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Journal articleStewart K, Carmona CP, Clements C, et al., 2023,
Functional diversity metrics can perform well with highly incomplete data sets
, Methods in Ecology and Evolution, Vol: 14, Pages: 2856-2872Characterising 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
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Journal articleMayfield MM, Lau JA, Tobias JA, et al., 2023,
What Can Evolutionary History Tell Us about the Functioning of Ecological Communities? The ASN Presidential Debate
, AMERICAN NATURALIST, ISSN: 0003-0147 -
Journal articleCruz-Silva E, Harrison SP, Prentice IC, et 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 articleBurton VJ, Baselga A, De Palma A, et 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 articleO'Gorman EJ, Zhao L, Kordas RL, et al., 2023,
Warming indirectly simplifies food webs through effects on apex predators
, NATURE ECOLOGY & EVOLUTION, ISSN: 2397-334X -
Journal articleDevenish AJM, Schmitter P, Jellason NP, et al., 2023,
One hundred priority questions for the development of sustainable food systems in Sub-Saharan Africa
, Land, Vol: 12, ISSN: 2073-445XSub-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.
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Journal articleSavolainen V, 2023,
Environmental DNA helps reveal reef shark distribution across a remote archipelago
, Ecological Indicators, Vol: 154, Pages: 1-10, ISSN: 1470-160XEnvironmental 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
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Journal articleEgli M, Rapp Wright H, Oloyede O, et 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: 0160-4120The 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.
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Journal articleHaas 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 articleKvasnica J, Matula R, Rejzek M, et al., 2023,
Multi-stemming enhances tree survival and growth in Borneo's logged forests
, FOREST ECOLOGY AND MANAGEMENT, Vol: 544, ISSN: 0378-1127 -
Journal articleDunne EM, Thompson SED, Butler RJ, et 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: 2397-334XEstimates 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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Journal articleZhou L, Liu F, Tan Y, et al., 2023,
Aluminum-induced changes in the net carbon fixation and carbon decomposition of a nitrogen-fixing cyanobacterium Trichodesmium erythraeum
, Biogeochemistry, Vol: 165, Pages: 277-290, ISSN: 0168-2563 -
Journal articleLaurenceau-Cornec EC, Mongin M, Trull TW, et al., 2023,
Concepts Toward a Global Mechanistic Mapping of Ocean Carbon Export
, GLOBAL BIOGEOCHEMICAL CYCLES, Vol: 37, ISSN: 0886-6236 -
Journal articleGonzalez A, Vihervaara P, Balvanera P, et al., 2023,
A global biodiversity observing system to unite monitoring and guide action
, NATURE ECOLOGY & EVOLUTION, ISSN: 2397-334X- Author Web Link
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Journal articleRosindell J, 2023,
Indicators to monitor the status of the Tree of Life
, Conservation Biology, ISSN: 0888-8892 -
Journal articleRuehr S, Keenan TF, Williams C, et al., 2023,
Evidence and attribution of the enhanced land carbon sink
, Nature Reviews Earth & Environment, Vol: 4, Pages: 518-534, ISSN: 2662-138XClimate change has been partially mitigated by an increasing net land carbon sink in the terrestrial biosphere; understanding the processes that drive the land carbon sink is thus essential for protecting, managing, and projecting this important ecosystem service. In this Review, we examine evidence for an enhanced land carbon sink and attribute the observed response to drivers and processes. The land carbon sink has doubled from 1.2 ± 0.5 PgC yr-1 in the 1960s to 3.1 ± 0.6 PgC yr-1 in the 2010s. This trend results largely from carbon dioxide (CO2) fertilization increasing photosynthesis (driving an increase in the annual land carbon sink of >2PgC globally since 1900), mainly in tropical forest regions, and elevated temperatures reducing cold-limitation, mainly at higher latitudes. Continued long term land carbon sequestration is possible through the end of this century under multiple emissions scenarios, especially if nature-based climate solutions and appropriate ecosystem management are deployed. A new generation of globally distributed field experiments are needed to improve understanding of future carbon sink potential by measuring belowground carbon release, the response to CO2 enrichment, and long-term shifts in carbon allocation and turnover .
