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  • Journal article
    Blundo C, Carilla J, Grau R, Malizia A, Malizia L, Osinaga-Acosta O, Bird M, Bradford M, Catchpole D, Ford A, Graham A, Hilbert D, Kemp J, Laurance S, Laurance W, Ishida FY, Marshall A, Waite C, Woell H, Bastin J-F, Bauters M, Beeckman H, Boeckx P, Bogaert J, De Canniere C, de Haulleville T, Doucet J-L, Hardy O, Hubau W, Kearsley E, Verbeeck H, Vleminckx J, Brewer SW, Alarcon A, Araujo-Murakami A, Arets E, Arroyo L, Chavez E, Fredericksen T, Villaroel RG, Sibauty GG, Killeen T, Licona JC, Lleigue J, Mendoza C, Murakami S, Gutierrez AP, Pardo G, Pena-Carlos M, Poorter L, Toledo M, Cayo JV, Viscarra LJ, Vos V, Ahumada J, Almeida E, Almeida J, Oliveira EAD, Cruz WAD, Oliveira AAD, Carvalho FA, Obermuller FA, Andrade A, Carvalho FA, Vieira SA, Aquino AC, Aragao L, Araujo AC, Assis MA, Gomes JAMA, Baccaro F, Camargo PBD, Barni P, Barroso J, Bernacci LC, Bordin K, Medeiros MBD, Broggio I, Camargo JL, Cardoso D, Carniello MA, Rochelle ALC, Castilho C, Castro AAJF, Castro W, Ribeiro SC, Costa F, Oliveira RCD, Coutinho I, Cunha J, da Costa L, Ferreira LDC, Silva RDC, Simbine MDGZ, Kamimura VDA, Lima HCD, Melo LDO, de Queiroz L, Lima JRDS, Santo MDE, Domingues T, Prestes NCDS, Carneiro SES, Elias F, Eliseu G, Emilio T, Farrapo CL, Fernandes L, Ferreira G, Ferreira J, Ferreira L, Ferreira S, Simon MF, Freitas MA, Garcia QS, Manzatto AG, Graca P, Guilherme F, Hase E, Higuchi N, Iguatemy M, Barbosa RI, Jaramillo M, Joly C, Klipel J, Do Amaral IL, Levis C, Lima AS, Dan ML, Lopes A, Madeiros H, Magnusson WE, dos Santos RM, Marimon B, Junior BHM, Grillo RMM, Martinelli L, Reis SM, Medeiros S, Meira-Junior M, Metzker T, Morandi P, Do Nascimento NM, Moura M, Muller SC, Nagy L, Nascimento H, Nascimento M, Lima AN, De Araujo RO, Silva JO, Pansonato M, Sabino GP, De Abreu KMP, Rodrigues PJFP, Piedade M, Rodrigues D, Pinto JRR, Quesada C, Ramos E, Ramos R, Rodrigues P, De Sousa TR, Salomao R, Santana F, Scaranello M, Bergamin RS, Schietti J, Schongart J, Schwartz G, Silva N, Silveira Met al., 2021,

    Taking the pulse of Earth's tropical forests using networks of highly distributed plots

    , BIOLOGICAL CONSERVATION, Vol: 260, ISSN: 0006-3207
  • Journal article
    Hill SL, Pinkerton MH, Ballerini T, Cavan EL, Gurney LJ, Martins I, Xavier JCet al., 2021,

    Robust model-based indicators of regional differences in food-web structure in the Southern Ocean

    , JOURNAL OF MARINE SYSTEMS, Vol: 220, ISSN: 0924-7963
  • Journal article
    Eberhart-Hertel LJ, Rodrigues LF, Krietsch J, Eberhart-Hertel AG, Cruz-López M, Vázquez-Rojas KA, González-Medina E, Schroeder J, Küpper Cet al., 2021,

    Egg size variation in a long-lived polyandrous shorebird in the context of senescence and breeding phenology

    <jats:p>We have withdrawn this manuscript due to a duplicate posting of manuscript number 240150. Therefore, we do not wish this work to be cited as reference for the project. If you have any questions, please contact Luke J. Eberhart-Hertel at<jats:email>luke.eberhart@orn.mpg.de</jats:email></jats:p>

  • Journal article
    Christensen A, Piggott M, Sebille EV, Reeuwijk MV, Pawar Set al., 2021,

    Investigating microscale patchiness of motile microbes driven by the interaction of turbulence and gyrotaxis in a 3D simulated convective mixed layer.

