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  • Journal article
    Gonzalez A, Vihervaara P, Balvanera P, Bates AE, Bayraktarov E, Bellingham PJ, Bruder A, Campbell J, Catchen MD, Cavender-Bares J, Chase J, Coops N, Costello MJ, Czucz B, Delavaud A, Dornelas M, Dubois G, Duffy EJ, Eggermont H, Fernandez M, Fernandez N, Ferrier S, Geller GN, Gill M, Gravel D, Guerra CA, Guralnick R, Harfoot M, Hirsch T, Hoban S, Hughes AC, Hugo W, Hunter ME, Isbell F, Jetz W, Juergens N, Kissling WD, Krug CB, Kullberg P, Le Bras Y, Leung B, Londono-Murcia MC, Lord J-M, Loreau M, Luers A, Ma K, MacDonald AJ, Maes J, McGeoch M, Mihoub JB, Millette KL, Molnar Z, Montes E, Mori AS, Muller-Karger FE, Muraoka H, Nakaoka M, Navarro L, Newbold T, Niamir A, Obura D, O'Connor M, Paganini M, Pelletier D, Pereira H, Poisot T, Pollock LJ, Purvis A, Radulovici A, Rocchini D, Roeoesli C, Schaepman M, Schaepman-Strub G, Schmeller DS, Schmiedel U, Schneider FD, Shakya MM, Skidmore A, Skowno AL, Takeuchi Y, Tuanmu M-N, Turak E, Turner W, Urban MC, Urbina-Cardona N, Valbuena R, Van de Putte A, van Havre B, Wingate VR, Wright E, Torrelio CZet al., 2024,

    A global biodiversity observing system to unite monitoring and guide action (AUG, 10.1038/s41559-023-02171-0, 2023)

    , NATURE ECOLOGY & EVOLUTION, Vol: 8, Pages: 175-175, ISSN: 2397-334X
  • Journal article
    Ren Y, Wang H, Harrison SP, Prentice IC, Atkin OK, Smith NG, Mengoli G, Stefanski A, Reich PBet al., 2024,

    Reduced global plant respiration due to the acclimation of leaf dark respiration coupled to photosynthesis

    , New Phytologist, Vol: 241, Pages: 578-591, ISSN: 0028-646X

    Leaf dark respiration (Rd) acclimates to environmental changes. However, the magnitude, controls and time scales of acclimation remain unclear and are inconsistently treated in ecosystem models. We hypothesized that Rd and Rubisco carboxylation capacity (Vcmax) at 25°C (Rd,25, Vcmax,25) are coordinated so that Rd,25 variations support Vcmax,25 at a level allowing full light use, with Vcmax,25 reflecting daytime conditions (for photosynthesis), and Rd,25/Vcmax,25 reflecting night-time conditions (for starch degradation and sucrose export). We tested this hypothesis temporally using a 5-yr warming experiment, and spatially using an extensive field-measurement data set. We compared the results to three published alternatives: Rd,25 declines linearly with daily average prior temperature; Rd at average prior night temperatures tends towards a constant value; and Rd,25/Vcmax,25 is constant. Our hypothesis accounted for more variation in observed Rd,25 over time (R2 = 0.74) and space (R2 = 0.68) than the alternatives. Night-time temperature dominated the seasonal time-course of Rd, with an apparent response time scale of c. 2 wk. Vcmax dominated the spatial patterns. Our acclimation hypothesis results in a smaller increase in global Rd in response to rising CO2 and warming than is projected by the two of three alternative hypotheses, and by current models.

