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  • Journal article
    Dearden RP, den Blaauwen JL, Sansom IJ, Burrow CJ, Davidson RG, Newman MJ, Ko A, Brazeau MDet al., 2021,

    A revision of Vernicomacanthus Miles with comments on the characters of stem-group chondrichthyans

    , PAPERS IN PALAEONTOLOGY, Vol: 7, Pages: 1949-1976, ISSN: 2056-2799
  • Journal article
    Liang C, Marghoub A, Kever L, Bertazzo S, Abzhanov A, Vickaryous M, Herrel A, Evans SE, Moazen Met al., 2021,

    Lizard osteoderms - Morphological characterisation, biomimetic design and manufacturing based on three species

    , BIOINSPIRATION & BIOMIMETICS, Vol: 16, ISSN: 1748-3182
  • Journal article
    Folkard-Tapp H, Banks-Leite C, Cavan EL, 2021,

    Nature-based Solutions to tackle climate change and restore biodiversity

    , JOURNAL OF APPLIED ECOLOGY, Vol: 58, Pages: 2344-2348, ISSN: 0021-8901
  • Journal article
    Stachewicz JD, Fountain-Jones NM, Koontz A, Woolf H, Pearse WD, Gallinat ASet al., 2021,

    Strong trait correlation and phylogenetic signal in North American ground beetle (Carabidae) morphology

    , ECOSPHERE, Vol: 12, ISSN: 2150-8925
  • Journal article
    Lechon-Alonso P, Clegg T, Cook J, Smith TP, Pawar Set al., 2021,

    The role of competition versus cooperation in microbial community coalescence

    , PLOS COMPUTATIONAL BIOLOGY, Vol: 17, ISSN: 1553-734X
  • Journal article
    Gallinat AS, Ellwood ER, Heberling JM, Miller-Rushing AJ, Pearse WD, Primack RBet al., 2021,

    Macrophenology: insights into the broad-scale patterns, drivers, and consequences of phenology

    , AMERICAN JOURNAL OF BOTANY, Vol: 108, Pages: 2112-2126, ISSN: 0002-9122
  • Journal article
    Overcast I, Ruffley M, Rosindell J, Harmon L, Borges PA, Emerson BC, Etienne RS, Gillespie R, Krehenwinkel H, Mahler DL, Massol F, Parent CE, Patino J, Peter B, Week B, Wagner C, Hickerson MJ, Rominger Aet al., 2021,

    A unified model of species abundance, genetic diversity, and functional diversity reveals the mechanisms structuring ecological communities

    , Molecular Ecology Resources, Vol: 21, Pages: 2782-2800, ISSN: 1471-8278

    Biodiversity accumulates hierarchically by means of ecological and evolutionary processes and feedbacks. Within ecological communities drift, dispersal, speciation, and selection operate simultaneously to shape patterns of biodiversity. Reconciling the relative importance of these is hindered by current models and inference methods, which tend to focus on a subset of processes and their resulting predictions. Here we introduce massive ecoevolutionary synthesis simulations (MESS), a unified mechanistic model of community assembly, rooted in classic island biogeography theory, which makes temporally explicit joint predictions across three biodiversity data axes: (i) species richness and abundances, (ii) population genetic diversities, and (iii) trait variation in a phylogenetic context. Using simulations we demonstrate that each data axis captures information at different timescales, and that integrating these axes enables discriminating among previously unidentifiable community assembly models. MESS is unique in generating predictions of community-scale genetic diversity, and in characterizing joint patterns of genetic diversity, abundance, and trait values. MESS unlocks the full potential for investigation of biodiversity processes using multidimensional community data including a genetic component, such as might be produced by contemporary eDNA or metabarcoding studies. We combine MESS with supervised machine learning to fit the parameters of the model to real data and infer processes underlying how biodiversity accumulates, using communities of tropical trees, arthropods, and gastropods as case studies that span a range of data availability scenarios, and spatial and taxonomic scales.

  • Journal article
    Qiao S, Wang H, Prentice IC, Harrison Set al., 2021,

    Optimality-based modelling of climate impacts on global potential wheat yield.

