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  • Journal article
    Jackson MC, Pawar S, Woodward G, 2021,

    The temporal dynamics of multiple stressor effects: from individuals to ecosystems

    , Trends in Ecology and Evolution, Vol: 36, Pages: 402-410, ISSN: 0169-5347

    Multiple stressors, such as warming and invasions, often occur together and have nonadditive effects. Most studies to date assume that stressors operate in perfect synchrony, but this will rarely be the case in reality. Stressor sequence and overlap will have implications for ecological memory - the ability of past stressors to influence future responses. Moreover, stressors are usually defined in an anthropocentric context: what we consider a short-term stressor, such as a flood, will span multiple generations of microbes. We argue that to predict responses to multiple stressors from individuals to the whole ecosystem, it is necessary to consider metabolic rates, which determine the timescales at which individuals operate and therefore, ultimately, the ecological memory at different levels of ecological organization.

  • Journal article
    Boyle MJW, Bishop TR, Luke SH, van Breugel M, Evans TA, Pfeifer M, Fayle TM, Hardwick SR, Lane-Shaw RI, Yusah KM, Ashford ICR, Ashford OS, Garnett E, Turner EC, Wilkinson CL, Chung AYC, Ewers RMet al., 2021,

    Localised climate change defines ant communities in human-modified tropical landscapes

    , Functional Ecology, Vol: 35, Pages: 1094-1108, ISSN: 0269-8463

    Logging and habitat conversion create hotter microclimates in tropical forest landscapes, representing a powerful form of localised anthropogenic climate change. It is widely believed that these emergent conditions are responsible for driving changes in communities of organisms found in modified tropical forests, although the empirical evidence base for this is lacking.Here we investigated how interactions between the physiological traits of genera and the environmental temperatures they experience lead to functional and compositional changes in communities of ants, a key organism in tropical forest ecosystems.We found that the abundance and activity of ant genera along a gradient of forest disturbance in Sabah, Malaysian Borneo, was defined by an interaction between their thermal tolerance (CTmax) and environmental temperature. In more disturbed, warmer habitats, genera with high CTmax had increased relative abundance and functional activity, and those with low CTmax had decreased relative abundance and functional activity.This interaction determined abundance changes between primary and logged forest that differed in daily maximum temperature by a modest 1.1°C, and strengthened as the change in microclimate increased with disturbance. Between habitats that differed by 5.6°C (primary forest to oil palm) and 4.5°C (logged forest to oil palm), a 1°C difference in CTmax among genera led to a 23% and 16% change in relative abundance, and a 22% and 17% difference in functional activity. CTmax was negatively correlated with body size and trophic position, with ants becoming significantly smaller and less predatory as microclimate temperatures increased.Our results provide evidence to support the widely held, but never directly tested, assumption that physiological tolerances underpin the influence of disturbance‐induced microclimate change on the abundance and function of invertebrates in tropical landscapes.

  • Journal article
    Savolainen V, Allen R, Binstead M, Arnold R, Priestley Vet al., 2021,

    Quick detection of a rare species: forensic swabs of survey tubes for hazel dormouse Muscardinus avellanarius urine

    , Methods in Ecology and Evolution, Vol: 12, Pages: 818-827, ISSN: 2041-210X

    1. Effective conservation decisions rely on accurate survey data, but methods can be resource‐intensive and risk false negative results. Presence of the threatened hazel dormouse (England, UK) is typically confirmed by looking for its nest in survey tubes, over a 6‐month period. As an alternative, environmental DNA (eDNA) surveys have proven benefits in efficiency and accuracy for other taxa, but generally rely on the extraction and amplification of DNA from water, soil or sediment, which are not yet dependable samples for rare terrestrial mammals like the hazel dormouse.2. At a known occupancy site, paper‐lined survey tubes were used to capture a DNA sample. Like other species of rodent, the hazel dormouse excretes urine freely, and this was highlighted by ultraviolet torch, swabbed from the paper, extracted and hazel dormouse eDNA amplified by quantitative polymerase chain reaction (qPCR).3. Hazel dormouse presence was confirmed in this way in three out of 50 tubes within 8 days. Detection by conventional nest survey occurred on day 63 when a hazel dormouse nest was found in a single survey tube. We calculate that amplification of eDNA left behind in tubes increased survey efficiency here at least 12‐fold.4. Synthesis and applications. In this study we demonstrate that eDNA swabbed from a clean substrate placed in survey apparatus can significantly hasten the detection of a rare species. This method has the potential to broaden the application of eDNA to other terrestrial vertebrates, including surveys at large spatiotemporal scales. Beyond presence/absence, the non‐invasive DNA sample could also offer insights into sex ratio, abundance, behaviour and population genetics.