    <jats:title>Abstract</jats:title> <jats:p>Microbes play a primary role in aquatic ecosystems and biogeochemical cycles. Spatial patchiness is a critical factor underlying these activities, influencing biological productivity, nutrient cycling and dynamics across trophic levels. Incorporating spatial dynamics into microbial models is a long-standing challenge, particularly where small-scale turbulence is involved. Here, we combine a fully 3D direct numerical simulation of convective mixed layer turbulence, with an individual-based microbial model to test the key hypothesis that the coupling of gyrotactic motility and turbulence drives intense microscale patchiness. The fluid model simulates turbulent convection caused by heat loss through the fluid surface, for example during the night, during autumnal or winter cooling or during a cold-air outbreak. We find that under such conditions, turbulence-driven patchiness is depth-structured and requires high motility: Near the fluid surface, intense convective turbulence overpowers motility, homogenising motile and non-motile microbes approximately equally. At greater depth, in conditions analogous to a thermocline, highly motile microbes can be over twice as patch-concentrated as non-motile microbes, and can substantially amplify their swimming velocity by efficiently exploiting fast-moving packets of fluid. Our results substantiate the predictions of earlier studies, and demonstrate that turbulence-driven patchiness is not a ubiquitous consequence of motility but rather a delicate balance of motility and turbulent intensity.</jats:p>

  • Journal article
    League G, Pitch S, Geyer J, Baxter L, Montijo J, Rowland J, Johnson L, Murdock C, Cator Let al., 2021,

    Sexual selection theory meets disease vector control: Testing harmonic convergence as a “good genes” signal in Aedes aegypti mosquitoes

    , PLoS Neglected Tropical Diseases, ISSN: 1935-2727

    Background:The mosquito Aedes aegypti is a medically important, globally distributed vector of the viruses that cause dengue, yellow fever, chikungunya, and Zika. Although reproduction and mate choice are key components of vector population dynamics and control, our understanding of the mechanisms of sexual selection in mosquitoes remains poor. In “good genes” models of sexual selection, females use male cues as an indicator of both mate and offspring genetic quality. Recent studies in Ae. aegypti provide evidence that male wingbeats may signal aspects of offspring quality and performance during mate selection in a process known as harmonic convergence. However, the extent to which harmonic convergence may signal overall inherent quality of mates and their offspring remains unknown.Methodology/Principal findings:To examine this, we measured the relationship between acoustic signaling and a broad panel of parent and offspring fitness traits in two generations of field-derived Ae. aegypti originating from dengue-endemic field sites in Thailand. Our data show that in this population of mosquitoes, harmonic convergence does not signal male fertility, female fecundity, or male flight performance traits, which despite displaying robust variability in both parents and their offspring were only weakly heritable.Conclusions/Significance:Together, our findings suggest that vector reproductive control programs should treat harmonic convergence as an indicator of some, but not all aspects of inherent quality, and that sexual selection likely affects Ae. aegypti in a trait-, population-, and environment-dependent manner.

  • Journal article
    Zhou L, Liu F, Liu Q, Fortin C, Tan Y, Huang L, Campbell PGCet al., 2021,

    Aluminum increases net carbon fixation by marine diatoms and decreases their decomposition: Evidence for the iron-aluminum hypothesis

    , LIMNOLOGY AND OCEANOGRAPHY, Vol: 66, Pages: 2712-2727, ISSN: 0024-3590
  • Journal article
    Shah T, Schneider JV, Zizka G, Maurin O, Baker W, Forest F, Brewer GE, Savolainen V, Darbyshire I, Larridon Iet al., 2021,

    Joining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits

    , AMERICAN JOURNAL OF BOTANY, Vol: 108, Pages: 1201-1216, ISSN: 0002-9122
  • Journal article
    Leroi AM, Lambert B, Rosindell J, Kokkoris GDet al., 2021,

    Neutral Theory is a tool that should be wielded with care

    , NATURE HUMAN BEHAVIOUR, Vol: 5, Pages: 809-809, ISSN: 2397-3374
  • Journal article
    Kuhn-Régnier A, Voulgarakis A, Nowack P, Forkel M, Prentice IC, Harrison SPet al., 2021,

    Quantifying the Importance of antecedent fuel-related vegetationproperties for burnt area using random forests