    , Environmental Research Letters, Vol: 16, Pages: 1-13, ISSN: 1748-9326

    Evaluation of potential crop yields is important for global food security assessment because it represents the biophysical 'ceiling' determined by variety, climate and ambient CO2. Statistical approaches have limitations when assessing future potential yields, while large differences between results obtained using process-based models reflect uncertainties in model parameterisations. Here we simulate the potential yield of wheat across the present-day wheat-growing areas, using a new global model that couples a parameter-sparse, optimality-based representation of gross primary production (GPP) to empirical functions relating GPP, biomass production and yield. The model reconciles the transparency and parsimony of statistical models with a mechanistic grounding in the standard model of C3 photosynthesis, and seamlessly integrates photosynthetic acclimation and CO2 fertilization effects. The model accurately predicted the CO2 response observed in FACE experiments, and captured the magnitude and spatial pattern of EARTHSTAT 'attainable yield' data in 2000 CE better than process-based models in ISIMIP. Global simulations of potential yield during 1981–2016 were analysed in parallel with global historical data on actual yield, in order to test the hypothesis that environmental effects on modelled potential yields would also be shown in observed actual yields. Higher temperatures are thereby shown to have negatively affected (potential and actual) yields over much of the world. Greater solar radiation is associated with higher yields in humid regions, but lower yields in semi-arid regions. Greater precipitation is associated with higher yields in semi-arid regions. The effect of rising CO2 is reflected in increasing actual yield, but trends in actual yield are stronger than the CO2 effect in many regions, presumably because they also include effects of crop breeding and improved management. We present this hybrid modelling approach as a useful addition to the toolki

  • Journal article
    Tan S, Wang H, Prentice IC, Yang Ket al., 2021,

    Land-surface evapotranspiration from a first-principles primary production model

    , Environmental Research Letters, Vol: 16, Pages: 1-11, ISSN: 1748-9326

    Evapotranspiration (ET) links the water and carbon cycles in the atmosphere, hydrosphere, and biosphere. In this study, we develop an ET modelling framework based on the idea that the transpiration and carbon uptake are closely coupled, as predicted by the 'least-cost hypothesis' that canopy conductance acclimates to environmental variations. According to eco-evolutionary optimality theory, which has been previously applied in monitoring and modelling land-surface processes, the total costs (per unit carbon fixed) for maintaining transpiration and carboxylation capacities should be minimized. We calculate gross primary production (GPP) assuming that the light- and Rubisco-limited rates of photosynthesis, described by the classical biochemical model of photosynthesis, are coordinated on an approximately weekly time scale. Transpiration (T) is then calculated via acclimated canopy conductance, with no need for plant type- or biome-specific parameters. ET is finally calculated from T using an empirical function of light, temperature, soil water content and foliage cover to predict the T/ET ratio at each site. The GPP estimates were well supported by (weekly) GPP data at 20 widely distributed eddy-covariance flux sites (228 site-years), with correlation coefficients (r) = 0.81 and root-mean-square error (RMSE) = 18.7 gC week−1 and Nash-Sutcliffe efficiency (NSE) = 0.61. Predicted ET was also well supported, with r =0.85, RMSE = 5.5 mm week–1 and NSE = 0.66. Estimated T/ET ratios (0.43–0.74) showed significant positive relationships to radiation, precipitation and green vegetation cover and negative relationships to temperature and modelled T (r = 0.84). Aspects of this framework could be improved, notably the estimation of T/ET. Nonetheless, we see the application of eco-evolutionary principles as a promising direction for water resources research, eliminating the uncertainty introduced by the need to specify multiple parameters, and leveraging the pow

  • Journal article
    De Palma A, Hoskins A, Gonzalez RE, Borger L, Newbold T, Sanchez-Ortiz K, Ferrier S, Purvis Aet al., 2021,

    Annual changes in the Biodiversity Intactness Index in tropical and subtropical forest biomes, 2001-2012

    , SCIENTIFIC REPORTS, Vol: 11, ISSN: 2045-2322
  • Journal article
    Stemkovski M, Bell JR, Ellwood ER, Inouye BD, Kobori H, Lee SD, Lloyd-Evans T, Primack RB, Templ B, Pearse WDet al., 2021,