  • Journal article
    Kawaguchi S, Atkinson A, Bahlburg D, Bernard KS, Cavan EL, Cox MJ, Hill SL, Meyer B, Veytia Det al., 2024,

    Climate change impacts on Antarctic krill behaviour and population dynamics

    , NATURE REVIEWS EARTH & ENVIRONMENT, Vol: 5, Pages: 43-58
  • Journal article
    Preston-Allen RGG, Hakkinen H, Canellas-Dols L, Juarez EIAY, Orme CDL, Pettorelli Net al., 2024,

    Geography, taxonomy, extinction risk and exposure of fully migratory birds to droughts and cyclones

    , GLOBAL ECOLOGY AND BIOGEOGRAPHY, Vol: 33, Pages: 63-73, ISSN: 1466-822X
  • Journal article
    Coathup M, Savolainen V, 2024,

    Ecological speciation in sympatric palms: 5. Evidence for pleiotropic speciation genes using gene knockout and high-throughput phenotyping

    , Evolutionary Journal of the Linnean Society, Vol: 3, ISSN: 2752-938X

    Theoretical models predict that sympatric, ecological speciation may be facilitated more readily when so-called ‘magic traits’ are present, linking traits under divergent selection with assortative mating. Such traits might be encoded by pleiotropic genes, that is, genes that affect multiple, apparently unrelated, phenotypes. However, few convincing examples of sympatric speciation exist, and empirical evidence for the role of magic traits in driving such speciation is rare. One of the strongest cases of sympatric speciation is the Howea palms of Lord Howe Island, Australia, comprising the sister species H. belmoreana and H. forsteriana, which have diverged due to soil substrate preferences and flowering time displacement. By carrying out high-throughput phenotyping experiments using 1,830 Arabidopsis thaliana plants with knockouts of candidate Howea ‘speciation genes’, here we investigate the role that pleiotropy may have played in the speciation process. We identify several genes that show signatures of adaptive divergence between the Howea species and demonstrate pleiotropic roles in soil stress tolerance and flowering time, consistent with the Howea speciation scenario – notably, Howea orthologs of the A. thaliana loci At2-MMP, DCL1, RCD1, SAL1, and SIZ1. Empirical evidence is provided, therefore, for a range of pleiotropic genes with the potential to have driven sympatric speciation by generating magic traits which link divergent selection to non-random mating.

  • Journal article
    Chow LJ, Nesbit ML, Hill T, Tranter C, Evison SEF, Hughes WOH, Graystock Pet al., 2024,

    Identification of fungi isolated from commercial bumblebee colonies

    , PeerJ, Vol: 12, ISSN: 2167-8359

    Fungi can have important beneficial and detrimental effects on animals, yet our understanding of the diversity and function of most bee-associated fungi is poor. Over 2 million bumblebee colonies are traded globally every year, but the presence and transport of viable fungi within them is unknown. Here, we explored whether any culturable fungi could be isolated from commercial bumblebee nests. We collected samples of various substrates from within 14 bumblebee colonies, including the honey, honey cup wall, egg cup wall, and frass then placed them on agar and recorded any growth. Fungal morphotypes were then subcultured and their ITS region sequenced for identification. Overall, we cultured 11 fungal species from the various nest substrates. These included both pathogenic and non-pathogenic fungi, such as Aspergillus sp., Penicillium sp., and Candida sp. Our results provide the first insights into the diversity of viable fungal communities in commercial bumblebee nests. Further research is needed to determine if these fungi are unique to commercial colonies or prevalent in wild bumblebee nests, and crucially to determine the ecological and evolutionary implications of these fungi in host colonies.

  • Journal article
    Gonzalez-Ferreras AM, Barquin J, Blyth PSA, Hawksley J, Kinsella H, Lauridsen R, Morris OF, Penas FJ, Thomas GE, Woodward G, Zhao L, O'Gorman EJet al., 2023,

    Chronic exposure to environmental temperature attenuates the thermal sensitivity of salmonids

    , NATURE COMMUNICATIONS, Vol: 14
  • Book chapter
    Shocket M, Caldwell J, Huxley P, Lippi C, Windram F, Keyel Aet al., 2023,

    Modelling the effects of climate and climate change on transmission of vector-borne disease

    , Planetary health approaches to understand and control vector-borne diseases, Editors: Fornace, Conn, Mureb, Chaves, Logan, Publisher: BRILL, Pages: 253-318, ISBN: 9789004688650