  • Journal article
    Wei D, Gonzalez-Samperiz P, Gil-Romera G, Harrison SP, Prentice ICet al., 2021,

    Seasonal temperature and moisture changes in interior semi-arid Spain from the last interglacial to the late Holocene

    , Quaternary Research, Vol: 101, Pages: 143-155, ISSN: 0033-5894

    The El Cañizar de Villarquemado pollen record covers the last part of MIS 6 to the late Holocene. We use Tolerance-Weighted Averaging Partial Least-Squares (TWA-PLS) to reconstruct mean temperature of the coldest month (MTCO) and growing degree days above 0° C (GDD0) and the ratio of annual precipitation to annual potential evapotranspiration (MI), accounting for the ecophysiological effect of changing CO2 on water-use efficiency. Rapid summer warming occurred during the Zeifen-Kattegat Oscillation at the transition to MIS 5. Summers were cold during MIS 4 and MIS 2, but some intervals of MIS 3 had summers as warm as the warmest phases of MIS 5 or the Holocene. Winter temperatures declined from MIS 4 to MIS 2. Changes in temperature seasonality within MIS 5 and MIS 1 are consistent with insolation seasonality changes. Conditions became progressively more humid during MIS 5, and MIS 4 was also humid although MIS 3 was more arid. Changes in MI and GDD0 are anti-correlated, with increased MI during summer warming intervals. Comparison with other records shows glacial-interglacial changes were not unform across the circum-Mediterranean region but available quantitative reconstructions are insufficient to determine if east-west differences reflect the circulation-driven precipitation dipole seen in recent decades.

  • Journal article
    Flintham E, Savolainen V, Mullon C, 2021,

    Dispersal alters the nature and scope of sexually antagonistic variation

    , The American Naturalist, Vol: 197, Pages: 543-559, ISSN: 0003-0147

    Intralocus sexual conflict, or sexual antagonism, occurs when alleles have opposing fitness effects in the two sexes. Previous theory suggests that sexual antagonism is a driver of genetic variation by generating balancing selection. However, most of these studies assume that populations are well mixed, neglecting the effects of spatial subdivision. Here, we use mathematical modeling to show that limited dispersal changes evolution at sexually antagonistic autosomal and X-linked loci as a result of inbreeding and sex-specific kin competition. We find that if the sexes disperse at different rates, kin competition within the philopatric sex biases intralocus conflict in favor of the more dispersive sex. Furthermore, kin competition diminishes the strength of balancing selection relative to genetic drift, reducing genetic variation in small subdivided populations. Meanwhile, by decreasing heterozygosity, inbreeding reduces the scope for sexually antagonistic polymorphism due to nonadditive allelic effects, and this occurs to a greater extent on the X chromosome than autosomes. Overall, our results indicate that spatial structure is a relevant factor in predicting where sexually antagonistic alleles might be observed. We suggest that sex-specific dispersal ecology and demography can contribute to interspecific and intragenomic variation in sexual antagonism.

  • Conference paper
    Morris Z, Abzhanov A, Pierce S, 2021,

    Embryonic origins of the flattened skull table and snout in Crocodylia

    , Experimental Biology Meeting, Publisher: WILEY, ISSN: 0892-6638
  • Journal article
    Fediajevaite J, Priestley V, Arnold R, Savolainen Vet al., 2021,

    Meta-analysis shows that environmental DNA outperforms traditional surveys, but warrants better reporting standards

    , Ecology and Evolution, Vol: 11, Pages: 4803-4815, ISSN: 2045-7758

    1. Decades of environmental DNA (eDNA) method application, spanning a wide variety of taxa and habitats, has advanced our understanding of eDNA and underlined its value as a tool for conservation practitioners. The general consensus is that eDNA methods are more accurate and cost‐effective than traditional survey methods. However, they are formally approved for just a few species globally (e.g., Bighead Carp, Silver Carp, Great Crested Newt). We conducted a meta‐analysis of studies that directly compare eDNA with traditional surveys to evaluate the assertion that eDNA methods are consistently “better.”2. Environmental DNA publications for multiple species or single macro‐organism detection were identified using the Web of Science, by searching “eDNA” and “environmental DNA” across papers published between 1970 and 2020. The methods used, focal taxa, habitats surveyed, and quantitative and categorical results were collated and analyzed to determine whether and under what circumstances eDNA outperforms traditional surveys.3. Results show that eDNA methods are cheaper, more sensitive, and detect more species than traditional methods. This is, however, taxa‐dependent, with amphibians having the highest potential for detection by eDNA survey. Perhaps most strikingly, of the 535 papers reviewed just 49 quantified the probability of detection for both eDNA and traditional survey methods and studies were three times more likely to give qualitative statements of performance.4. Synthesis and applications: The results of this meta‐analysis demonstrate that where there is a direct comparison, eDNA surveys of macro‐organisms are more accurate and efficient than traditional surveys. This conclusion, however, is based on just a fraction of available eDNA papers as most do not offer this granularity. We recommend that conclusions are substantiated with comparable and quantitative data. Where a direct comparison has not been made, we caution a

