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  • 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>

  • Journal article
    Rosindell J, Manson K, Gumbs R, Pearse WD, Steel Met al., 2022,

    Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage

    <jats:title>A<jats:sc>bstract</jats:sc></jats:title><jats:p>Phylogenetic metrics are essential tools used in the study of ecology, evolution and conservation. Phylogenetic diversity (PD) in particular is one of the most prominent measures of biodiversity, and is based on the idea that biological features accumulate along the edges of phylogenetic trees that are summed. We argue that PD and many other phylogenetic biodiversity metrics fail to capture an essential process that we term attrition. Attrition is the gradual loss of features through causes other than extinction. Here we introduce ‘EvoHeritage’, a generalisation of PD that is founded on the joint processes of accumulation and attrition of features. We argue that whilst PD measures evolutionary history, EvoHeritage is required to capture a more pertinent subset of evolutionary history including only components that have survived attrition. We show that EvoHeritage is not the same as PD on a tree with scaled edges; instead, accumulation and attrition interact in a more complex non-monophyletic way that cannot be captured by edge lengths alone. This leads us to speculate that the one dimensional edge lengths of classic trees may be insufficiently flexible to capture the nuances of evolutionary processes. We derive a measure of EvoHeritage and show that it elegantly reproduces species richness and PD at opposite ends of a continuum based on the intensity of attrition. We demonstrate the utility of EvoHeritage in ecology as a predictor of community productivity compared with species richness and PD. We also show how EvoHeritage can quantify living fossils and resolve their associated controversy. We suggest how the existing calculus of PD-based metrics and other phylogenetic biodiversity metrics can and should be recast in terms of EvoHeritage accumulation and attrition.</jats:p><jats:sec><jats:title>Candidate cover image</jats:title><jats:fig

  • Journal article
    Rubin C-J, Enbody ED, Dobreva MP, Abzhanov A, Davis BW, Lamichhaney S, Pettersson M, Sendell-Price AT, Sprehn CG, Valle CA, Vasco K, Wallerman O, Grant BR, Grant PR, Andersson Let al., 2022,

    Rapid adaptive radiation of Darwin's finches depends on ancestral genetic modules

    , SCIENCE ADVANCES, Vol: 8, ISSN: 2375-2548
  • Journal article
    Barker J, Davies J, Goralczyk M, Patel S, O'Connor J, Evans J, Sharp R, Gollock M, Wood FR, Rosindell J, Bartlett C, Garner BJ, Jones D, Quigley D, Wray Bet al., 2022,

    The distribution, ecology and predicted habitat use of the Critically Endangered angelshark (Squatina squatina) in coastal waters of Wales and the central Irish Sea

    , Journal of Fish Biology, Vol: 101, Pages: 640-658, ISSN: 0022-1112

    The angelshark (Squatina squatina) has the northernmost range of any angel shark species, but there is limited information on its distribution, habitat use and ecology at higher latitudes. To address this, Angel Shark Project: Wales gathered 2231 S. squatina records and 142 anecdotal resources from fishers, coastal communities and archives. These spanned the coastal waters of Wales and the central Irish Sea and were dated from 1812 to 2020, with 97.62% of records within 11.1 km (6 nm) of the coast. Commercial, recreational and charter boat fishers provided the majority of S. squatina records (97.18%), with significantly more sightings from three decades (1970s, 1980s and 1990s) and in the months of September, June, August and July (in descending order). The coastal area between Bardsey Island and Strumble Head had the most S. squatina records (n = 1279), with notable concentrations also found in Carmarthen Bay, Conwy Bay and the Outer Severn Estuary. Species distribution models (SDM) identified four environmental variables that had significant influence on S. squatina distribution, depth, chlorophyll-a concentration, sea surface temperature (SST) and salinity, and these varied between the quarters (Q) of the year. SDM model outputs predicted a larger congruous area of suitable habitat in Q3 (3176 km2) compared to Q2 (2051 km2), with suitability along the three glacial moraines (Sarn Badrig, Sarn-y-Bwch and Sarn Cynfelyn) strongly presented. Comparison of modelled environmental variables at the location of S. squatina records for each Q identified reductions in depth and salinity, and increases in chlorophyll-a and SST when comparing Q2 or Q3 with Q1 or Q4. This shift may suggest S. squatina are making seasonal movements to shallow coastal waters in Q2 and Q3. This is supported by 23 anecdotal resources and may be driven by reproductive behaviour, as there were 85 records of S. squatina individuals ≤60 cm in the dataset, inferred as recently b

  • Journal article
    Cheng S, Jin Y, Harrison S, Quilodrán Casas C, Prentice C, Guo Y-K, Arcucci Ret al., 2022,