    Mathematical and statistical models are critical tools for both understanding how climate can influence patterns of vector-borne disease transmission, and predicting how climate change might affect these patterns in the future. This chapter focuses primarily on quantitative approaches for modelling the effects of climate on mosquito-borne disease (MBD), although we also briefly consider tick-borne disease. We initially describe how the biological mechanisms that contribute to transmission of vector-borne disease can respond to changes in climate and other environmental factors. Importantly, transmission of MBD responds nonlinearly over gradients of both temperature and rainfall. When building or interpreting models for the effects of climate on MBD dynamics, it is important to consider that the effects of temperature and rainfall on disease may be positive, negative, or both depending on circumstance. This context-dependence can limit the transferability of models beyond the setting in which they were fit. Next, we provide an overview of important concepts and approaches for modelling vector-borne diseases using mechanistic and statistical models. This includes the most commonly used modelling methods, techniques for model evaluation and validation, and climate re-analysis products used as model predictors. The best choices of methods for model construction and evaluation depend on the goals of the model and the structure of the underlying data, including their spatial and temporal scales. Then, we explore three case studies of MBD in more detail and use them to illustrate representative modelling approaches across a gradient of spatiotemporal scales: (1) local time series models of dengue fever in San Juan, Puerto Rico; (2) regional models of West Nile virus in the United States; and (3) continental and global models for how climate change may impact future transmission risk for malaria and dengue fever. Finally, we note some key challenges, knowledge gaps, and res

  • Journal article
    Eberhart-Hertel LJ, Rodrigues LF, Krietsch J, Hertel AG, Cruz-Lopez M, Vazquez-Rojas KA, Gonzalez-Medina E, Schroeder J, Kuepper Cet al., 2023,

    Egg size variation in the context of polyandry: a case study using long-term field data from snowy plovers

    , EVOLUTION, Vol: 77, Pages: 2590-2605, ISSN: 0014-3820
  • Journal article
    Ruehr S, Keenan TF, Williams C, Zhou Y, Lu X, Bastos A, Canadell JG, Prentice IC, Sitch S, Terrer Cet al., 2023,

    Publisher Correction: Evidence and attribution of the enhanced land carbon sink (Nature Reviews Earth & Environment, (2023), 4, 8, (518-534), 10.1038/s43017-023-00456-3)

    , Nature Reviews Earth and Environment, Vol: 4

    Correction to: Nature Reviews Earth & Environment, published online 25 July 2023. In the version of the article initially published, the y-axis labels in Fig. 7b, now reading “+” and “–”, read “234” and “254”, respectively. This has been corrected in the HTML and PDF versions of the article.

  • Journal article
    Delabre I, Lyons-White J, Melot C, Veggeberg EI, Alexander A, Schleper MCC, Ewers RMM, Knight ATTet al., 2023,

    Should I stay or should I go? Understanding stakeholder dis/engagement for deforestation-free palm oil

    , Business Strategy and the Environment, Vol: 32, Pages: 5128-5145, ISSN: 0964-4733

    Addressing tropical deforestation in the palm oil sector involves a diverse range of stakeholders who engage or disengage with each other. Palm oil global value chain (GVC) firms (plantation companies, traders and processors, and consumer goods manufacturers and retailers), as well as nongovernmental organisations, financial institutions, consultancies and certification bodies, pursue their respective organisations' agendas through engagement practices, including through coalitions, in a palm oil sustainability network (POSN). Building on interviews with different stakeholder groups, this qualitative study characterises and critically analyses ‘stakeholder engagement’ by examining (1) the priority targets for engagement among different POSN stakeholders, (2) how mechanisms and tools are used in POSN stakeholder engagement or disengagement for addressing deforestation, and (3) the implications of stakeholder engagement or disengagement for addressing deforestation. Engagement and disengagement practices are shaped by and reshape GVC governance, with powerful stakeholders emerging as knowledge brokers and norm setters, raising important challenges for how deforestation is addressed.

