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  • Journal article
    Norman DL, Bischoff PH, Wearn OR, Ewers RM, Rowcliffe JM, Evans B, Sethi S, Chapman PM, Freeman Ret al., 2023,

    Can CNN-based species classification generalise across variation in habitat within a camera trap survey?

    , Methods in Ecology and Evolution, Vol: 14, Pages: 242-251, ISSN: 2041-210X

    Camera trap surveys are a popular ecological monitoring tool that produce vast numbers of images making their annotation extremely time-consuming. Advances in machine learning, in the form of convolutional neural networks, have demonstrated potential for automated image classification, reducing processing time. These networks often have a poor ability to generalise, however, which could impact assessments of species in habitats undergoing change.Here, we (i) compare the performance of three network architectures in identifying species in camera trap images taken from tropical forest of varying disturbance intensities; (ii) explore the impacts of training dataset configuration; (iii) use habitat disturbance categories to investigate network generalisability and (iv) test whether classification performance and generalisability improve when using images cropped to bounding boxes.Overall accuracy (72.8%) was improved by excluding the rarest species and by adding extra training images (76.3% and 82.8%, respectively). Generalisability to new camera locations within a disturbance level was poor (mean F1-score: 0.32). Performance across unseen habitat disturbance levels was worse (mean F1-score: 0.27). Training the network on multiple disturbance levels improved generalisability (mean F1-score on unseen disturbance levels: 0.41). Cropping images to bounding boxes improved overall performance (F1-score: 0.77 vs. 0.47) and generalisability (mean F1-score on unseen disturbance levels: 0.73), but at a cost of losing images that contained animals which the detector failed to detect.These results suggest researchers should consider using an object detector before passing images to a classifier, and an improvement in classification might be seen if labelled images from other studies are added to their training data. Composition of training data was shown to be influential, but including rarer classes did not compromise performance on common classes, providing support for the inclu

  • Journal article
    Ali JR, Blonder BW, Pigot AL, Tobias JAet al., 2023,

    Bird extinctions threaten to cause disproportionate reductions of functional diversity and uniqueness

    , FUNCTIONAL ECOLOGY, Vol: 37, Pages: 162-175, ISSN: 0269-8463
  • Journal article
    Zhu Z, Wang H, Harrison SP, Prentice IC, Qiao S, Tan Set al., 2023,

    Optimality principles explaining divergent responses of alpine vegetation to environmental change

    , Global Change Biology, Vol: 29, Pages: 126-142, ISSN: 1354-1013

    Recent increases in vegetation greenness over much of the world reflect increasing CO2 globally and warming in cold areas. However, the strength of the response to both CO2 and warming in those areas appears to be declining for unclear reasons, contributing to large uncertainties in predicting how vegetation will respond to future global changes. Here, we investigated the changes of satellite-observed peak season absorbed photosynthetically active radiation (Fmax) on the Tibetan Plateau between 1982 and 2016. Although climate trends are similar across the Plateau, we identified robust divergent responses (a greening of 0.31 ± 0.14% year−1 in drier regions and a browning of 0.12 ± 0.08% year−1 in wetter regions). Using an eco-evolutionary optimality (EEO) concept of plant acclimation/adaptation, we propose a parsimonious modelling framework that quantitatively explains these changes in terms of water and energy limitations. Our model captured the variations in Fmax with a correlation coefficient (r) of .76 and a root mean squared error of .12 and predicted the divergent trends of greening (0.32 ± 0.19% year−1) and browning (0.07 ± 0.06% year−1). We also predicted the observed reduced sensitivities of Fmax to precipitation and temperature. The model allows us to explain these changes: Enhanced growing season cumulative radiation has opposite effects on water use and energy uptake. Increased precipitation has an overwhelmingly positive effect in drier regions, whereas warming reduces Fmax in wetter regions by increasing the cost of building and maintaining leaf area. Rising CO2 stimulates vegetation growth by enhancing water-use efficiency, but its effect on photosynthesis saturates. The large decrease in the sensitivity of vegetation to climate reflects a shift from water to energy limitation. Our study demonstrates the potential of EEO approaches to reveal the

  • Journal article
    Shah T, Mashimba FH, Suleiman HO, Mbailwa YS, Savolainen V, Larridon I, Darbyshire Iet al., 2023,