    Disorder or a new order: how climate change affects phenological variability

    <jats:title>Abstract</jats:title><jats:p>Advancing spring phenology is a well-documented consequence of anthropogenic climate change, but it is not well understood how climate change will affect the variability of phenology year-to-year. Species’ phenological timings reflect adaptation to a broad suite of abiotic needs (e.g. thermal energy) and biotic interactions (e.g. predation and pollination), and changes in patterns of variability may disrupt those adaptations and interactions. Here, we present a geographically and taxonomically broad analysis of phenological shifts, temperature sensitivity, and changes in inter-annual variance encompassing nearly 10,000 long-term phenology time-series representing over 1,000 species across much of the northern hemisphere. We show that early-season species in colder and less seasonal regions were the most sensitive to temperature change and had the least variable phenologies. The timings of leaf-out, flowering, insect first-occurrence, and bird arrival have all shifted earlier and tend to be less variable in warmer years. This has led leaf-out and flower phenology to become moderately but significantly less variable over time. These simultaneous changes in phenological averages and the variation around them have the potential to influence mismatches among interacting species that are difficult to anticipate if shifts in average are studied in isolation.</jats:p>

  • Working paper
    Smith TP, Stemkovski M, Koontz A, Pearse WDet al., 2021,

    AREAdata: a worldwide climate dataset averaged across spatial units at different scales through time

    <jats:title>ABSTRACT</jats:title><jats:p>In an era of increasingly cross-discipline collaborative science, it is imperative to produce data resources which can be quickly and easily utilised by non-specialists. In particular, climate data often require heavy processing before they can be used for analyses. Here we describe AREAdata, a free-to-use online global climate dataset, pre-processed to provide the averages of various climate variables across differing administrative units (<jats:italic>e</jats:italic>.<jats:italic>g</jats:italic>., countries, states). These are daily estimates, based on the Copernicus Climate Data Store’s ERA-5 data, regularly updated to the near-present and provided as direct downloads from our website (<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://pearselab.github.io/areadata/">https://pearselab.github.io/areadata/</jats:ext-link>). The daily climate estimates from AREAdata are consistent with other openly available data, but at much finer-grained spatial and temporal scales than available elsewhere. AREAdata complements the existing suite of climate resources by providing these data in a form more readily usable by researchers unfamiliar with GIS data-processing methods, and we anticipate these resources being of particular use to environmental and epidemiological researchers.</jats:p>

  • Journal article
    Heath R, Orme DS, Sethi CSL, Ewers RM, Picinali Let al., 2021,

    How index selection, compression, and recording schedule impact the description of ecological soundscapes

    , Evolutionary Ecology, Vol: 11, Pages: 13206-13217, ISSN: 0269-7653

    Acoustic indices derived from environmental soundscape recordings are being used to monitor ecosystem health and vocal animal biodiversity. Soundscape data can quickly become very expensive and difficult to manage, so data compression or temporal down-sampling are sometimes employed to reduce data storage and transmission costs. These parameters vary widely between experiments, with the consequences of this variation remaining mostly unknown.We analyse field recordings from North-Eastern Borneo across a gradient of historical land use. We quantify the impact of experimental parameters (MP3 compression, recording length and temporal subsetting) on soundscape descriptors (Analytical Indices and a convolutional neural net derived AudioSet Fingerprint). Both descriptor types were tested for their robustness to parameter alteration and their usability in a soundscape classification task.We find that compression and recording length both drive considerable variation in calculated index values. However, we find that the effects of this variation and temporal subsetting on the performance of classification models is minor: performance is much more strongly determined by acoustic index choice, with Audioset fingerprinting offering substantially greater (12%–16%) levels of classifier accuracy, precision and recall.We advise using the AudioSet Fingerprint in soundscape analysis, finding superior and consistent performance even on small pools of data. If data storage is a bottleneck to a study, we recommend Variable Bit Rate encoded compression (quality = 0) to reduce file size to 23% file size without affecting most Analytical Index values. The AudioSet Fingerprint can be compressed further to a Constant Bit Rate encoding of 64 kb/s (8% file size) without any detectable effect. These recommendations allow the efficient use of restricted data storage whilst permitting comparability of results between different studies.