  • Journal article
    Tudge SJ, Harris ZM, Murphy RJ, Purvis A, De Palma Aet al., 2023,

    Global trends in biodiversity with tree plantation age

    , GLOBAL ECOLOGY AND CONSERVATION, Vol: 48
  • Journal article
    Keenan TF, Luo X, Stocker BD, De Kauwe MG, Medlyn BE, Prentice IC, Smith NG, Terrer C, Wang H, Zhang Y, Zhou Set al., 2023,

    A constraint on historic growth in global photosynthesis due to rising CO2

    , Nature Climate Change, Vol: 13, Pages: 1376-1381, ISSN: 1758-678X

    Theory predicts that rising CO2 increases global photosynthesis, a process known as CO2 fertilization, and that this is responsible for a large proportion of the current terrestrial carbon sink. The estimated magnitude of the historic CO2 fertilization, however, differs by an order ofmagnitude between long-term proxies, remote sensing-based estimates and terrestrial biosphere models. Here we constrain the likely historic effect of CO2 on global photosynthesis by combining terrestrial biosphere models, ecological optimality theory, remote sensing approaches and an emergent constraint based on global carbon budget estimates. Our analysis suggests that CO2 fertilization increased global annual terrestrial photosynthesis by 13.5 ± 3.5%, or 15.9 ± 2.9 Pg C u(mean ± standard deviation) between 1981 and 2020. Our results help resolve conflicting estimates of the historic sensitivity of global terrestrial photosynthesis to CO2 and highlight the large impact anthropogenic emissions have had on ecosystems worldwide.

  • Journal article
    Peng Y, Prentice IC, Bloomfield KJ, Campioli M, Guo Z, Sun Y, Tian D, Wang X, Vicca S, Stocker BDet al., 2023,

    Global terrestrial nitrogen uptake and nitrogen use efficiency

    , Journal of Ecology, Vol: 111, Pages: 2676-2693, ISSN: 0022-0477

    1. Plant biomass production (BP), nitrogen uptake (Nup) and their ratio, nitrogen use efficiency (NUE), must be quantified to understand how nitrogen (N) cycling constrains terrestrial carbon (C) uptake. But the controls of key plant processes determining Nup and NUE, including BP, C and N allocation, tissue C:N ratios and N resorption efficiency (NRE), remain poorly known. 2. We compiled measurements from 804 forest and grassland sites and derived regression models for each of these processes with growth temperature, vapour pressure deficit, stand age, soil C:N ratio, fAPAR (remotely sensed fraction of photosynthetically active radiation absorbed by green vegetation) and growing-season average daily incident photosynthetic photon flux density (gPPFD) (effectively the seasonal concentration of light availability, which increases polewards) as predictors. An empirical model for leaf N was based on optimal photosynthetic capacity (a function of gPPFD and climate) and observed leaf mass-per-area. The models were used to produce global maps of Nup and NUE. 3. Global BP was estimated as 72 Pg C/yr; Nup as 950 Tg N/yr; and NUE as 76 gC/gN. Forest BP was found to increase with growth temperature and fAPAR and to decrease with stand age, soil C:N ratio and gPPFD. Forest NUE is controlled primarily by climate through its effect on C allocation – especially to leaves, being richer in N than other tissues. NUE is greater in colder climates, where N is less readily available, because belowground allocation is increased. NUE is also greater in drier climates because leaf allocation is reduced. NRE is enhanced (further promoting NUE) in both cold and dry climates. 4. These findings can provide observationally based benchmarks for model representations of C–N cycle coupling. State-of-the-art vegetation models in the TRENDY ensemble showed variable performance against these benchmarks, and models including coupled C–N cycling produced relatively poor simulations o

  • Journal article
    Dimitrov D, Xu X, Su X, Shrestha N, Liu Y, Kennedy JD, Lyu L, Nogues-Bravo D, Rosindell J, Yang Y, Fjeldsa J, Liu J, Schmid B, Fang J, Rahbek C, Wang Zet al., 2023,

    Diversification of flowering plants in space and time

    , NATURE COMMUNICATIONS, Vol: 14
  • Journal article
    Xu H, Wang H, Prentice IC, Harrison SPet al., 2023,