    , Biogeosciences, Vol: 8, ISSN: 1726-4170

    The seasonal and longer-term dynamics of fuel accumulation affect fire seasonality and the occurrence of extreme wildfires. Failure to account for their influence mayhelp to explain why state-of-the-art fire models do not simulate the length and timing of the fire season or interannual variability in burnt area well. We investigated the impact of accounting for different timescales of fuel production and accumulation on burnt area using a suite of random forest regression models that included the immediateimpact of climate, vegetation, and human influences in agiven month and tested the impact of various combinationsof antecedent conditions in four productivity-related vegetation indices and in antecedent moisture conditions. Analyses were conducted for the period from 2010 to 2015 inclusive. Inclusion of antecedent vegetation conditions representing fuel build-up led to an improvement of the global,climatological out-of-sample R2from 0.579 to 0.701, but theinclusion of antecedent vegetation conditions on timescales≥ 1 year had no impact on simulated burnt area. Currentmoisture levels were the dominant influence on fuel drying. Additionally, antecedent moisture levels were importantfor fuel build-up. The models also enabled the visualisationof interactions between variables, such as the importanceof antecedent productivity coupled with instantaneous drying. The length of the period which needs to be consideredvaries across biomes; fuel-limited regions are sensitive to antecedent conditions that determine fuel build-up over longertime periods (∼ 4 months), while moisture-limited regionsare more sensitive to current conditions that regulate fuel drying.

  • Journal article
    Kuhn- Regnier A, Voulgarakis A, Nowack P, Forkel M, Prentice IC, Harrison Set al., 2021,

    The importance of antecedent vegetation and drought conditions as global drivers of burnt areas

    , Biogeosciences, Vol: 18, Pages: 3861-3879, ISSN: 1726-4170

    The seasonal and longer-term dynamics of fuel accumulation affect fire seasonality and the occurrence of extreme wildfires. Failure to account for their influence may help to explain why state-of-the-art fire models do not simulate the length and timing of the fire season or interannual variability in burnt area well. We investigated the impact of accounting for different timescales of fuel production and accumulation on burnt area using a suite of random forest regression models that included the immediate impact of climate, vegetation, and human influences in a given month and tested the impact of various combinations of antecedent conditions in four productivity-related vegetation indices and in antecedent moisture conditions. Analyses were conducted for the period from 2010 to 2015 inclusive. Inclusion of antecedent vegetation conditions representing fuel build-up led to an improvement of the global, climatological out-of-sample R2 from 0.579 to 0.701, but the inclusion of antecedent vegetation conditions on timescales ≥ 1 year had no impact on simulated burnt area. Current moisture levels were the dominant influence on fuel drying. Additionally, antecedent moisture levels were important for fuel build-up. The models also enabled the visualisation of interactions between variables, such as the importance of antecedent productivity coupled with instantaneous drying. The length of the period which needs to be considered varies across biomes; fuel-limited regions are sensitive to antecedent conditions that determine fuel build-up over longer time periods (∼ 4 months), while moisture-limited regions are more sensitive to current conditions that regulate fuel drying.

  • Journal article
    Rurangwa ML, Aguirre-Gutierrez J, Matthews TJ, Niyigaba P, Wayman JP, Tobias JA, Whittaker RJet al., 2021,

    Effects of land-use change on avian taxonomic, functional and phylogenetic diversity in a tropical montane rainforest

    , Diversity and Distributions: a journal of conservation biogeography, Vol: 27, Pages: 1732-1746, ISSN: 1366-9516

    AimAlthough land use change is a leading cause of biodiversity loss worldwide, there is scant information on the extent to which it has affected the structure and composition of bird communities in the Afrotropical region. This study aimed to quantify the effects of habitat transformation on taxonomic, functional and phylogenetic diversity in Afrotropical bird communities.LocationNyungwe landscape, a montane rainforest with adjoining farmland in south-west Rwanda.MethodsData on bird occurrence, abundance and functional traits were collected in 2017/18 using point counts. We also collected data on habitat and morphological traits for all bird species recorded. We quantified bird diversity using a range of metrics, including the inverse Simpson index, functional dispersion and the standardized effect size of mean nearest taxon distance.ResultsIn comparison with primary forest areas, even low levels of land use change altered species composition and reduced species diversity. Although overall functional diversity and phylogenetic diversity were similar across land use types, we found a significant contraction of trophic and locomotory trait structures of bird communities in restored areas and cultivated areas, respectively. Soil moisture, elevation and lower vegetation height were major factors influencing taxonomic, functional and phylogenetic dimensions of bird communities, although their effects varied across these dimensions.Main conclusionsThe sensitivity of forest species to minor habitat disturbance emphasizes the value of conserving primary vegetation. Long-term conservation of bird communities in Afromontane ecosystems requires halting wide-scale destruction of primary forest, promoting vegetation heterogeneity in the ecological restoration of degraded habitats and adopting wildlife-friendly agricultural practices. Our results suggest that monitoring and conservation in these landscapes can be refined using taxonomic, functional and phylogenetic diversity metr