  • Journal article
    Huxley PJ, Murray KA, Pawar S, Cator LJet al., 2021,

    The effect of resource limitation on the temperature-dependence of mosquito population fitness

    , Proceedings of the Royal Society B: Biological Sciences, Vol: 288, ISSN: 0962-8452

    Laboratory-derived temperature dependencies of life history traits are increasingly being usedto make mechanistic predictions for how climatic warming will affect vector-borne diseasedynamics, partially by affecting abundance dynamics of the vector population. Thesetemperature-trait relationships are typically estimated from juvenile populations reared onoptimal resource supply, even though natural populations of vectors are expected toexperience variation in resource supply, including intermittent resource limitation. Usinglaboratory experiments on the mosquito Aedes aegypti, a principal arbovirus vector,combined with stage-structured population modelling, we show that low-resource supply inthe juvenile life stages significantly depresses the vector’s maximal population growth rateacross the entire temperature range (22–32°C) and causes it to peak at a lower temperaturethan at high-resource supply. This effect is primarily driven by an increase in juvenilemortality and development time, combined with a decrease in adult size with temperature atlow-resource supply. Our study suggests that most projections of temperature-dependentvector abundance and disease transmission are likely to be biased because they are based ontraits measured under optimal resource supply. Our results provide compelling evidence forfuture studies to consider resource supply when predicting the effects of climate and habitatchange on vector-borne disease transmission, disease vectors and other arthropods.

  • Journal article
    Cook J, Pawar S, Endres RG, 2021,

    Thermodynamic constraints on the assembly and diversity of microbial ecosystems are different near to and far from equilibrium

    <jats:title>Abstract</jats:title><jats:p>Non-equilibrium thermodynamics has long been an area of substantial interest to ecologists because most fundamental biological processes, such as protein synthesis and respiration, are inherently energy-consuming. However, most of this interest has focused on developing coarse ecosystem-level maximisation principles, providing little insight into underlying mechanisms that lead to such emergent constraints. Microbial communities are a natural system to decipher this mechanistic basis because their interactions in the form of substrate consumption, metabolite production, and cross-feeding can be described explicitly in thermodynamic terms. Previous work has considered how thermodynamic constraints impact competition between pairs of species, but restrained from analysing how this manifests in complex dynamical systems. To address this gap, we develop a thermodynamic microbial community model with fully reversible reaction kinetics, which allows direct consideration of free-energy dissipation. This also allows species to interact via products rather than just substrates, increasing the dynamical complexity, and allowing a more nuanced classification of interaction types to emerge. Using this model, we find that community diversity increases with substrate lability, because greater free-energy availability allows for faster generation of niches. Thus, more niches are generated in the time frame of community establishment, leading to higher final species diversity. We also find that allowing species to make use of near-to-equilibrium reactions increases diversity in a low free-energy regime. In such a regime, two new thermodynamic interaction types that we identify here reach comparable strengths to the conventional (competition and facilitation) types, emphasising the key role that thermodynamics plays in community dynamics. Our results suggest that accounting for realistic thermodynamic constraints is vital fo

  • Journal article
    Benitez-Lopez A, Santini L, Gallego-Zamorano J, Mila B, Walkden P, Huijbregts MAJ, Tobias JAet al., 2021,

    The island rule explains consistent patterns of body size evolution in terrestrial vertebrates

    , Nature Ecology and Evolution, Vol: 5, Pages: 768-+, ISSN: 2397-334X

    Island faunas can be characterized by gigantism in small animals and dwarfism in large animals, but the extent to which this so-called ‘island rule’ provides a general explanation for evolutionary trajectories on islands remains contentious. Here we use a phylogenetic meta-analysis to assess patterns and drivers of body size evolution across a global sample of paired island–mainland populations of terrestrial vertebrates. We show that ‘island rule’ effects are widespread in mammals, birds and reptiles, but less evident in amphibians, which mostly tend towards gigantism. We also found that the magnitude of insular dwarfism and gigantism is mediated by climate as well as island size and isolation, with more pronounced effects in smaller, more remote islands for mammals and reptiles. We conclude that the island rule is pervasive across vertebrates, but that the implications for body size evolution are nuanced and depend on an array of context-dependent ecological pressures and environmental conditions.

