicaloptimality theory is available at https://github.com/SmithEcophysLab/optimal_vcmax_R (Smith, 2020).
  • Journal article
    Cheng S, Prentice IC, Huang Y, Jin Y, Guo Y-K, Arcucci Ret al., 2022,

    Data-driven surrogate model with latent data-assimilation: application to wildfire forecasting

    , Journal of Computational Physics, Vol: 464, ISSN: 0021-9991

    The large and catastrophic wildfires have been increasing across the globe in the recent decade, highlighting the importance of simulating and forecasting fire dynamics in near real-time. This is extremely challenging due to the complexities of physical models and geographical features. Running physics-based simulations for large wildfire events in near real-time are computationally expensive, if not infeasible. In this work, we develop and test a novel data-model integration scheme for fire progression forecasting, that combines Reduced-order modelling, recurrent neural networks (Long-Short-Term Memory), data assimilation, and error covariance tuning. The Reduced-order modelling and the machine learning surrogate model ensure the efficiency of the proposed approach while the data assimilation enables the system to adjust the simulation with observations. We applied this algorithm to simulate and forecast three recent large wildfire events in California from 2017 to 2020. The deep-learning-based surrogate model runs around 1000 times faster than the Cellular Automata simulation which is used to generate training data-sets. The daily fire perimeters derived from satellite observation are used as observation data in Latent Assimilation to adjust the fire forecasting in near real-time. An error covariance tuning algorithm is also performed in the reduced space to estimate prior simulation and observation errors. The evolution of the averaged relative root mean square error (R-RMSE) shows that data assimilation and covariance tuning reduce the RMSE by about 50% and considerably improves the forecasting accuracy. As a first attempt at a reduced order wildfire spread forecasting, our exploratory work showed the potential of data-driven machine learning models to speed up fire forecasting for various applications.
  • Journal article
    Dong N, Wright IJ, Chen JM, Luo X, Wang H, Keenan T, Smith NG, Prentice ICet al., 2022,

    Rising CO2 and warming reduce global canopy deman for nitrogen

    , New Phytologist, Vol: 235, Pages: 1692-1700, ISSN: 0028-646X

    Nitrogen (N) limitation has been considered as a constraint on terrestrial carbon uptake in response to rising CO2 and climate change. By extension, it has been suggested that declining carboxylation capacity (Vcmax) and leaf N content in enhanced-CO2 experiments and satellite records signify increasing N limitation of primary production. We predicted Vcmax using the coordination hypothesis, and estimated changes in leaf-level photosynthetic N for 1982–2016 assuming proportionality with leaf-level Vcmax at 25˚C. Whole-canopy photosynthetic N was derived using satellite-based leaf area index (LAI) data and an empirical extinction coefficient for Vcmax, and converted to annual N demand using estimated leaf turnover times. The predicted spatial pattern of Vcmax shares key features with an independent reconstruction from remotely-sensed leaf chlorophyll content. Predicted leaf photosynthetic N declined by 0.27 % yr-1, while observed leaf (total) N declined by 0.2–0.25 % yr-1. Predicted global canopy N (and N demand) declined from 1996 onwards, despite increasing LAI. Leaf-level responses to rising CO2, and to a lesser extent temperature, may have reduced the canopy requirement for N by more than rising LAI has increased it. This finding provides an alternative explanation for declining leaf N that does not depend on increasing N limitation.
  • Journal article
    Triantis KA, Rigal F, Whittaker RJ, Hume JP, Sheard C, Poursanidis D, Rolland J, Sfenthourakis S, Matthews TJ, Thebaud C, Tobias JAet al., 2022,

    Deterministic assembly and anthropogenic extinctions drive convergence of island bird communities

    , GLOBAL ECOLOGY AND BIOGEOGRAPHY, Vol: 31, Pages: 1741-1755, ISSN: 1466-822X
  • Journal article
    Liu M, Prentice IC, Menviel L, Harrison SPet al., 2022,