  • Journal article
    Smith TP, Flaxman S, Gallinat AS, Kinosian SP, Stemkovski M, Unwin HJT, Watson OJ, Whittaker C, Cattarino L, Dorigatti I, Tristem M, Pearse WDet al., 2021,

    Temperature and population density influence SARS-CoV-2 transmission in the absence of nonpharmaceutical interventions

    , Proceedings of the National Academy of Sciences of USA, Vol: 118, Pages: 1-8, ISSN: 0027-8424

    As COVID-19 continues to spread across the world, it is increasingly important to understand the factors that influence its transmission. Seasonal variation driven by responses to changing environment has been shown to affect the transmission intensity of several coronaviruses. However, the impact of the environment on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains largely unknown, and thus seasonal variation remains a source of uncertainty in forecasts of SARS-CoV-2 transmission. Here we address this issue by assessing the association of temperature, humidity, ultraviolet radiation, and population density with estimates of transmission rate (R). Using data from the United States, we explore correlates of transmission across US states using comparative regression and integrative epidemiological modeling. We find that policy intervention (“lockdown”) and reductions in individuals’ mobility are the major predictors of SARS-CoV-2 transmission rates, but, in their absence, lower temperatures and higher population densities are correlated with increased SARS-CoV-2 transmission. Our results show that summer weather cannot be considered a substitute for mitigation policies, but that lower autumn and winter temperatures may lead to an increase in transmission intensity in the absence of policy interventions or behavioral changes. We outline how this information may improve the forecasting of COVID-19, reveal its future seasonal dynamics, and inform intervention policies.

  • Journal article
    O'Loughlin SM, Forster AJ, Fuchs S, Dottorini T, Nolan T, Crisanti A, Burt Aet al., 2021,

    Ultra-conserved sequences in the genomes of highly diverse <i>Anopheles</i> mosquitoes, with implications for malaria vector control

    , G3-GENES GENOMES GENETICS, Vol: 11, ISSN: 2160-1836
  • Journal article
    Huaraca Huasco W, Riutta T, Girardin CAJ, Hancco Pacha F, Puma Vilca BL, Moore S, Rifai SW, del Aguila-Pasquel J, Araujo Murakami A, Freitag R, Morel AC, Demissie S, Doughty CE, Oliveras I, Galiano Cabrera DF, Durand Baca L, Farfan Amezquita F, Silva Espejo JE, da Costa ACL, Oblitas Mendoza E, Quesada CA, Evouna Ondo F, Edzang Ndong J, Jeffery KJ, Mihindou V, White LJT, N'ssi Bengone N, Ibrahim F, Addo-Danso SD, Duah-Gyamfi A, Djaney Djagbletey G, Owusu-Afriyie K, Amissah L, Mbou AT, Marthews TR, Metcalfe DB, Aragao LEO, Marimon-Junior BH, Marimon BS, Majalap N, Adu-Bredu S, Abernethy KA, Silman M, Ewers RM, Meir P, Malhi Yet al., 2021,

    Fine root dynamics across pantropical rainforest ecosystems

    , Global Change Biology, Vol: 27, Pages: 3657-3680, ISSN: 1354-1013

    Fine roots constitute a significant component of the net primary productivity (NPP) of forest ecosystems but are much less studied than aboveground NPP. Comparisons across sites and regions are also hampered by inconsistent methodologies, especially in tropical areas. Here, we present a novel dataset of fine root biomass, productivity, residence time, and allocation in tropical old-growth rainforest sites worldwide, measured using consistent methods, and examine how these variables are related to consistently determined soil and climatic characteristics. Our pantropical dataset spans intensive monitoring plots in lowland (wet, semi-deciduous, and deciduous) and montane tropical forests in South America, Africa, and Southeast Asia (n = 47). Large spatial variation in fine root dynamics was observed across montane and lowland forest types. In lowland forests, we found a strong positive linear relationship between fine root productivity and sand content, this relationship was even stronger when we considered the fractional allocation of total NPP to fine roots, demonstrating that understanding allocation adds explanatory power to understanding fine root productivity and total NPP. Fine root residence time was a function of multiple factors: soil sand content, soil pH, and maximum water deficit, with longest residence times in acidic, sandy, and water-stressed soils. In tropical montane forests, on the other hand, a different set of relationships prevailed, highlighting the very different nature of montane and lowland forest biomes. Root productivity was a strong positive linear function of mean annual temperature, root residence time was a strong positive function of soil nitrogen content in montane forests, and lastly decreasing soil P content increased allocation of productivity to fine roots. In contrast to the lowlands, environmental conditions were a better predictor for fine root productivity than for fractional allocation of total NPP to fine roots, suggesting t