    Parameter flexible wildfire prediction using machine learning techniques: forward and inverse modelling

    , Remote Sensing, Vol: 14, ISSN: 2072-4292

    Parameter identification for wildfire forecasting models often relies on case-by-case tuning or posterior diagnosis/analysis, which can be computationally expensive due to the complexity of the forward prediction model. In this paper, we introduce an efficient parameter flexible fire prediction algorithm based on machine learning and reduced order modelling techniques. Using a training dataset generated by physics-based fire simulations, the method forecasts burned area at different time steps with a low computational cost. We then address the bottleneck of efficient parameter estimation by developing a novel inverse approach relying on data assimilation techniques (latent assimilation) in the reduced order space. The forward and the inverse modellings are tested on two recent large wildfire events in California. Satellite observations are used to validate the forward prediction approach and identify the model parameters. By combining these forward and inverse approaches, the system manages to integrate real-time observations for parameter adjustment, leading to more accurate future predictions.

  • Journal article
    Geci R, Willis K, Burt A, 2022,

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

    <jats:title>Abstract</jats:title><jats:p>The sterile insect technique (SIT) has been successful in controlling some pest species but is not practicable for many others due to the large numbers of individuals that need to be reared and released. Previous computer modelling has demonstrated that the release of males carrying a Y-linked editor that kills or sterilises female descendants could be orders of magnitude more efficient than SIT while still remaining spatially restricted, particularly if combined with an autosomal sex distorter. In principle, further gains in efficiency could be achieved by using a self-propagating double drive design, in which each of the two components (the Y-linked editor and the sex ratio distorter) boosted the transmission of the other. To better understand the expected dynamics and impact of releasing constructs of this new design, we have analysed a deterministic population genetic and population dynamic model. Our modelling demonstrates that this design can suppress a population from very low release rates, with no invasion threshold. Importantly, the design can work even if homing rates are low and sex chromosomes are silenced at meiosis, potentially expanding the range of species amenable to such control. Moreover, the predicted dynamics and impacts can be exquisitely sensitive to relatively small (e.g., 25%) changes in allele frequencies in the target population, which could be exploited for sequence-based population targeting. Analysis of published <jats:italic>Anopheles gambiae</jats:italic> genome sequences indicates that even for weakly differentiated populations with an F<jats:sub>ST</jats:sub> of 0.02 there may be thousands of suitably differentiated genomic sites that could be used to restrict the spread and impact of a release. Our proposed design, which extends an already promising development pathway based on Y-linked editors, is therefore a potentially useful addition to the menu

  • Journal article
    Jones S, Bell T, Coleman CM, Harris D, Woodward G, Worledge L, Roberts H, McElhinney L, Aegerter J, Ransome E, Savolainen Vet al., 2022,

    Testing bats in rehabilitation for SARS-CoV-2 before release into the wild

    , Conservation Science and Practice, Vol: 4, ISSN: 2578-4854

    Several studies have suggested SARS-CoV-2 originated from a viral ancestor in bats, but whether transmission occurred directly or via an intermediary host to humans remains unknown. Concerns of spillover of SARS-CoV-2 into wild bat populations are hindering bat rehabilitation and conservation efforts in the United Kingdom and elsewhere. Current protocols state that animals cared for by individuals who have tested positive for SARS-CoV-2 cannot be released into the wild and must be isolated to reduce the risk of transmission to wild populations. Here, we propose a reverse transcription-quantitative polymerase chain reaction (RT-qPCR)-based protocol for detection of SARS-CoV-2 in bats, using fecal sampling. Bats from the United Kingdom were tested following suspected exposure to SARS-CoV-2 and tested negative for the virus. With current UK and international legislation, the identification of SARS-CoV-2 infection in wild animals is becoming increasingly important, and protocols such as the one developed here will help improve understanding and mitigation of SARS-CoV-2 in the future.