  • Working paper
    Smith TP, Mombrikotb S, Ransome E, Kontopoulos D-G, Pawar S, Bell Tet al., 2021,

    Latent functional diversity may accelerate microbial community responses to environmental fluctuations

    , Publisher: Cold Spring Harbor Laboratory

    Whether and how whole ecological communities can respond to climate change remains an open question. With their fast generation times and abundant functional diversity, microbes in particular harbor great potential to exhibit community-level adaptation through a combination of strain-level adaptation, phenotypic plasticity, and species sorting. However, the relative importance of these mechanisms remains unclear. Here, through a novel laboratory experiment, we show that bacterial communities can exhibit a remarkable degree of community-level adaptability through a combination of phenotypic plasticity and species sorting alone. Specifically, by culturing soil communities from a single location at six temperatures between 4°C and 50°C, we find that multiple strains well adapted to different temperatures can be isolated from the community, without immigration or strain-level adaptation. This is made possible by the ability of strains with different physiological and life history traits to “switch on” under suitable conditions, with phylogenetically distinct K-specialist taxa favoured under cooler conditions, and r-specialist taxa in warmer conditions. Our findings provide new insights into microbial community adaptation, and suggest that microbial community function is likely to respond rapidly to climatic fluctuations, through changes in species composition during repeated community assembly dynamics.

  • Journal article
    Peng Y, Bloomfield K, Cernusak L, Dominques T, Prentice ICet al., 2021,

    Global climate and nutrient controls of photosynthetic capacity

    , Communications Biology, Vol: 4, ISSN: 2399-3642

    There is huge uncertainty about how global exchanges of carbon between the atmosphere and land will respond to continuing environmental change. A better representation of photosynthetic capacity is required for Earth System models to simulate carbon assimilation reliably. Here we use a global leaf-trait dataset to test whether photosynthetic capacity is quantitatively predictable from climate, based on optimality principles; and to explore how this prediction is modified by soil properties, including indices of nitrogen and phosphorus availability, measured in situ. The maximum rate of carboxylation standardized to 25 °C (Vcmax25) was found to be proportional to growing-season irradiance, and to increase—as predicted—towards both colder and drier climates. Individual species’ departures from predicted Vcmax25 covaried with area-based leaf nitrogen (Narea) but community-mean Vcmax25 was unrelated to Narea, which in turn was unrelated to the soil C:N ratio. In contrast, leaves with low area-based phosphorus (Parea) had low Vcmax25 (both between and within communities), and Parea increased with total soil P. These findings do not support the assumption, adopted in some ecosystem and Earth System models, that leaf-level photosynthetic capacity depends on soil N supply. They do, however, support a previously-noted relationship between photosynthesis and soil P supply.

  • Journal article
    Neate-Clegg MHC, Jones SE, Tobias JA, Newmark WD, Sekercioglu CHet al., 2021,

    Ecological correlates of elevational range shifts in tropical birds

    , Frontiers in Ecology and Evolution, Vol: 9, Pages: 1-16, ISSN: 2296-701X

    Globally, birds have been shown to respond to climate change by shifting their elevational distributions. This phenomenon is especially prevalent in the tropics, where elevational gradients are often hotspots of diversity and endemism. Empirical evidence has suggested that elevational range shifts are far from uniform across species, varying greatly in the direction (upslope vs. downslope) and rate of change (speed of elevational shift). However, little is known about the drivers of these variable responses to climate change, limiting our ability to accurately project changes in the future. Here, we compile empirical estimates of elevational shift rates (m/yr) for 421 bird species from eight study sites across the tropics. On average, species shifted their mean elevations upslope by 1.63 ± 0.30 m/yr, their upper limits by 1.62 m ± 0.38 m/yr, and their lower limits by 2.81 ± 0.42 m/yr. Upslope shift rates increased in smaller-bodied, less territorial species, whereas larger species were more likely to shift downslope. When considering absolute shift rates, rates were fastest for species with high dispersal ability, low foraging strata, and wide elevational ranges. Our results indicate that elevational shift rates are associated with species’ traits, particularly body size, dispersal ability, and territoriality. However, these effects vary substantially across sites, suggesting that responses of tropical montane bird communities to climate change are complex and best predicted within the local or regional context.