    A taxonomic revision of the ecologically important<i> Ochna</i><i> holstii</i> (Ochnaceae) complex using molecular and morphological data

    , PLANT ECOLOGY AND EVOLUTION, Vol: 156, Pages: 174-200, ISSN: 2032-3913
  • Journal article
    Wang H, Harrison SP, Li M, Prentice IC, Qiao S, Wang R, Xu H, Mengoli G, Peng Y, Yang Yet al., 2022,

    The China plant trait database version 2

    , Scientific Data, Vol: 9, ISSN: 2052-4463

    Plant functional traits represent adaptive strategies to the environment, linked to biophysical and biogeochemical processes and ecosystem functioning. Compilations of trait data facilitate research in multiple fields from plant ecology through to land-surface modelling. Here we present version 2 of the China Plant Trait Database, which contains information on morphometric, physical, chemical, photosynthetic and hydraulic traits from 1529 unique species in 140 sites spanning a diversity of vegetation types. Version 2 has five improvements compared to the previous version: (1) new data from a 4-km elevation transect on the edge of Tibetan Plateau, including alpine vegetation types not sampled previously; (2) inclusion of traits related to hydraulic processes, including specific sapwood conductance, the area ratio of sapwood to leaf, wood density and turgor loss point; (3) inclusion of information on soil properties to complement the existing data on climate and vegetation (4) assessments and flagging the reliability of individual trait measurements; and (5) inclusion of standardized templates for systematical field sampling and measurements.

  • Journal article
    Malhi Y, Riutta T, Wearn OR, Deere NJ, Mitchell SL, Bernard H, Majalap N, Nilus R, Davies ZG, Ewers RM, Struebig MJet al., 2022,

    Logged tropical forests have amplified and diverse ecosystem energetics

    , Nature, Vol: 612, Pages: 707-713, ISSN: 0028-0836

    Old-growth tropical forests are widely recognized as being immensely important for their biodiversity and high biomass1. Conversely, logged tropical forests are usually characterized as degraded ecosystems2. However, whether logging results in a degradation in ecosystem functions is less clear: shifts in the strength and resilience of key ecosystem processes in large suites of species have rarely been assessed in an ecologically integrated and quantitative framework. Here we adopt an ecosystem energetics lens to gain new insight into the impacts of tropical forest disturbance on a key integrative aspect of ecological function: food pathways and community structure of birds and mammals. We focus on a gradient spanning old-growth and logged forests and oil palm plantations in Borneo. In logged forest there is a 2.5-fold increase in total resource consumption by both birds and mammals compared to that in old-growth forests, probably driven by greater resource accessibility and vegetation palatability. Most principal energetic pathways maintain high species diversity and redundancy, implying maintained resilience. Conversion of logged forest into oil palm plantation results in the collapse of most energetic pathways. Far from being degraded ecosystems, even heavily logged forests can be vibrant and diverse ecosystems with enhanced levels of ecological function.

  • Journal article
    Díaz S, Kattge J, Cornelissen JHC, Wright IJ, Lavorel S, Dray S, Reu B, Kleyer M, Wirth C, Prentice IC, Garnier E, Bönisch G, Westoby M, Poorter H, Reich PB, Moles AT, Dickie J, Zanne AE, Chave J, Wright SJ, Sheremetiev SN, Jactel H, Baraloto C, Cerabolini BEL, Pierce S, Shipley B, Casanoves F, Joswig JS, Günther A, Falczuk V, Rüger N, Mahecha MD, Gorné LD, Amiaud B, Atkin OK, Bahn M, Baldocchi D, Beckmann M, Blonder B, Bond W, Bond-Lamberty B, Brown K, Burrascano S, Byun C, Campetella G, Cavender-Bares J, Chapin FS, Choat B, Coomes DA, Cornwell WK, Craine J, Craven D, Dainese M, de Araujo AC, de Vries FT, Domingues TF, Enquist BJ, Fagúndez J, Fang J, Fernández-Méndez F, Fernandez-Piedade MT, Ford H, Forey E, Freschet GT, Gachet S, Gallagher R, Green W, Guerin GR, Gutiérrez AG, Harrison SP, Hattingh WN, He T, Hickler T, Higgins SI, Higuchi P, Ilic J, Jackson RB, Jalili A, Jansen S, Koike F, König C, Kraft N, Kramer K, Kreft H, Kühn I, Kurokawa H, Lamb EG, Laughlin DC, Leishman M, Lewis S, Louault F, Malhado ACM, Manning P, Meir P, Mencuccini M, Messier J, Miller R, Minden V, Molofsky J, Montgomery R, Montserrat-Martí G, Moretti M, Müller S, Niinemets Ü, Ogaya R, Öllerer K, Onipchenko V, Onoda Y, Ozinga WA, Pausas JG, Peco B, Penuelas J, Pillar VD, Pladevall C, Römermann C, Sack L, Salinas N, Sandel B, Sardans J, Schamp B, Scherer-Lorenzen M, Schulze E-D, Schweingruber F, Shiodera S, Sosinski Ê, Soudzilovskaia N, Spasojevic MJ, Swaine E, Swenson N, Tautenhahn S, Thompson K, Totte A, Urrutia-Jalabert R, Valladares F, van Bodegom P, Vasseur F, Verheyen K, Vile D, Violle C, von Holle B, Weigelt P, Weiher E, Wiemann MC, Williams M, Wright J, Zotz Get al., 2022,