  • Journal article
    Sanchez AC, Jones SK, Purvis A, Estrada-Carmona N, De Palma Aet al., 2022,

    Landscape complexity and functional groups moderate the effect of diversified farming on biodiversity: A global meta-analysis

    , AGRICULTURE ECOSYSTEMS & ENVIRONMENT, Vol: 332, ISSN: 0167-8809
  • Journal article
    Marghoub A, Williams CJA, Leite JV, Kirby AC, Kever L, Porro LB, Barrett PM, Bertazzo S, Abzhanov A, Vickaryous M, Herrel A, Evans SE, Moazen Met al., 2022,

    Unravelling the structural variation of lizard osteoderms

    , ACTA BIOMATERIALIA, Vol: 146, Pages: 306-316, ISSN: 1742-7061
  • Journal article
    Rurangwa ML, Niyigaba P, Tobias JA, Whittaker RJet al., 2022,

    Functional and phylogenetic diversity of an agricultural matrix avifauna: The role of habitat heterogeneity in Afrotropical farmland

    , Ecology and Evolution, Vol: 12, ISSN: 2045-7758

    Varied strategies to alleviate the loss of farmland biodiversity have been tested, yet there is still insufficient evidence supporting their effectiveness, especially when considering phylogenetic and functional diversity alongside traditional taxonomic diversity metrics. This conservation challenge is accentuated in the Afrotropics by the rapid agricultural expansion and intensification for the production of cash crops and by a comparative lack of research. In this study, we assessed how farming practices influence avian phylogenetic and functional diversity. We conducted point-count surveys to assess avian diversity in monocultures of tea and mixed crop farming systems surrounding the Nyungwe rainforest in south-west Rwanda, allowing us to investigate the drivers of avian diversity at farm level. Species composition was found to be moderately different between farm types, with mixed crop farms supporting higher phylogenetic diversity than tea plantations. There were no significant seasonal differences in species composition, functional or phylogenetic diversity. Overall, functional diversity did not differ between farm types, but the dispersion of trophic-related traits was significantly higher in mixed crop farms. Both functional and phylogenetic diversity were influenced by floristic diversity, vegetation height, tree number, and elevation to varying degrees. Our results also (i) highlight the role of farmland heterogeneity (e.g., crop species composition, height, and tree cover extent) in encouraging avian functional and phylogenetic diversity in the Afrotropics and (ii) indicate that the generally negative biodiversity impacts of monoculture agriculture can be partially alleviated by extensive agroforestry with an emphasis on indigenous tree species.

  • Journal article
    Aguirre-Gutierrez J, Berenguer E, Menor IO, Bauman D, Corral-Rivas JJ, Guadalupe Nava-Miranda M, Both S, Ndong JE, Ondo FE, Bengone NN, Mihinhou V, Dalling JW, Heineman K, Figueiredo A, Gonzalez-M R, Norden N, Hurtado-M AB, Gonzalez D, Salgado-Negret B, Reis SM, Moraes de Seixas MM, Farfan-Rios W, Shenkin A, Riutta T, Girardin CAJ, Moore S, Abernethy K, Asner GP, Bentley LP, Burslem DFRP, Cernusak LA, Enquist BJ, Ewers RM, Ferreira J, Jeffery KJ, Joly CA, Marimon-Junior BH, Martin RE, Morandi PS, Phillips OL, Bennett AC, Lewis SL, Quesada CA, Marimon BS, Kissling WD, Silman M, Teh YA, White LJT, Salinas N, Coomes DA, Barlow J, Adu-Bredu S, Malhi Yet al., 2022,

    Functional susceptibility of tropical forests to climate change

    , NATURE ECOLOGY & EVOLUTION, Vol: 6, Pages: 878-+, ISSN: 2397-334X
  • Journal article
    Christensen AK, Piggott M, van Sebille E, van Reeuwijk M, Pawar Set al., 2022,

    Investigating microscale patchiness of motile microbes under turbulence in a simulated convective mixed layer

    , PLOS COMPUTATIONAL BIOLOGY, Vol: 18, ISSN: 1553-734X
  • Journal article
    Parra-Sanchez E, Banks-Leite C, 2022,

    Value of human-modified forests for the conservation of canopy epiphytes

    , BIOTROPICA, Vol: 54, Pages: 958-968, ISSN: 0006-3606
  • Journal article
    Cruz-Silva E, Harrison SP, Marinova-Wolff E, Prentice ICet al., 2022,

    A new method based on surface- sample pollen data for reconstructing palaeovegetation patterns.