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Journal articleAlif Ž, Crees JJ, White RL, et al., 2023,
Understanding local knowledge and attitudes toward potential reintroduction of a former British wetland bird
, People and Nature, Vol: 5, Pages: 1220-1233, ISSN: 2575-8314Stakeholder acceptance and support is essential for long-term success in species reintroductions, and assessing social feasibility of reintroductions within human-occupied landscapes is an integral component of effective decision-making.The Dalmatian pelican Pelecanus crispus is an extirpated British bird, and possible pelican reintroduction to British wetlands is under discussion. Any reintroduction planning must first assess local community awareness, attitudes, and acceptance of potential pelican arrival and associated habitat management, as part of wider socio-ecological feasibility assessment. Pelicans are distinctive species with potential to increase support for wetland conservation, but might provoke conflict through real or perceived competition with landscape users such as fishers; such conflict is already seen within Britain between fishers and cormorants.We conducted an online survey of 590 respondents in the Somerset Levels and East Anglian Fens, Britain's largest wetland landscapes, to understand local views on pelican reintroduction, other reintroductions and wetland restoration, and to investigate correlates of varying attitudes toward coexistence with pelicans and five other waterbirds (grey heron, Eurasian bittern, little egret, common crane, great cormorant).Respondents had generally positive views about previous reintroductions of other species, and had overall positive attitudes toward all six waterbirds. Two-thirds of respondents supported or strongly supported pelican reintroduction, but both benefits and concerns were identified in relation to its possible reintroduction. Anglers and hunters were more likely to hold negative attitudes toward pelicans, other waterbirds and wetland restoration. However, although anglers raised more concerns, they were not more likely to be unsupportive toward reintroduction. More socio-demographic predictors were associated with negative attitudes toward restoration required to establish pelican habitat, sugges
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Journal articleBellotto-Trigo FC, Uezu A, Hatfield JH, et al., 2023,
Intraspecific variation in sensitivity to habitat fragmentation is influenced by forest cover and distance to the range edge
, BIOLOGICAL CONSERVATION, Vol: 284, ISSN: 0006-3207 -
Journal articleFattorini R, Egan PA, Rosindell J, et al., 2023,
Grayanotoxin I variation across tissues and species of Rhododendron suggests pollinator-herbivore defence trade-offs
, Phytochemistry: the international journal of plant chemistry, plant biochemistry and molecular biology, Vol: 212, Pages: 1-7, ISSN: 0031-9422Grayanotoxin I (GTX I) is a major toxin in leaves of Rhododendron species, where it provides a defence against insect and vertebrate herbivores. Surprisingly, it is also present in R. ponticum nectar, and this can hold important implications for plant-pollinator mutualisms. However, knowledge of GTX I distributions across the genus Rhododendron and in different plant materials is currently limited, despite the important ecological function of this toxin. Here we characterise GTX I expression in the leaves, petals, and nectar of seven Rhododendron species. Our results indicated interspecific variation in GTX I concentration across all species. GTX I concentrations were consistently higher in leaves compared to petals and nectar. Our findings provide preliminary evidence for phenotypic correlation between GTX I concentrations in defensive tissues (leaves and petals) and floral rewards (nectar), suggesting that Rhododendron species may commonly experience functional trade-offs between herbivore defence and pollinator attraction.
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Journal articlePearse WD, Stemkovski M, Lee BRR, et al., 2023,
Consistent, linear phenological shifts across a century of observations in South Korea
, NEW PHYTOLOGIST, Vol: 239, Pages: 824-829, ISSN: 0028-646X -
Journal articleSethi SS, Bick A, Ewers RM, et al., 2023,
Limits to the accurate and generalizable use of soundscapes to monitor biodiversity
, Nature Ecology and Evolution, Vol: 7, Pages: 1373-1378, ISSN: 2397-334XAlthough eco-acoustic monitoring has the potential to deliver biodiversity insight on vast scales, existing analytical approaches behave unpredictably across studies. We collated 8,023 audio recordings with paired manual avifaunal point counts to investigate whether soundscapes could be used to monitor biodiversity across diverse ecosystems. We found that neither univariate indices nor machine learning models were predictive of species richness across datasets but soundscape change was consistently indicative of community change. Our findings indicate that there are no common features of biodiverse soundscapes and that soundscape monitoring should be used cautiously and in conjunction with more reliable in-person ecological surveys.
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Journal articleDobson S, Dunning J, Burke T, et al., 2023,
Indirect genetic effects increase heritability estimates for male and female extra-pair reproduction
, EVOLUTION, Vol: 77, Pages: 1893-1901, ISSN: 0014-3820 -
Journal articleClive J, Flintham E, Savolainen V, 2023,
Same-sex sociosexual behaviour is widespread and heritable in male rhesus macaques
, Nature Ecology and Evolution, Vol: 7, Pages: 1287-1301, ISSN: 2397-334XNumerous reports have documented the occurrence of same-sex sociosexual behaviour (SSB) across animal species. However, the distribution of the behaviour within a species is needed to test the theories describing its evolution and maintenance, in particular whether the behaviour is heritable and can therefore evolve by natural selection. Here, we collected detailed observations across three years of social and mounting behaviour of 236 male semi-wild rhesus macaques, which we combined with a pedigree dating back to 1938, to show that SSB was both repeatable (19.35%) and heritable (6.4%). Demographic factors (age and group structure) explained SSB variation only marginally. Furthermore, we found a positive genetic correlation between same-sex mounter and mountee activities, indicating a common basis to different forms of SSB. Finally, we found no evidence of fitness costs to SSB, but show instead that the behaviour mediated coalitionary partnerships that have been linked with improved reproductive success. Together, our results demonstrate that SSB is frequent in rhesus macaques, can evolve, and is not costly, indicating that SSB may be a common feature of primate reproductive ecology.