  • Journal article
    Fuchs S, Garrood WT, Beber A, Hammond A, Galizi R, Gribble M, Morselli G, Hui T-YJ, Willis K, Kranjc N, Burt A, Crisanti A, Nolan T, Malik HSet al., 2021,

    Resistance to a CRISPR-based gene drive at an evolutionarily conserved site is revealed by mimicking genotype fixation

    , PLoS Genetics, Vol: 17, Pages: 1-19, ISSN: 1553-7390

    CRISPR-based homing gene drives can be designed to disrupt essential genes whilst biasing their own inheritance, leading to suppression of mosquito populations in the laboratory. This class of gene drives relies on CRISPR-Cas9 cleavage of a target sequence and copying (‘homing’) therein of the gene drive element from the homologous chromosome. However, target site mutations that are resistant to cleavage yet maintain the function of the essential gene are expected to be strongly selected for. Targeting functionally constrained regions where mutations are not easily tolerated should lower the probability of resistance. Evolutionary conservation at the sequence level is often a reliable indicator of functional constraint, though the actual level of underlying constraint between one conserved sequence and another can vary widely. Here we generated a novel adult lethal gene drive (ALGD) in the malaria vector Anopheles gambiae, targeting an ultra-conserved target site in a haplosufficient essential gene (AGAP029113) required during mosquito development, which fulfils many of the criteria for the target of a population suppression gene drive. We then designed a selection regime to experimentally assess the likelihood of generation and subsequent selection of gene drive resistant mutations at its target site. We simulated, in a caged population, a scenario where the gene drive was approaching fixation, where selection for resistance is expected to be strongest. Continuous sampling of the target locus revealed that a single, restorative, in-frame nucleotide substitution was selected. Our findings show that ultra-conservation alone need not be predictive of a site that is refractory to target site resistance. Our strategy to evaluate resistance in vivo could help to validate candidate gene drive targets for their resilience to resistance and help to improve predictions of the invasion dynamics of gene drives in field populations.

  • Journal article
    Rother L, Kraft N, Smith DB, el Jundi B, Gill RJ, Pfeiffer Ket al., 2021,

    A micro-CT-based standard brain atlas of the bumblebee

    , Cell and Tissue Research, Vol: 386, Pages: 29-45, ISSN: 0302-766X

    <jats:title>Abstract</jats:title><jats:p>In recent years, bumblebees have become a prominent insect model organism for a variety of biological disciplines, particularly to investigate learning behaviors as well as visual performance. Understanding these behaviors and their underlying neurobiological principles requires a clear understanding of brain anatomy. Furthermore, to be able to compare neuronal branching patterns across individuals, a common framework is required, which has led to the development of 3D standard brain atlases in most of the neurobiological insect model species. Yet, no bumblebee 3D standard brain atlas has been generated. Here we present a brain atlas for the buff-tailed bumblebee <jats:italic>Bombus terrestris</jats:italic> using micro-computed tomography (micro-CT) scans as a source for the raw data sets, rather than traditional confocal microscopy, to produce the first ever micro-CT-based insect brain atlas. We illustrate the advantages of the micro-CT technique, namely, identical native resolution in the three cardinal planes and 3D structure being better preserved. Our <jats:italic>Bombus terrestris</jats:italic> brain atlas consists of 30 neuropils reconstructed from ten individual worker bees, with micro-CT allowing us to segment neuropils completely intact, including the lamina, which is a tissue structure often damaged when dissecting for immunolabeling. Our brain atlas can serve as a platform to facilitate future neuroscience studies in bumblebees and illustrates the advantages of micro-CT for specific applications in insect neuroanatomy.</jats:p>

  • Journal article
    Smith TP, Clegg T, Bell T, Pawar Set al., 2021,

    Systematic variation in the temperature dependence of bacterial carbon use efficiency

    , ECOLOGY LETTERS, Vol: 24, Pages: 2123-2133, ISSN: 1461-023X
  • Journal article
    Hui T-YJ, Brenas JH, Burt A, 2021,