    Leaf carbon and nitrogen stoichiometric variation alongenvironmental gradients

    , Biogeosciences, Vol: 20, Pages: 4511-4525, ISSN: 1726-4170

    Leaf stoichiometric traits are central to ecosystem function and biogeochemical cycling, yet no accepted theory predicts their variation along environmental gradients. Using data in the China Plant Trait Database version 2, we aimed to characterize variation in leaf carbon and nitrogen per unit mass (Cmass, Nmass) and their ratio, and to test an eco-evolutionary optimality model for Nmass. Community-mean trait values were related to climate variables by multiple linear regression. Climatic optima and tolerances of major genera were estimated; Pagel’s λ was used to quantify phylogenetic controls, and Bayesian phylogenetic linear mixed models to assess the contributions of climate, species identity and phylogeny. Optimality-based predictions of community-mean Nmass were compared to observed values. All traits showed strong phylogenetic signals. Climate explained only 18 % of C : N ratio variation among species but 45 % among communities, highlighting the role of taxonomic replacement in mediating community-level responses. Geographic distributions of deciduous taxa separated primarily by moisture, evergreens by temperature. Cmass increased with irradiance, but decreased with moisture and temperature. Nmass declined with all three variables. C : N ratio variations were dominated by Nmass. The coefficients relating Nmass to the ratio of maximum carboxylation capacity at 25 °C (Vcmax25) and leaf mass per area (Ma) were influenced by leaf area index. The optimality model captured 68 % and 53 % of variation between communities for Vcmax25 and Ma respectively, and 30 % for Nmass. We conclude that stoichiometric variations along climate gradients are achieved largely by environmental selection among species and clades with different characteristic trait values. Variations in leaf C : N ratio are mainly determined by Nmass, and optimality-based modelling shows useful predictive ability for community-mean Nmass. These findings should help to improve the repres

  • Journal article
    Brazeau M, Castiello M, El Fassi El Fehri A, Hamilton L, Ivanov AO, Johanson Z, Friedman Met al., 2023,

    Fossil evidence for a pharyngeal origin of the vertebrate pectoral girdle

    , Nature, Vol: 623, Pages: 550-554, ISSN: 0028-0836

    The origin of vertebrate paired appendages is one of the most investigated and debated examples of evolutionary novelty. Paired appendages are widely considered key innovations that allowed new opportunities for controlled swimming and gill ventilation and were prerequisites for the eventual transition from water to land. The last 150 years of debate has been shaped by two contentious theories: the ventrolateral fin-fold hypothesis and the archipterygium hypothesis. The latter proposes that fins and girdles evolved from an ancestral gill arch. Although tantalizing developmental evidence has revived interest in this idea, it is apparently unsupported by fossil evidence. Here we present fossil evidence of a pharyngeal basis for the vertebrate shoulder girdle. We use CT scanning to reveal details of the braincase of Kolymaspis sibirica, a placoderm fish from the Early Devonian of Siberia that suggests a pharyngeal component of the shoulder. We combine these findings with refreshed comparative anatomy of placoderms and jawless outgroups to place the origin of the shoulder girdle on the sixth branchial arch. These findings provide a novel framework for understanding the origin of the pectoral girdle. Our new evidence clarifies the location of the presumptive head-trunk interface in jawless fishes and explains the constraint on branchial arch number in gnathostomes. The results revive a key aspect of the archipterygium hypothesis, but also reconciles it with the ventrolateral fin fold model.