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Journal articleJohansson J, Arce A, Gill R, 2023,
How competition between overlapping generations can influence optimal egg-laying strategies in annual social insects
, Oecologia, Vol: 202, Pages: 535-547, ISSN: 0029-8549Annual social insects are an integral functional group of organisms, particularly in temperate environments. An emblematic part of their annual cycle is the social phase, during which the colony-founding queen rears workers that later assist her in rearing sexual progeny (gynes and drones). In many annual social insects, such as species of bees, wasps, and other groups, developing larvae are provisioned gradually as they develop (progressive provisioning) leading to multiple larval generations being reared simultaneously. We present a model for how the queen in such cases should optimize her egg-laying rate throughout the social phase depending on number-size trade-offs, colony age-structure, and energy balance. Complementing previous theory on optimal allocation between workers vs. sexuals in annual social insects and on temporal egg-laying patterns in solitary insects, we elucidate how resource competition among overlapping larval generations can influence optimal egg-laying strategies. With model parameters informed by knowledge of a common bumblebee species, the optimal egg-laying schedule consists of two temporally separated early broods followed by a more continuous rearing phase, matching empirical observations. However, eggs should initially be laid continuously at a gradually increasing rate when resources are scarce or mortality risks high and in cases where larvae are fully supplied with resources at the egg-laying stage (mass-provisioning). These factors, alongside sexual:worker body size ratios, further determine the overall trend in egg-laying rates over the colony cycle. Our analysis provides an inroad to study and mechanistically understand variation in colony development strategies within and across species of annual social insects.
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Journal articleGranville NR, Banks-Leite C, 2023,
Mangrove propagules are limited in their capacity to disperse across long distances
, JOURNAL OF TROPICAL ECOLOGY, Vol: 39, ISSN: 0266-4674 -
Journal articlede Lorm TA, Horswill C, Rabaiotti D, et al., 2023,
Optimizing the automated recognition of individual animals to support population monitoring
, Ecology and Evolution, Vol: 13, ISSN: 2045-7758Reliable estimates of population size and demographic rates are central to assessing the status of threatened species. However, obtaining individual-based demographic rates requires long-term data, which is often costly and difficult to collect. Photographic data offer an inexpensive, noninvasive method for individual-based monitoring of species with unique markings, and could therefore increase available demographic data for many species. However, selecting suitable images and identifying individuals from photographic catalogs is prohibitively time-consuming. Automated identification software can significantly speed up this process. Nevertheless, automated methods for selecting suitable images are lacking, as are studies comparing the performance of the most prominent identification software packages. In this study, we develop a framework that automatically selects images suitable for individual identification, and compare the performance of three commonly used identification software packages; Hotspotter, I3S-Pattern, and WildID. As a case study, we consider the African wild dog, Lycaon pictus, a species whose conservation is limited by a lack of cost-effective large-scale monitoring. To evaluate intraspecific variation in the performance of software packages, we compare identification accuracy between two populations (in Kenya and Zimbabwe) that have markedly different coat coloration patterns. The process of selecting suitable images was automated using convolutional neural networks that crop individuals from images, filter out unsuitable images, separate left and right flanks, and remove image backgrounds. Hotspotter had the highest image-matching accuracy for both populations. However, the accuracy was significantly lower for the Kenyan population (62%), compared to the Zimbabwean population (88%). Our automated image preprocessing has immediate application for expanding monitoring based on image matching. However, the difference in accuracy between population
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Journal articleDong N, Dechant B, Wang H, et al., 2023,
Global leaf-trait mapping based on optimality theory
, Global Ecology and Biogeography, Vol: 32, Pages: 1152-1162, ISSN: 1466-822XAimLeaf traits are central to plant function, and key variables in ecosystem models. However recently published global trait maps, made by applying statistical or machine-learning techniques to large compilations of trait and environmental data, differ substantially from one another. This paper aims to demonstrate the potential of an alternative approach, based on eco-evolutionary optimality theory, to yield predictions of spatio-temporal patterns in leaf traits that can be independently evaluated.InnovationGlobal patterns of community-mean specific leaf area (SLA) and photosynthetic capacity (Vcmax) are predicted from climate via existing optimality models. Then leaf nitrogen per unit area (Narea) and mass (Nmass) are inferred using their (previously derived) empirical relationships to SLA and Vcmax. Trait data are thus reserved for testing model predictions across sites. