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  • 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>
  • 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.

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