  • Other
    Blackford KR, Kasoar M, Burton C, Burke E, Prentice IC, Voulgarakis Aet al., 2023,

    Supplementary material to "INFERNO-peat v1.0.0: A representation of northern high latitude peat fires in the JULES-INFERNO global fire model"

  • Journal article
    Mwima R, Hui T-YJ, Nanteza A, Burt A, Kayondo JKet al., 2023,

    Potential persistence mechanisms of the major Anopheles gambiae species complex malaria vectors in sub-Saharan Africa: a narrative review

    , Malaria Journal, Vol: 22, ISSN: 1475-2875

    The source of malaria vector populations that re-establish at the beginning of the rainy season is still unclear yet knowledge of mosquito behaviour is required to effectively institute control measures. Alternative hypotheses like aestivation, local refugia, migration between neighbouring sites, and long-distance migration (LDM) are stipulated to support mosquito persistence. This work assessed the malaria vector persistence dynamics and examined various studies done on vector survival  via these hypotheses; aestivation, local refugia, local or long-distance migration across sub-Saharan Africa, explored a range of methods used, ecological parameters and highlighted the knowledge trends and gaps. The results about a particular persistence mechanism that supports the re-establishment of Anopheles gambiae, Anopheles coluzzii or Anopheles arabiensis in sub-Saharan Africa were not conclusive given that each method used had its limitations. For example, the Mark-Release-Recapture (MRR) method whose challenge is a low recapture rate that affects its accuracy, and the use of time series analysis through field collections whose challenge is the uncertainty about whether not finding mosquitoes during the dry season is a weakness of the conventional sampling methods used or because of hidden shelters. This, therefore, calls for further investigations emphasizing the use of ecological experiments under controlled conditions in the laboratory or semi-field, and genetic approaches, as they are known to complement each other. This review, therefore, unveils and assesses the uncertainties that influence the different malaria vector persistence mechanisms and provides recommendations for future studies.

  • Journal article
    Mayfield MM, Lau JA, Tobias JA, Ives AR, Strauss SYet al., 2023,

    What Can Evolutionary History Tell Us about the Functioning of Ecological Communities? The ASN Presidential Debate

    , AMERICAN NATURALIST, ISSN: 0003-0147
  • Journal article
    Stewart K, Carmona CP, Clements C, Venditti C, Tobias JA, González-Suárez Met al., 2023,

    Functional diversity metrics can perform well with highly incomplete data sets

    , Methods in Ecology and Evolution, Vol: 14, Pages: 2856-2872

    Characterising changes in functional diversity at large spatial scales provides insight into the impact of human activity on ecosystem structure and function. However, the approach is often based on trait data sets that are incomplete and unrepresentative, with uncertain impacts on functional diversity estimates. To address this knowledge gap, we simulated random and biased removal of data from three empirical trait data sets: an avian data set (9579 species), a plant data set (2185 species) and a crocodilian data set (25 species). For these data sets, we assessed whether functional diversity metrics were robust to data incompleteness with and without using imputation to fill data gaps. We compared two metrics each calculated with two methods: functional richness (calculated with convex hulls and trait probabilities densities) and functional divergence (calculated with distance-based Rao and trait probability densities). Without imputation, estimates of functional diversity (richness and divergence) for birds and plants were robust when 20%–70% of species had missing data for four out of 11 and two out of six continuous traits, respectively, depending on the severity of bias and method used. However, when missing traits were imputed, functional diversity metrics consistently remained representative of the true value when 70% of bird species were missing data for four out of 11 traits and when 50% of plant species were missing data for two out of six traits. Trait probability densities and distance-based Rao were particularly robust to missingness and bias when combined with imputation. Convex hull-based estimations of functional richness were less reliable. When applied to a smaller data set (crocodilians, 25 species), all functional diversity metrics were much more sensitive to missing data. Expanding global morphometric data sets to represent more taxa and traits, and to quantify intraspecific variation, remains a priority. In the meantime, our results show

  • Journal article
    Cruz-Silva E, Harrison SP, Prentice IC, Marinova E, Bartlein PJ, Renssen H, Zhang Yet al., 2023,

    Pollen-based reconstructions of Holocene climate trends in the eastern Mediterranean region

    , CLIMATE OF THE PAST, Vol: 19, Pages: 2093-2108, ISSN: 1814-9324
  • Journal article
    Burton VJ, Baselga A, De Palma A, Phillips HRP, Mulder C, Eggleton P, Purvis Aet al., 2023,

    Effects of land use and soil properties on taxon richness and abundance of soil assemblages