    , Journal of Biogeography, Vol: 49, Pages: 1381-1396, ISSN: 0305-0270

    Aim: Amongst the various techniques available to reconstruct past vegetation at regional to continental scales, biomisation has been the most widely used because it does not require an extensive modern pollen data set. However, it has well well-known limitations including its dependence on expert judgement for the assignment of pollen taxa to plant functional types (PFTs) and PFTs to biomes. Here we present a new method that combines the strengths of biomisation with those of the alternative dissimilarity-based techniques. This new technique quantifies the likelihood that a sample belongs to a given biome, and allows discrimination of non-analogue vegetation types. Location: The Eastern Mediterranean-Black Sea Caspian Corridor (EMBSeCBIO) region, 28°-49°N, 20°- 62°E. Methods: Modern pollen samples assigned to biomes based on potential natural vegetation data, are used to characterize biomes according to the within-biome means and standard deviations of the abundances of each taxon. These are used to calculate a dissimilarity index between any given pollen sample and every biome, and thus assign a pollen sample to the most likely biome. We also calculate a threshold value for each biome which identifies samples that fall outside the acceptable range of likelihoods for biome assignment and hence can be used to distinguish non-analogue vegetation. We have applied the new technique to the EMBSeCBIO region to compare the performance of the new method with existing reconstructions. Results: The technique captured changes in the importance of individual taxa along environmental gradients. The balanced accuracy obtained for the EMBSeCBIO region using the new method was better than that obtained using biomisation (77% versus 65%). When the method was applied to high resolution fossil records, 70% of the evaluated entities showed more temporally stable biome assignments than obtained with the biomisation method. The technique also identifies likely non analogu

  • Journal article
    Weeks BC, O'Brien BK, Chu JJ, Claramunt S, Sheard C, Tobias JAet al., 2022,

    Morphological adaptations linked to flight efficiency and aerial lifestyle determine natal dispersal distance in birds

    , Functional Ecology, Vol: 36, Pages: 1681-1689, ISSN: 0269-8463

    Natal dispersal—the movement from birthplace to breeding location—is often considered the most significant dispersal event in an animal's lifetime. Natal dispersal distances may be shaped by a variety of intrinsic and extrinsic factors, and remain poorly quantified in most groups, highlighting the need for indices that capture variation in dispersal among species.In birds, it is hypothesized that dispersal distance can be predicted by flight efficiency, which can be estimated using wing morphology. However, the use of morphological indices to predict dispersal remains contentious and the mechanistic links between flight efficiency and natal dispersal are unclear.Here, we use phylogenetic comparative models to test whether hand-wing index (HWI, a morphological proxy for wing aspect ratio) predicts natal dispersal distance across a global sample of 114 bird species. In addition, we assess whether HWI is correlated with flight usage in foraging and daily routines.We find that HWI is a strong predictor of both natal dispersal distance and a more aerial lifestyle.Our results support the use of HWI as a valid proxy for relative natal dispersal distance, and also suggest that evolutionary adaptation to aerial lifestyles is a major factor connecting flight efficiency with patterns of natal dispersal.

  • Journal article
    Cheng S, Jin Y, Harrison SP, Quilodran-Casas C, Prentice IC, Guo Y-K, Arcucci Ret al., 2022,

    Parameter flexible wildfire prediction using machine learning techniques:forward and inverse modelling

    , Remote Sensing, ISSN: 2072-4292
  • Journal article
    Iglesias-Carrasco M, Tobias JA, Duchene DA, 2022,

    Bird lineages colonizing urban habitats have diversified at high rates across deep time

    , Global Ecology and Biogeography, Vol: 31, Pages: 1784-1793, ISSN: 1466-822X

    AimUrbanization exposes species to novel ecological conditions. Some species thrive in urban areas, whereas many others are excluded from these human-made environments. Previous analyses suggest that the ability to cope with rapid environmental change is associated with long-term patterns of diversification, but whether the suite of traits associated with the ability to colonize urban environments is linked to this process remains poorly understood.LocationWorld.Time periodCurrent.Major taxa studiedPasserine birds.MethodsWe applied macroevolutionary models to a large dataset of passerine birds to compare the evolutionary history of urban-tolerant species with that of urban-avoidant species. Specifically, we examined models of state-dependent speciation and extinction to assess the macroevolution of urban tolerance as a binary trait, in addition to models of quantitative trait-dependent diversification based on relative urban abundance. We also ran simulation-based model assessments to explore potential sources of bias.ResultsWe provide evidence that historically, species with traits promoting urban colonization have undergone faster diversification than urban-avoidant species, indicating that urbanization favours clades with a historical tendency towards rapid speciation or reduced extinction. In addition, we find that past transitions towards states that currently impede urban colonization by passerines have been more frequent than in the opposite direction. Furthermore, we find a portion of urban-avoidant passerines to be recent and to undergo fast diversification. All highly supported models give this result consistently.Main conclusionsUrbanization is mainly associated with the loss of lineages that are inherently more vulnerable to extinction over deep time, whereas cities tend to be colonized by less vulnerable lineages, for which urbanization might be neutral or positive in terms of longer-term diversification. Urban avoidance is associated with high rates of

  • Journal article
    Keenan TFC, Luo X, De Kauwe MG, Medlyn BE, Prentice IC, Stocker BD, Smith NG, Terrer C, Wang H, Zhang Y, Zhou Set al., 2022,