    Contemporary Ne estimation using temporally spaced data with linked loci

    , Molecular Ecology Resources, Vol: 21, Pages: 2221-2230, ISSN: 1471-8278

    The contemporary effective population size Ne is important in many disciplines including population genetics, conservation science and pest management. One of the mostpopular methods of estimating this quantity uses temporal changes in allele frequencydue to genetic drift. A significant assumption of the existing methods is the independence among loci while constructing confidence intervals (CI), which restricts the typesof species or genetic data applicable to the methods. Although genetic linkage doesnot bias point Ne estimates, applying these methods to linked loci can yield unreliableCI that are far too narrow. We extend the current methods to enable the use of manylinked loci to produce precise contemporary Ne estimates, while preserving the targeted CI width and coverage. This is achieved by deriving the covariance of changes inallele frequency at linked loci in the face of recombination and sampling errors, suchthat the extra sampling variance due to between-locus correlation is properly handled. Extensive simulations are used to verify the new method. We apply the methodto two temporally spaced genomic data sets of Anopheles mosquitoes collected froma cluster of villages in Burkina Faso between 2012 and 2014. With over 33,000 linkedloci considered, the Ne estimate for Anopheles coluzzii is 9,242 (95% CI 5,702–24,282),and for Anopheles gambiae it is 4,826 (95% CI 3,602–7,353).

  • Journal article
    Daniel F, Prentice IC, Gallagher R, Wenk E, Bloomfield K, Dong Net al., 2021,

    AusTraits, a curated plant trait database for the Australian flora.

    , Scientific Data, Vol: 8, Pages: 1-20, ISSN: 2052-4463

    We introduce the AusTraits database - a compilation of values of plant traits for taxa in theAustralian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across28640 taxa from field campaigns, published literature, taxonomic monographs, andindividual taxon descriptions. Traits vary in scope from physiological measures ofperformance (e.g. photosynthetic gas exchange, water-use efficiency) to morphologicalattributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecologicalvariation. AusTraits contains curated and harmonised individual- and species-levelmeasurements coupled to, where available, contextual information on site properties andexperimental conditions. This article provides information on version 3.0.2 of AusTraitswhich contains data for 997808 trait-by-taxon combinations. We envision AusTraits as anongoing collaborative initiative for easily archiving and sharing trait data and also providesa template for other national or regional initiatives globally to fill persistent gaps in traitknowledge.

  • Journal article
    Kordas R, Pawar S, Woodward G, O'Gorman Eet al., 2021,

    Metabolic plasticity can amplify ecosystem responses to global warming

    <jats:title>Abstract</jats:title> <jats:p>Organisms have the capacity to alter their physiological response to warming through acclimation or adaptation, but empirical evidence for this metabolic plasticity across species within food webs is lacking, and a generalisable framework does not exist for modelling its ecosystem-level consequences. Here we show that the ability of organisms to raise their metabolic rate following chronic exposure to warming decreases with increasing body size. Chronic exposure to higher temperatures also increases the sensitivity of organisms to short-term warming, irrespective of their body size. A mathematical model parameterised with these findings shows that metabolic plasticity could account for an additional 60% of ecosystem energy flux with just +2 °C of warming. This could explain why ecosystem respiration continues to rise in long-term warming experiments and highlights the need to embed metabolic plasticity in predictive models of global warming impacts on ecosystems.</jats:p>

  • Journal article
    Harrison S, Cramer W, Franklin O, Prentice IC, Wang H, Brannstrom A, de Boer H, Dieckmann U, Joshi J, Keenan T, Lavergne A, Manzoni S, Mengoli G, Morfopoulos C, Penuelas J, Dietsch S, Rebel K, Ryu Y, Smith N, Stocker B, Wright Iet al., 2021,

    Eco-evolutionary optimality as a means to improve vegetation and land-surface models

    , New Phytologist, Vol: 231, Pages: 2125-2141, ISSN: 0028-646X

    Global vegetation and land-surface models embody interdisciplinary scientific understanding of the behaviour of plants and ecosystems, and are indispensable to project the impacts of environmental change on vegetation and the interactions between vegetation and climate. However, systematic errors and persistently large differences among carbon and water cycle projections by different models highlight the limitations of current process formulations. In this review, focusing on core plant functions in the terrestrial carbon and water cycles, we show how unifying hypotheses derived from eco-evolutionary optimality (EEO) principles can provide novel, parameter-sparse representations of plant and vegetation processes. We present case studies that demonstrate how EEO generate parsimonious representations of core, leaf-level processes that are individually testable and supported by evidence. EEO approaches to photosynthesis and primary production, dark respiration, and stomatal behaviour are ripe for implementation in global models. EEO approaches to other important traits, including the leaf economics spectrum and applications of EEO at the community level are active research areas. Independently tested modules emerging from EEO studies could profitably be integrated into modelling frameworks that account for the multiple time scales on which plants and plant communities adjust to environmental change.