  • Journal article
    Tobias JA, Donald PF, Martin RW, Butchart SHM, Collar NJet al., 2021,

    Performance of a points-based scoring system for assessing species limits in birds

    , Ornithology, Vol: 138, Pages: 1-14, ISSN: 2732-4613

    Species are fundamental to biology, conservation, and environmental legislation; yet, there is often disagreement on how and where species limits should be drawn. Even sophisticated molecular methods have limitations, particularly in the context of geographically isolated lineages or inadequate sampling of loci. With extinction rates rising, methods are needed to assess species limits rapidly but robustly. Tobias et al. devised a points-based system to compare phenotypic divergence between taxa against the level of divergence in sympatric species, establishing a threshold to guide taxonomic assessments at a global scale. The method has received a mixed reception. To evaluate its performance, we identified 397 novel taxonomic splits from 328 parent taxa made by application of the criteria (in 2014‒2016) and searched for subsequent publications investigating the same taxa with molecular and/or phenotypic data. Only 71 (18%) novel splits from 60 parent taxa have since been investigated by independent studies, suggesting that publication of splits underpinned by the criteria in 2014–2016 accelerated taxonomic decisions by at least 33 years. In the evaluated cases, independent analyses explicitly or implicitly supported species status in 62 (87.3%) of 71 splits, with the level of support increasing to 97.2% when excluding subsequent studies limited only to molecular data, and reaching 100% when the points-based criteria were applied using recommended sample sizes. Despite the fact that the training set used to calibrate the criteria was heavily weighted toward passerines, splits of passerines and non-passerines received equally strong support from independent research. We conclude that the method provides a useful tool for quantifying phenotypic divergence and fast-tracking robust taxonomic decisions at a global scale.

  • Journal article
    Cator L, Wyer C, Harrington L, 2021,

    Mosquito Sexual Selection and Reproductive Control Programs

    , Trends in Parasitology, Vol: 37, Pages: 330-339, ISSN: 0169-4758

    The field of mosquito mating biology has experienced a considerable expansion in the past decade. Recent work has generated many key insights about specific aspects of mating behavior and physiology. Here, we synthesize these findings and classify swarming mosquito systems as polygynous. Male mating success is highly variable in swarms and evidence suggests that it is likely determined by both scramble competition between males and female choice. Incorporating this new understanding will improve both implementation and long-term stability of reproductive control tools.

  • Journal article
    Barneche DR, Hulatt CJ, Dossena M, Padfield D, Woodward G, Trimmer M, Yvon-Durocher Get al., 2021,

    Warming impairs trophic transfer efficiency in a long-term field experiment

    , NATURE, Vol: 592, Pages: 76-+, ISSN: 0028-0836
  • Journal article
    Connolly JB, Mumford JD, Fuchs S, Turner G, Beech C, North AR, Burt Aet al., 2021,

    Systematic identification of plausible pathways to potential harm via problem formulation for investigational releases of a population suppression gene drive to control the human malaria vector <i>Anopheles gambiae</i> in West Africa

    , MALARIA JOURNAL, Vol: 20
  • Journal article
    Padfield D, O'Sullivan H, Pawar S, 2021,

    rTPC and nls.multstart: A new pipeline to fit thermal performance curves in r

    , METHODS IN ECOLOGY AND EVOLUTION, Vol: 12, Pages: 1138-1143, ISSN: 2041-210X
  • Journal article
    Koontz A, Pearse WD, Wolf P, 2021,

    Pronounced Genetic Separation Among Varieties of the<i>Primula cusickiana</i>Species Complex, a Great Basin Endemic

    <jats:title>Abstract</jats:title><jats:p>Distinguishing between unique species and populations with strong genetic structure is a common challenge in population genetics, especially in fragmented habitats where allopatric speciation may be widespread and distinct groups may be morphologically similar. Such is often the case with species complexes across sky island environments. In these scenarios, biogeography may help to explain the relations between species complex members, and RADseq methods are commonly used to compare closely related species across thousands of genetic loci. Here we use RADseq to clarify the relations between geographically distinct but morphologically similar varieties of the<jats:italic>Primula cusickiana</jats:italic>species complex, and to contextualize past findings of strong genetic structure among populations within varieties. Our genomic analyses demonstrate pronounced separation between isolated populations of this Great Basin endemic, indicating that the current varietal classification of complex members is inaccurate and emphasizing their conservation importance. We discuss how these results correspond to recent biogeographical models used to describe the distribution of other sky island taxa in western North America. Our findings also fit into a wider trend observed for alpine<jats:italic>Primula</jats:italic>species complexes, and we consider how heterostylous breeding systems may be contributing to frequent diversification via allopatric speciation in this genus.</jats:p>

  • Journal article
    Wayman JP, Sadler JP, Pugh TAM, Martin TE, Tobias JA, Matthews TJet al., 2021,

    Identifying the drivers of spatial taxonomic and functional beta-diversity of British breeding birds