    , EUROPEAN JOURNAL OF SOIL SCIENCE, Vol: 74, ISSN: 1351-0754
  • Journal article
    O'Gorman EJ, Zhao L, Kordas RL, Dudgeon S, Woodward Get al., 2023,

    Warming indirectly simplifies food webs through effects on apex predators

    , NATURE ECOLOGY & EVOLUTION, ISSN: 2397-334X
  • Journal article
    Devenish AJM, Schmitter P, Jellason NP, Esmail N, Abdi NM, Adanu SK, Adolph B, Al-Zubi M, Amali AA, Barron J, Chapman ASA, Chausson AM, Chibesa M, Davies J, Dugan E, Edwards GI, Egeru A, Gebrehiwot T, Griffiths GH, Haile A, Hunga HG, Igbine L, Jarju OM, Keya F, Khalifa M, Ledoux WA, Lejissa LT, Loupa P, Lwanga J, Mapedza ED, Marchant R, McLoud T, Mukuyu P, Musah LM, Mwanza M, Mwitwa J, Neina D, Newbold T, Njogo S, Robinson EJZ, Singini W, Umar BB, Wesonga F, Willcock S, Yang J, Tobias JAet al., 2023,

    One hundred priority questions for the development of sustainable food systems in Sub-Saharan Africa

    , Land, Vol: 12, ISSN: 2073-445X

    Sub-Saharan Africa is facing an expected doubling of human population and tripling of food demand over the next quarter century, posing a range of severe environmental, political, and socio-economic challenges. In some cases, key Sustainable Development Goals (SDGs) are in direct conflict, raising difficult policy and funding decisions, particularly in relation to trade-offs between food production, social inequality, and ecosystem health. In this study, we used a horizon-scanning approach to identify 100 practical or research-focused questions that, if answered, would have the greatest positive impact on addressing these trade-offs and ensuring future productivity and resilience of food-production systems across sub-Saharan Africa. Through direct canvassing of opinions, we obtained 1339 questions from 331 experts based in 55 countries. We then used online voting and participatory workshops to produce a final list of 100 questions divided into 12 thematic sections spanning topics from gender inequality to technological adoption and climate change. Using data on the background of respondents, we show that perspectives and priorities can vary, but they are largely consistent across different professional and geographical contexts. We hope these questions provide a template for establishing new research directions and prioritising funding decisions in sub-Saharan Africa.

  • Journal article
    Savolainen V, 2023,

    Environmental DNA helps reveal reef shark distribution across a remote archipelago

    , Ecological Indicators, Vol: 154, Pages: 1-10, ISSN: 1470-160X

    Environmental DNA (eDNA) methods are being increasingly used in proof-of-concept studies to detect shark species, many populations of which are experiencing severe declines. These methods are widely seen as the future of biodiversity monitoring, but they have yet to become established as routine monitoring techniques for elasmobranch species. Here, we developed species-specific quantitative PCR assays for the detection of grey reef shark (Carcharhinus amblyrhynchos) and silvertip shark (Carcharhinus albimarginatus). We assessed whether species-specific eDNA methods could infer the distribution of the two species around the atolls of the Chagos Archipelago, which, despite being surrounded by a large marine protected area, experience contrasting levels of illegal fishing leading to heterogeneity in shark population densities. We found that eDNA detections were significantly reduced and sporadic around the northern atolls, which are under high pressure from illegal fishing. By contrast eDNA detections of both species were ubiquitous and consistent around the highly protected atoll Diego Garcia. We postulate that current levels of illegal, unreported and unregulated (IUU) fishing is having a significant impact on the shark community in the northern atolls and suppressing local reef shark populations. In the northern atolls we also employed visual and acoustic telemetry techniques to reveal the distribution of reef sharks. We found that despite eDNA samples being taken directly after visual surveys, detection results did not correlate, suggesting a need for further optimisation of eDNA methods for detecting sharks. However, both species were detected by eDNA in sites where they were not observed, highlighting that the scale of the sampling environment must be considered when inferring eDNA results and showing that eDNA methods can be used to fill gaps in data from more established monitoring techniques. We conclude that eDNA methods should be used in combination with oth