  • Journal article
    Tudge SJ, Purvis A, De Palma A, 2021,

    The impacts of biofuel crops on local biodiversity: a global synthesis

    , BIODIVERSITY AND CONSERVATION, Vol: 30, Pages: 2863-2883, ISSN: 0960-3115
  • Journal article
    Hordley LA, Gillings S, Petchey OL, Tobias JA, Oliver THet al., 2021,

    Diversity of response and effect traits provides complementary information about avian community dynamics linked to ecological function

    , Functional Ecology, Vol: 35, Pages: 1938-1950, ISSN: 0269-8463

    Functional diversity metrics based on species traits are widely used to investigate ecosystem functioning. In theory, such metrics have different implications depending on whether they are calculated from traits mediating responses to environmental change (response traits) or those regulating function (effect traits), yet trait choice in diversity metrics is rarely scrutinized.Here, we compile effect and response traits for British bird species supplying two key ecological services—seed dispersal and insect predation—to assess the relationship between functional diversity and both mean and stability of community abundance over time.As predicted, functional diversity correlates with stability in community abundance of seed dispersers when calculated using response traits. However, we found a negative relationship between functional diversity and mean community abundance of seed dispersers when calculated using effect traits. Subsequently, when combining all traits together, we found inconsistent results with functional diversity correlating with reduced stability in insectivores, but greater stability in seed dispersers.Our findings suggest that trait choice should be considered more carefully when applying such metrics in ecosystem management.

  • Journal article
    Culina A, Adriaensen F, Bailey LD, Burgess MD, Charmantier A, Cole EF, Eeva T, Matthysen E, Nater CR, Sheldon BC, Saether B-E, Vriend SJG, Zajkova Z, Adamík P, Aplin LM, Angulo E, Artemyev A, Barba E, Barišić S, Belda E, Bilgin CC, Bleu J, Both C, Bouwhuis S, Branston CJ, Broggi J, Burke T, Bushuev A, Camacho C, Campobello D, Canal D, Cantarero A, Caro SP, Cauchoix M, Chaine A, Cichoń M, Ćiković D, Cusimano CA, Deimel C, Dhondt AA, Dingemanse NJ, Doligez B, Dominoni DM, Doutrelant C, Drobniak SM, Dubiec A, Eens M, Einar Erikstad K, Espín S, Farine DR, Figuerola J, Kavak Gülbeyaz P, Grégoire A, Hartley IR, Hau M, Hegyi G, Hille S, Hinde CA, Holtmann B, Ilyina T, Isaksson C, Iserbyt A, Ivankina E, Kania W, Kempenaers B, Kerimov A, Komdeur J, Korsten P, Král M, Krist M, Lambrechts M, Lara CE, Leivits A, Liker A, Lodjak J, Mägi M, Mainwaring MC, Mänd R, Massa B, Massemin S, Martínez-Padilla J, Mazgajski TD, Mennerat A, Moreno J, Mouchet A, Nakagawa S, Nilsson J-Å, Nilsson JF, Cláudia Norte A, van Oers K, Orell M, Potti J, Quinn JL, Réale D, Kristin Reiertsen T, Rosivall B, Russell AF, Rytkönen S, Sánchez-Virosta P, Santos ESA, Schroeder J, Senar JC, Seress G, Slagsvold T, Szulkin M, Teplitsky C, Tilgar V, Tolstoguzov A, Török J, Valcu M, Vatka E, Verhulst S, Watson H, Yuta T, Zamora-Marín JM, Visser MEet al., 2021,

    Connecting the data landscape of long-term ecological studies: The SPI-Birds data hub.