    , Frontiers in Ecology and Evolution, Vol: 9, Pages: 1-16, ISSN: 2296-701X

    Spatial variation in community composition may be driven by a variety of processes, including environmental filtering and dispersal limitation. While work has been conducted on the relative importance of these processes on various taxa and at varying resolutions, tests using high-resolution empirical data across large spatial extents are sparse. Here, we use a dataset on the presence/absence of breeding bird species collected at the 10 km × 10 km scale across the whole of Britain. Pairwise spatial taxonomic and functional beta diversity, and the constituent components of each (turnover and nestedness/richness loss or gain), were calculated alongside two other measures of functional change (mean nearest taxon distance and mean pairwise distance). Predictor variables included climate and land use measures, as well as a measure of elevation, human influence, and habitat diversity. Generalized dissimilarity modeling was used to analyze the contribution of each predictor variable to variation in the different beta diversity metrics. Overall, we found that there was a moderate and unique proportion of the variance explained by geographical distance per se, which could highlight the role of dispersal limitation in community dissimilarity. Climate, land use, and human influence all also contributed to the observed patterns, but a large proportion of the explained variance in beta diversity was shared between these variables and geographical distance. However, both taxonomic nestedness and functional nestedness were uniquely predicted by a combination of land use, human influence, elevation, and climate variables, indicating a key role for environmental filtering. These findings may have important conservation implications in the face of a warming climate and future land use change.

  • Journal article
    Perkins DM, Durance I, Jackson M, Jones JI, Lauridsen RB, Layer-Dobra K, Reiss J, Thompson MSA, Woodward Get al., 2021,

    Systematic variation in food web body-size structure linked to external subsidies

    , BIOLOGY LETTERS, Vol: 17, ISSN: 1744-9561
  • Journal article
    Cael BB, Cavan EL, Britten GL, 2021,

    Reconciling the Size-Dependence of Marine Particle Sinking Speed

  • Journal article
    Smith TP, Dorigatti I, Mishra S, Volz E, Walker PGT, Ragonnet-Cronin M, Tristem M, Pearse WDet al., 2021,

    Environmental drivers of SARS-CoV-2 lineage B.1.1.7 transmission intensity

    <jats:title>Abstract</jats:title><jats:p>Previous work has shown that environment affects SARS-CoV-2 transmission, but it is unclear whether emerging strains show similar responses. Here we show that, like other SARS-CoV-2 strains, lineage B.1.1.7 spread with greater transmission in colder and more densely populated parts of England. However, we also find evidence of B.1.1.7 having a transmission advantage at warmer temperatures compared to other strains. This implies that spring and summer conditions are unlikely to slow B.1.1.7’s invasion in Europe and across the Northern hemisphere - an important consideration for public health interventions.</jats:p>

  • Journal article
    Nunes MH, Jucker T, Riutta T, Svatek M, Kvasnica J, Rejzek M, Matula R, Majalap N, Ewers RM, Swinfield T, Valbuena R, Vaughn NR, Asner GP, Coomes DAet al., 2021,

    Recovery of logged forest fragments in a human-modified tropical landscape during the 2015-16 El Nino

    , Nature Communications, Vol: 12, Pages: 1-11, ISSN: 2041-1723

    The past 40 years in Southeast Asia have seen about 50% of lowland rainforests converted to oil palm and other plantations, and much of the remaining forest heavily logged. Little is known about how fragmentation influences recovery and whether climate change will hamper restoration. Here, we use repeat airborne LiDAR surveys spanning the hot and dry 2015-16 El Niño Southern Oscillation event to measure canopy height growth across 3,300 ha of regenerating tropical forests spanning a logging intensity gradient in Malaysian Borneo. We show that the drought led to increased leaf shedding and branch fall. Short forest, regenerating after heavy logging, continued to grow despite higher evaporative demand, except when it was located close to oil palm plantations. Edge effects from the plantations extended over 300 metres into the forests. Forest growth on hilltops and slopes was particularly impacted by the combination of fragmentation and drought, but even riparian forests located within 40 m of oil palm plantations lost canopy height during the drought. Our results suggest that small patches of logged forest within plantation landscapes will be slow to recover, particularly as ENSO events are becoming more frequent.