  • Journal article
    Kuhn-Régnier A, Voulgarakis A, Nowack P, Forkel M, Prentice IC, Harrison SPet al., 2021,

    Supplementary material to &quot;Quantifying the Importance of Antecedent Fuel-Related VegetationProperties for Burnt Area using Random Forests&quot;

    , Biogeosciences, ISSN: 1726-4170
  • Journal article
    Luiselli J, Overcast I, Rominger A, Ruffley M, Morlon H, Rosindell Jet al., 2021,

    Detecting the ecological footprint of selection

    <jats:title>Abstract</jats:title><jats:p>The structure of communities is influenced by many ecological and evolutionary processes, but the way this manifests in classic biodiversity patterns often remains unclear. Here, we aim to distinguish the ecological footprint of selection – through competition or environmental filtering – from that of neutral processes that are invariant to species identity. We build on existing Massive Eco-evolutionary Synthesis Simulations (MESS), which uses information from three biodiversity axes – species abundances, genetic diversity, and trait variation – to distinguish between mechanistic processes. In order to correctly detect and characterise competition, we add a new and more realistic form of competition that explicitly compares the traits of each pair of individuals. Our results are qualitatively different to those of previous work in which competition is based on the distance of each individual’s trait to the community mean. We find that our new form of competition is easier to identify in empirical data compared to the alternatives. This is especially true when trait data are available and used in the inference procedure. Our findings hint that signatures in empirical data previously attributed to neutrality may in fact be the result of pairwise-acting selective forces. We conclude that gathering more different types of data, together with more advanced mechanistic models and inference as done here, could be the key to unravelling the mechanisms of community assembly.</jats:p>

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

    Ecosystem photosynthesis in land-surface models: a first-principles approach

    , Publisher: Cold Spring Harbor Laboratory

    Vegetation regulates land-atmosphere water and energy exchanges and is an essential component of land-surface models (LSMs). However, LSMs have been handicapped by assumptions that equate acclimated photosynthetic responses to environment with fast responses observable in the laboratory. These time scales can be distinguished by including specific representations of acclimation, but at the cost of further increasing parameter requirements. Here we develop an alternative approach based on optimality principles that predict the acclimation of carboxylation and electron-transport capacities, and a variable controlling the response of leaf-level carbon dioxide drawdown to vapour pressure deficit (VPD), to variations in growth conditions on a weekly to monthly time scale. In the “P model”, an optimality-based light-use efficiency model for gross primary production (GPP) on this time scale, these acclimated responses are implicit. Here they are made explicit, allowing fast and slow response time-scales to be separated and GPP to be simulated at sub-daily timesteps. The resulting model mimics diurnal cycles of GPP recorded by eddy-covariance flux towers in a temperate grassland and boreal, temperate and tropical forests, with no parameter changes between biomes. Best performance is achieved when biochemical capacities are adjusted to match recent midday conditions. This model suggests a simple and parameter-sparse method to include both instantaneous and acclimated responses within an LSM framework, with many potential applications in weather, climate and carbon - cycle modelling.

  • Journal article
    Ewers RM, Nathan SKSS, Lee PAK, 2021,

    African swine fever ravaging Borneo's wild pigs

    , NATURE, Vol: 593, Pages: 37-37, ISSN: 0028-0836
  • Journal article
    Banks-Leite C, Larrosa C, Carrasco LR, Tambosi LR, Milner-Gulland Eet al., 2021,

    The suggestion that landscapes should contain 40% of forest cover lacks evidence and is problematic

    , Ecology Letters, Vol: 24, Pages: 1112-1113, ISSN: 1461-023X

    A recent review suggests that forest cover needs to be restored or maintained on at least 40% of land area. In the absence of empirical evidence to support this threshold, we discuss how this suggestion is unhelpful and potentially dangerous. We advocate for regionally defined thresholds to inform conservation and restoration.

  • 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.

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