    , Journal of Animal Ecology, Vol: 90, Pages: 2147-2160, ISSN: 0021-8790

    The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long-term studies of individually marked animals are not an exception. These studies are especially important as instrumental for understanding evolutionary and ecological processes in the wild. Furthermore, their number and global distribution provides a unique opportunity to assess the generality of patterns and to address broad-scale global issues (e.g. climate change). To solve data integration issues and enable a new scale of ecological and evolutionary research based on long-term studies of birds, we have created the SPI-Birds Network and Database (www.spibirds.org)-a large-scale initiative that connects data from, and researchers working on, studies of wild populations of individually recognizable (usually ringed) birds. Within year and a half since the establishment, SPI-Birds has recruited over 120 members, and currently hosts data on almost 1.5 million individual birds collected in 80 populations over 2,000 cumulative years, and counting. SPI-Birds acts as a data hub and a catalogue of studied populations. It prevents data loss, secures easy data finding, use and integration and thus facilitates collaboration and synthesis. We provide community-derived data and meta-data standards and improve data integrity guided by the principles of Findable, Accessible, Interoperable and Reusable (FAIR), and aligned with the existing metadata languages (e.g. ecological meta-data language). The encouraging community involvement stems from SPI-Bird's decentralized approach: research groups retain full control over data use and their way of data management, while SPI-Birds creates tailored pipelines to convert each unique data format into a standard format. We outline the lessons learned, so that other communities (e.g. those working on other taxa) can adapt our successful model. Creating community-specific hubs (such

  • Journal article
    Drury JP, Clavel J, Tobias JA, Rolland J, Sheard C, Morlon Het al., 2021,

    Tempo and mode of morphological evolution are decoupled from latitude in birds

    , PLoS Biology, Vol: 19, ISSN: 1544-9173

    The latitudinal diversity gradient is one of the most striking patterns in nature, yet its implications for morphological evolution are poorly understood. In particular, it has been proposed that an increased intensity of species interactions in tropical biota may either promote or constrain trait evolution, but which of these outcomes predominates remains uncertain. Here, we develop tools for fitting phylogenetic models of phenotypic evolution in which the impact of species interactions-namely, competition-can vary across lineages. Deploying these models on a global avian trait dataset to explore differences in trait divergence between tropical and temperate lineages, we find that the effect of latitude on the mode and tempo of morphological evolution is weak and clade- or trait dependent. Our results indicate that species interactions do not disproportionately impact morphological evolution in tropical bird families and question the validity of previously reported patterns of slower trait evolution in the tropics.

  • Journal article
    Luo X, Keenan T, Chen JM, Croft H, Smith N, Prentice IC, Walker A, Wang H, Wang R, Xu C, Zhang Yet al., 2021,

    Global variation in the fraction of leaf nitrogen allocated to photosynthesis

    , Nature Communications, Vol: 12, ISSN: 2041-1723

    Plants invest a considerable amount of leaf nitrogen in the photosynthetic enzyme ribulose-1,5- bisphosphate carboxylase-oxygenase (RuBisCO), forming a strong coupling of nitrogen and photosynthetic capacity. Variability in the nitrogen-photosynthesis relationship indicates different nitrogen use strategies of plants (i.e., the fraction nitrogen allocated to RuBisCO; fLNR), however, the reason for this remains unclear as widely different nitrogen use strategies are adopted in photosynthesis models. Here, we use a comprehensive database of in-situ observations, a remote sensing product of leaf chlorophyll and ancillary climate and soil data, to examine the global distribution in fLNR using a random forest model. We find global fLNR is 18.2 ± 6.2%, with its variation largely driven by negative dependence on leaf mass per area and positive dependence on leaf phosphorus. Some climate and soil factors (i.e., light, atmospheric dryness, soil pH, and sand) have considerable positive influences on fLNR regionally. This study provides insight into the nitrogen-photosynthesis relationship of plants globally and an improved understanding of the global distribution of photosynthetic potential.

  • Journal article
    Clive J, Wisden W, Savolainen V, 2021,

    The de-scent of sexuality: should we smell a rat?

    , Archives of Sexual Behavior: an interdisciplinary research journal, Vol: 50, Pages: 2283-2288, ISSN: 0004-0002

    In their Target Article, Pfau, Jordan, and Breedlove (2019) proposed a connection between the transient receptor potential cation channel 2 gene (TRPC2) and same-sex sexual behavior (SSSB) in primates. This novel theory is an attractive prospect for researchers investigating sexuality in the natural world. The proposal relies on evidence from proximate mechanism studies of TRPC2 knockout (KO) experiments in mice, in which non-functional TPRC2 alters the development of an olfactory sensory structure called the vomeronasal organ (VNO), resulting in an increase of SSSB in both males and females (Axel et al., 2002; Kimchi, Xu, & Dulac, 2007). In combination with an examination of TRPC2 sequence data and evolutionary relationships across primates, Pfau et al. proposed some hypotheses for the fitness consequences of SSSB in primates. Pfau et al. speculated that primates with multi-male/multi-female societies may have evolved via improved social cohesion facilitated by an increase in SSSB, mediated by non-functional TRPC2, and/or pleiotropy between increased SSSB and reduced same-sex aggression. Here, although we support some of these ideas by providing a more complete examination of TRPC2 in primates, we also advocate greater caution when interpreting available data on SSSB.