    Past rapid warmings as a constraint on greenhouse-gas climate feedbacks

    , Communications Earth & Environment, Vol: 3, ISSN: 2662-4435

    There are large uncertainties in the estimation of greenhouse-gas climate feedback. Recent observations do not provide strong constraints because they are short and complicated by human interventions, while model-based estimates differ considerably. Rapid climate changes during the last glacial period (Dansgaard-Oeschger events), observed near-globally, were comparable in both rate and magnitude to current and projected 21st century climate warming and therefore provide a relevant constraint on feedback strength. Here we use these events to quantify the centennial-scale feedback strength of CO2, CH4 and N2O by relating global mean temperature changes, simulated by an appropriately forced low-resolution climate model, to the radiative forcing of these greenhouse gases derived from their concentration changes in ice-core records. We derive feedback estimates (expressed as dimensionless gain) of 0.14 ± 0.04 for CO2, 0.10 ± 0.02 for CH4, and 0.09 ± 0.03 for N2O. This indicates that much lower or higher estimates of gains, particularly some previously published values for CO2, are unrealistic.
  • Journal article
    Palmer J, Samuelson AE, Gill RJ, Leadbeater E, Jansen VAAet al., 2022,

    Honeybees vary communication and collective decision making across landscapes

    <jats:title>Abstract</jats:title><jats:p>Honeybee (<jats:italic>Apis mellifera</jats:italic>) colony foraging decisions arise from the waggle dances of individual foragers, processed and filtered through a series of feedback loops that produce emergent collective behaviour. This process is an example of animal communication at the height of eusociality, yet a growing body of evidence suggests that its value for colony foraging success is heavily dependent on local ecology. Although colonies are thought to vary their use of the waggle dance in response to local ecological conditions, this is yet to be empirically established. Here, we quantify waggle dance use based on colony level dance-decoding and show that the impact of dance use on collective foraging is clear in some colonies but nearly negligible in others. We outline how these estimates of dance use can be combined with land-use data to explore the landscape characteristics that drive collective foraging. Our methodology provides a means to quantify the real-world importance of a celebrated example of animal communication and opens the door to the exploration of the selection pressures that may have driven the evolution of this remarkable collective behaviour.</jats:p>
  • Journal article
    Khatri BS, Burt A, 2022,

    A theory of resistance to multiplexed gene drive demonstrates the significant role of weakly deleterious natural genetic variation

    , PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 119, ISSN: 0027-8424
  • Journal article
    Dobson B, Barry S, Maes-Prior R, Mijic A, Woodward G, Pearse WDet al., 2022,

    Predicting catchment suitability for biodiversity at national scales

    , WATER RESEARCH, Vol: 221, ISSN: 0043-1354
  • Journal article
    Terlau J, Brose U, Antunes AC, Berti E, Boy T, Gauzens B, Pawar S, Pinsky M, Ryser R, Hirt MRet al., 2022,

    Integrating trait-based movement into mechanistic predictions of thermal performance

    <jats:title>Abstract</jats:title> <jats:p>Despite the diversity and functional importance of invertebrates, predicting their response to global warming remains challenging as it requires extensive measurements of physiological performance or rarely available high-resolution distribution data. Mechanistic models can help overcome these limitations by generalizing fundamental physiological processes. However, their predictions typically omit the effects of species interactions. Movement is a key process of species interactions underpinning animal performance in the real world. Here, we developed an empirically-grounded mechanistic model that incorporates allometric and thermodynamic constraints on movement and predator-prey interactions. We illustrate how it can be used to quantify the thermal performance of invertebrates under current and future climatic conditions. This trait-based approach (1) contributes to our understanding of the mechanisms underlying thermal fitness, (2) allows generalized predictions of thermal performance across invertebrate species worldwide and (3) can be used to inform species distribution models and thereby help infer species range limits under climate change.</jats:p>

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