  • Journal article
    Egli M, Rapp Wright H, Oloyede O, Francis W, Preston-Allen R, Friedman S, Woodward G, Piel FB, Barron LPet al., 2023,

    A One-Health environmental risk assessment of contaminants of emerging concern in London’s waterways throughout the SARS-CoV-2 pandemic

    , Environment International, Vol: 180, ISSN: 0160-4120

    The SARS-CoV-2 pandemic had huge impacts on global urban populations, activity and health, yet little is known about attendant consequences for urban river ecosystems. We detected significant changes in occurrence and risks from contaminants of emerging concern (CECs) in waterways across Greater London (UK) during the pandemic. We were able to rapidly identify and monitor large numbers of CECs in n=390 samples across 2019–2021 using novel direct-injection liquid chromatography-mass spectrometry methods for scalable targeted analysis, suspect screening and prioritisation of CEC risks. At total of 10,029 measured environmental concentrations (MECs) were obtained for 66 unique CECs. Pharmaceutical MECs decreased during lockdown in 2020 in the R. Thames (p≤0.001), but then increased significantly in 2021 (p ≤0.01). For the tributary rivers, the R. Lee, Beverley Brook, R. Wandle and R. Hogsmill were the most impacted primarily via wastewater treatment plant effluent and combined sewer overflows. For the R. Hosgmill in particular, pharmaceutical MEC trends were generally correlated with NHS prescription statistics, likely reflecting limited wastewater dilution. Suspect screening of ∼1,200 compounds tentatively identified 25 additional CECs at the five impacted sites, including metabolites such as O-desmethylvenlafaxine, an EU Watch List compound. Lastly, risk quotients (RQs) ≥0.1 were calculated for 21 compounds across the whole Greater London freshwater catchment, of which 7 were of medium risk (RQ ≥1.0) and three were in the high-risk category (RQ ≥10), including imidacloprid (RQ=19.6), azithromycin (15.7) and diclofenac (10.5). This is the largest spatiotemporal dataset of its kind for any major capital city globally and the first for Greater London, representing ∼16 % of the population of England, and delivering a foundational One Health case study in the third largest city in Europe across a global pandemic.

  • Journal article
    Haas O, Prentice IC, Harrison SP, 2023,

    The response of wildfire regimes to Last Glacial Maximum carbon dioxide and climate

    , BIOGEOSCIENCES, Vol: 20, Pages: 3981-3995, ISSN: 1726-4170
  • Journal article
    Kvasnica J, Matula R, Rejzek M, Ewers RM, Riutta T, Turner EC, Nilus R, Svatek Met al., 2023,

    Multi-stemming enhances tree survival and growth in Borneo's logged forests

    , FOREST ECOLOGY AND MANAGEMENT, Vol: 544, ISSN: 0378-1127
  • Journal article
    Dunne EM, Thompson SED, Butler RJ, Rosindell J, Close RAet al., 2023,

    Mechanistic neutral models show that sampling biases drive the apparent explosion of early tetrapod diversity

    , Nature Ecology and Evolution, Vol: 7, Pages: 1480-1489, ISSN: 2397-334X

    Estimates of deep-time biodiversity typically rely on statistical methods to mitigate the impacts of sampling biases in the fossil record. However, these methods are limited by the spatial and temporal scale of the underlying data. Here we use a spatially explicit mechanistic model, based on neutral theory, to test hypotheses of early tetrapod diversity change during the late Carboniferous and early Permian, critical intervals for the diversification of vertebrate life on land. Our simulations suggest that apparent increases in early tetrapod diversity were not driven by local endemism following the ‘Carboniferous rainforest collapse’. Instead, changes in face-value diversity can be explained by variation in sampling intensity through time. Our results further demonstrate the importance of accounting for sampling biases in analyses of the fossil record and highlight the vast potential of mechanistic models, including neutral models, for testing hypotheses in palaeobiology.

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