  • Journal article
    Gray REJ, Ewers RM, 2021,

    Monitoring forest phenology in a changing world

    , Forests, Vol: 12, Pages: 1-24, ISSN: 1999-4907

    Plant phenology is strongly interlinked with ecosystem processes and biodiversity. Like many other aspects of ecosystem functioning, it is affected by habitat and climate change, with both global change drivers altering the timings and frequency of phenological events. As such, there has been an increased focus in recent years to monitor phenology in different biomes. A range of approaches for monitoring phenology have been developed to increase our understanding on its role in ecosystems, ranging from the use of satellites and drones to collection traps, each with their own merits and limitations. Here, we outline the trade-offs between methods (spatial resolution, temporal resolution, cost, data processing), and discuss how their use can be optimised in different environments and for different goals. We also emphasise emerging technologies that will be the focus of monitoring in the years to follow and the challenges of monitoring phenology that still need to be addressed. We conclude that there is a need to integrate studies that incorporate multiple monitoring methods, allowing the strengths of one to compensate for the weaknesses of another, with a view to developing robust methods for upscaling phenological observations from point locations to biome and global scales and reconciling data from varied sources and environments. Such developments are needed if we are to accurately quantify the impacts of a changing world on plant phenology.

  • Journal article
    Dobreva MP, Lynton-Jenkins JG, Chaves JA, Tokita M, Bonneaud C, Abzhanov Aet al., 2021,

    Sex identification in embryos and adults of Darwin's finches

    , PLoS One, Vol: 16, Pages: 1-13, ISSN: 1932-6203

    Darwin’s finches are an iconic example of adaptive radiation and evolution under natural selection. Comparative genetic studies using embryos of Darwin’s finches have shed light on the possible evolutionary processes underlying the speciation of this clade. Molecular identification of the sex of embryonic samples is important for such studies, where this information often cannot be inferred otherwise. We tested a fast and simple chicken embryo protocol to extract DNA from Darwin’s finch embryos. In addition, we applied minor modifications to two of the previously reported PCR primer sets for CHD1, a gene used for sexing adult passerine birds. The sex of all 29 tested embryos of six species of Darwin’s finches was determined successfully by PCR, using both primer sets. Next to embryos, hatchlings and fledglings are also impossible to distinguish visually. This extends to juveniles of sexually dimorphic species which are yet to moult in adult-like plumage and beak colouration. Furthermore, four species of Darwin’s finches are monomorphic, males and females looking alike. Therefore, sex assessment in the field can be a source of error, especially with respect to juveniles and mature monomorphic birds outside of the mating season. We caught 567 juveniles and adults belonging to six species of Darwin’s finches and only 44% had unambiguous sex-specific morphology. We sexed 363 birds by PCR: individuals sexed based on marginal sex specific morphological traits; and birds which were impossible to classify in the field. PCR revealed that for birds with marginal sex specific traits, sexing in the field produced a 13% error rate. This demonstrates that PCR based sexing can improve field studies on Darwin’s finches, especially when individuals with unclear sex-related morphology are involved. The protocols used here provide an easy and reliable way to sex Darwin’s finches throughout ontogeny, from embryos to adults.

  • Journal article
    Joshi J, Stocker B, Hofhansl F, Zhou S, Brännström Å, Prentice IC, Dieckmann Uet al., 2021,

    Eco-evolutionary responses of plant communities to drought and rainfall variability

    <jats:p>&amp;lt;p&amp;gt;The future Earth is projected to experience elevated rainfall variability, with more frequent and intense droughts, as well as high-rainfall events. Increasing CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; concentrations are expected to raise terrestrial gross primary productivity (GPP), whereas water stress is expected to lower GPP. Plant responses to water stress vary strongly with timescale, and plants adapted to different environmental conditions differ in their functional responses. Here, we embed a unified optimality-based theory of stomatal conductance and biochemical acclimation of leaves we have recently developed [Joshi, J. et al. (2020) Towards a unified theory of plant photosynthesis and hydraulics. bioRxiv 2020.12.17.423132] in an eco-evolutionary vegetation-modelling framework, with the goal to investigate emergent functional diversity and associated GPP impacts under different rainfall regimes.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;The model of photosynthesis used here simultaneously predicts the stomatal responses and biochemical acclimation of leaves to atmospheric and soil-moisture conditions. Using three hydraulic traits and two cost parameters, it successfully predicts the simultaneous declines in CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; assimilation rate, stomatal conductance, and leaf photosynthetic capacity caused by drying soil. It also correctly predicts the responses of CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; assimilation rate, stomatal conductance, leaf water potential, and leaf photosynthetic capacity to vapour pressure deficit, temperature, ambient CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, light intensity, and elevation. Our model therefore captures the synergistic effects of atmospheric and soil drought, as well as of atmospheric CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; changes, on plant photosynthesis

  • Journal article
    Mengoli G, Agustí-Panareda A, Boussetta S, Harrison SP, Trotta C, Prentice ICet al., 2021,

    Application of an optimality-based model to operate at half-hourly timestep to implement plant acclimation within a land-surface modelling framework