    The global spectrum of plant form and function: enhanced species-level trait dataset

    , Scientific Data, Vol: 9, Pages: 1-18, ISSN: 2052-4463

    Here we provide the 'Global Spectrum of Plant Form and Function Dataset', containing species mean values for six vascular plant traits. Together, these traits -plant height, stem specific density, leaf area, leaf mass per area, leaf nitrogen content per dry mass, and diaspore (seed or spore) mass - define the primary axes of variation in plant form and function. The dataset is based on ca. 1 million trait records received via the TRY database (representing ca. 2,500 original publications) and additional unpublished data. It provides 92,159 species mean values for the six traits, covering 46,047 species. The data are complemented by higher-level taxonomic classification and six categorical traits (woodiness, growth form, succulence, adaptation to terrestrial or aquatic habitats, nutrition type and leaf type). Data quality management is based on a probabilistic approach combined with comprehensive validation against expert knowledge and external information. Intense data acquisition and thorough quality control produced the largest and, to our knowledge, most accurate compilation of empirically observed vascular plant species mean traits to date.

  • Journal article
    Buehne HST, Tobias JAA, Durant SMM, Pettorelli Net al., 2022,

    Indirect interactions between climate and cropland distribution shape fire size in West African grasslands

    , Landscape Ecology, Vol: 38, Pages: 1-16, ISSN: 0921-2973

    ContextClimate and land use changes often interact, yet our ability to predict their combined effects on biodiversity is currently limited. In particular, the combined effects of climate and land use on key ecosystem dynamics, such as disturbance regimes, that shape biodiversity across large spatial scales, are poorly understood.ObjectivesWe assess how indirect climate–land use interactions influence disturbance regimes by examining the mechanistic pathways by which climate and proximity to cropland interact to shape fire size in a West African grassland ecosystem, the W-Arly-Pendjari transboundary protected area complex.MethodsWe use remotely sensed indicators of burned area, rainfall, cropland distribution, and vegetation dynamics to test two spatially explicit hypotheses about the interaction between climate and land use effects on fire dynamics.ResultsWe demonstrate that in areas where wet season grass production (which is driven by rainfall) is higher, fires are larger, but that this relationship depends on the distance to cropland. Close to cropland, environmental drivers of fire size (wet season grass production, and progressive loss of fire fuel during the fire season) have little effect on fire size, as fuel breaks induced by cropland limit fire size.

  • Conference paper
    Waziri H, Kalaiarasan G, Wawman R, Hobbs F, Young G, Ransome E, Adcock I, Bhavsar P, Savolainen V, Porter A, Kumar P, Chung KFet al., 2022,

    Characterising SARS-CoV-2 transmission via aerosols and effective sampling methods for surveillance

    , 2022 ERS International Congress, Publisher: European Respiratory Society, ISSN: 0903-1936
  • Journal article
    Geci R, Willis K, Burt A, 2022,

    Gene drive designs for efficient and localisable population suppression using Y-linked editors

    , PLOS GENETICS, Vol: 18, ISSN: 1553-7404
  • 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

  • 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

  • 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>

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