    A constraint on historic growth in global photosynthesis due to increasing CO<sub>2</sub> (Retraction of Vol 600, Pg 253, 2021)

    , NATURE, Vol: 606, Pages: 420-420, ISSN: 0028-0836
  • Journal article
    Banks-Leite C, Betts MG, Ewers RM, Orme CDL, Pigot ALet al., 2022,

    The macroecology of landscape ecology

    , Trends in Ecology and Evolution, Vol: 37, ISSN: 0169-5347

    One of landscape ecology's main goals is to unveil how biodiversity is impacted by habitat transformation. However, the discipline suffers from significant context dependency in observed spatial and temporal trends, hindering progress towards understanding the mechanisms driving species declines and preventing the development of accurate estimates of future biodiversity change. Here, we discuss recent evidence that populations' and species' responses to habitat change at the landscape scale are modulated by factors and processes occurring at macroecological scales, such as historical disturbance rates, distance to geographic range edges, and climatic suitability. We suggest that placing landscape ecology studies in a macroecological lens will help to explain seemingly inconsistent results and will ultimately create better predictive models to help mitigate the biodiversity crisis.

  • Journal article
    Wang H, Wang R, Harrison SP, Prentice ICet al., 2022,

    Leaf morphological traits as adaptations to multiple climate gradients

    , Journal of Ecology, Vol: 110, Pages: 1344-1355, ISSN: 0022-0477

    1. Leaf morphological traits vary systematically along climatic gradients. However, recent studies in plant functional ecology have mainly analysed quantitative traits, while numerical models of species distributions and vegetation function have focused on traits associated with resource acquisition; both ignore the wider functional significance of leaf morphology.2. A data set comprising 22 leaf morphological traits for 662 woody species from 92 sites, representing all biomes present in China, was subjected to multivariate analysis in order to identify leading dimensions of trait covariation (correspondence analysis), quantify climatic and phylogenetic contributions (canonical correspondence analysis with variation partitioning), and characterize co-occurring trait syndromes (k-means clustering) and their climatic preferences. 3. Three axes accounted for > 20% of trait variation in both evergreen and deciduous species. Moisture index, precipitation seasonality and growing-season temperature accounted for 8–10% of trait variation; family 15–32%. Microphyll or larger, mid- to dark green leaves with drip-tips in wetter climates contrasted with nanophyll or smaller glaucous leaves without drip-tips in drier climates. Thick, entire leaves in less seasonal climates contrasted with thin, marginal dissected, aromatic, and involute/revolute leaves in more seasonal climates. Thick, involute, hairy leaves in colder climates contrasted with thin leaves with marked surface structures (surface patterning) in warmer climates. Distinctive trait clusters were linked to the driest and most seasonal climates, for example the clustering of picophyll, fleshy and succulent leaves in the driest climates and leptophyll, linear, dissected, revolute or involute, and aromatic leaves in regions with highly seasonal rainfall. Several trait clusters co-occurred in wetter climates, including clusters characterised by microphyll, moderately thick, patent, and entire leaves or notop

  • Journal article
    Deere NJ, Bicknell JE, Mitchell SL, Afendy A, Baking EL, Bernard H, Chung AYC, Ewers RM, Heroin H, Joseph N, Lewis OT, Luke SH, Milne S, Fikri AH, Parrett JM, Payne M, Rossiter SJ, Vairappan CS, Vian CV, Wilkinson CL, Williamson J, Wong ABH, Slade EM, Davies ZG, Struebig MJet al., 2022,

    Riparian buffers can help mitigate biodiversity declines in oil palm agriculture

    , Frontiers in Ecology and the Environment, Vol: 20, Pages: 459-466, ISSN: 1540-9295

    Agricultural expansion is a primary driver of biodiversity decline in forested regions of the tropics. Consequently, it is important to understand the conservation value of remnant forests in production landscapes. In a tropical landscape dominated by oil palm (Elaeis guineensis), we characterized faunal communities across eight taxa occurring within riparian forest buffers, which are legally protected alongside rivers, and compared them to nearby recovering logged forest. Buffer width was the main predictor of species richness and abundance, with widths of 40–100 m on each side of the river supporting broadly equivalent levels of biodiversity as compared to logged forest. However, width responses varied markedly among taxa, and buffers often lacked forest-dependent species. Much wider buffers than are currently mandated are needed to safeguard most species. The largest biodiversity gains are achieved by increasing relatively narrow buffers. To provide optimal conservation outcomes in tropical production landscapes, we encourage policy makers to prescribe width requirements for key taxa and different landscape contexts.

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