    <jats:p>&amp;lt;p&amp;gt;Vegetation and atmosphere are linked through the perpetual exchange of water, carbon and energy. An accurate representation of the processes involved in these exchanges is crucial in forecasting Earth system states. Although vegetation has become an undisputed key component in land-surface modelling (LSMs), the current generation of models differ in terms of how key processes are formulated. Plant processes react to environmental changes on multiple time scales. Here we differentiate a fast (minutes) and a slower (acclimated &amp;amp;#8211; weeks to months) response. Some current LSMs include plant acclimation, even though they require additional parameters to represent this response, but the majority of them represent only the fast response and assume that this also applies at longer time scales. Ignoring acclimation in this way could be the cause of inconsistent future projections. Our proposition is to include plant acclimation in a LSM schema, without having to include new plant-functional-type-dependent parameters. This is possible by using an alternative model development strategy based on eco-evolutionary theory, which explicitly predicts the acclimation of photosynthetic capacities and stomatal behaviour to environmental variations. So far, this theory has been tested only at weekly to monthly timescales. Here we develop and test an approach to apply an existing optimality-based model of gross primary production (GPP), the P model, at the sub-daily timestep necessary for use in an LSM, making an explicit differentiation between the fast and slow responses of photosynthesis and stomatal conductance. We test model performance in reproducing the diurnal cycle of GPP as recorded by flux tower measurements across different biomes, including boreal and tropical forests. The extended model requires only a few meteorological inputs, and a satellite-derived product for leaf area index or green vegetation cover. It is able to

  • Journal article
    Nóbrega R, Prentice IC, 2021,

    Developing a climate-driven root zone water stress function for different climates and ecosystems

    <jats:p>&amp;lt;p&amp;gt;Plant roots have less water available when soils have low moisture content and, consequently, limit their root-to-leaf water potential gradient to protect their xylem, which reduces H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O and CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; exchanges with the atmosphere. In vegetation, hydrological and land-surface models, plant responses to reduced available water in the soil have been implemented in various ways depending on data availability, type of ecosystem, and modelling assumptions. Most models use soil water stress functions &amp;amp;#8211; commonly known as beta functions &amp;amp;#8211; to reduce transpiration and carbon assimilation, by applying a factor that reflects the soil water availability for plants. These functions usually produce reasonably satisfactory results, but rely on the information on soil properties (e.g. wilting point and field capacity) that are not widely available. On a global level, soil information is mediocre, and data uncertainty is compensated by tuning parameters that rarely represent a physiological process. We propose instead the use of a beta function derived from a mass-balance approach focused on the root zone water capacity. This method quantifies the root zone water storage by calculating the accumulated water deficit based on the balance between water influxes and effluxes, and it does not require land-cover or soil information. We assessed how our approach performs compared to those other soil water stress functions. We used global datasets, including WDFE5 and PMLv2, to extract precipitation and evapotranspiration and compute water deficit. For most vegetation types and climates our approach yielded promising results. Worst results were found for some (semi-)arid sites due to the overestimation of the water deficit. We aim to deliver an approach that can be easily applied on global scales.&amp;lt;/p&a

  • Journal article
    Rurangwa ML, Matthews TJ, Niyigaba P, Tobias JA, Whittaker RJet al., 2021,

    Assessing tropical forest restoration after fire using birds as indicators: An afrotropical case study

    , Forest Ecology and Management, Vol: 483, Pages: 1-15, ISSN: 0378-1127

    The necessity to restore rainforest habitats degraded by anthropogenic fires is widely recognized, however, research on restoration approaches has mainly centred on the recovery of forest structural complexity. There is insufficient evidence on the efficacy of restoration methods in the recovery of the faunal diversity and features linked to key ecosystem functions. We assessed the taxonomic diversity and functional trait structure of bird assemblages in undisturbed primary forest and fire-affected habitats undergoing natural regeneration, as well as areas of assisted natural regeneration, in Nyungwe National Park, Rwanda. We compiled bird occurrence data from point-count sampling, and obtained morphological traits for all species in our assemblages using measurements taken from wild birds and museum specimens. We found marked differences in species composition between primary forest habitats and regenerating forest, with similarity increasing over time since perturbation. Taxonomic diversity was higher in primary forest, and similar between the two restoration approaches. Functional diversity was lower in assisted naturally regenerated habitats, although separate analyses within dietary guilds revealed no differences across habitats. Among desired restoration outcomes, tree species diversity was the leading positive driver of avian species diversity, fern coverage exerted negative effects, while canopy cover had a positive but weak influence. Our findings underscore the importance of preventing anthropogenic fires in tropical rainforest since their impacts on ecological processes are not easily reversed, as shown by the lack of improvement in avian diversity metrics under assisted naturally regeneration in relation to natural regeneration. We stress the need to document both floral and faunal recovery in order to aid informed decision-making on restoration methods.

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