  • Journal article
    Sato H, Kelly D, Mayor S, Calvo MM, Cowling S, Prentice ICet al., 2021,

    Dry corridors opened by fire and low CO2 in Amazonian rainforest during last glacial maximum

    , Nature Geoscience, Vol: 14, Pages: 578-585, ISSN: 1752-0894

    The dynamics of Amazonian rainforest over long timescales connects closely to its rich biodiversity. While palaeoecological studies have suggested its stability through the Pleistocene, palaeontological evidence indicates the past existence of major expansions of savanna and grassland. Here we present integrated modeling evidence for a grassier Neotropics during the Last Glacial Maximum (LGM), congruent with palaeoecological and biological studies. Vegetation re-constructions were generated using the Land Processes and eXchanges (LPX) model, driven by model reconstructions of LGM climate, and compared against palynological data. A factorial experiment was performed to quantify the impacts of fire and low CO2 on vegetation and model-data agreement. Fire and low CO2 both individually and interactively induced widespread expansion of savanna and grassland biomes while improving model-data agreement. The interactive effects of fire and low CO2 induced the greatest ‘savannafication’ of the Neotropics, providing integrated evidence for a number of biogeographically relevant open vegetation formations including two dry corridors; paths of savanna and grassland through and around Amazonia that facilitated major dispersal and evolutionary diversification events. Our results show a bimodality in tree cover that was driven by fire and further enhanced by ‘CO2 deprivation’, which suggests biome instability in this region of climate space.

  • Journal article
    Milodowski DT, Coomes DA, Swinfield T, Jucker T, Riutta T, Malhi Y, Svatek M, Kvasnica J, Burslem DFRP, Ewers RM, Teh YA, Williams Met al., 2021,

    The impact of logging on vertical canopy structure across a gradient of tropical forest degradation intensity in Borneo

    , JOURNAL OF APPLIED ECOLOGY, Vol: 58, Pages: 1764-1775, ISSN: 0021-8901
  • Journal article
    Tao R, Sack L, Rosindell J, 2021,

    Biogeographic drivers of evolutionary radiations

    , Frontiers in Ecology and Evolution, Vol: 9, Pages: 1-14, ISSN: 2296-701X

    Some lineages radiate spectacularly when colonising a region, but others do not. Large radiations are often attributed to species’adaptation into niches, but sometimes instead to other drivers, such as biogeography. Here we aim to disentangle the factorsdetermining radiation size, by modelling simplified scenarios without the complexity of explicit niches. We build a spatiallystructured neutral model free from niches and incorporating a form of protracted speciation that accounts for gene flow betweenpopulations. We characterise the behaviour of the model for a range of different networks of connectivity between patches. Wefind that a wide range of radiation sizes are possible depending on the combination of geographic isolation and species' dispersalability. For example, when considering isolated archipelagos, low rates of dispersal from the mainland result in decreasedcompetition and thus increased radiation size. Dispersal between habitat patches also has an important effect. At extremely lowdispersal rates, each habitat patch has its own endemic species, intermediate dispersal rates foster larger radiations. Asdispersal rates increase further, a critical point is reached at which identical lineages can vary greatly in radiation size due torare and stochastic dispersal events. At the critical point, some lineages remain a single species for a long time, whilst otherswith identical characteristics produce the largest radiations of all. The mechanism for this is a ‘radiation cascade’ in whichspeciation leads to reduced numbers of individuals per species, and thus reduced gene flow between conspecifics in isolatedpatches, leading to yet more speciation. Once a radiation cascade begins, it continues rapidly until it is arrested by a newequilibrium between speciation and extinction. We speculate that such cascades may occur more generally and are not onlypresent in neutral models. This may help to explain rapid radiation, and the extreme radiation si

  • Journal article
    Miller BA, Pearse WD, Flint CG, 2021,

    Saving the Forest from the Trees: Expert Views on Funding Restoration of Northern Arizona Ponderosa Pine Forests through Registered Carbon Offsets

    , FORESTS, Vol: 12

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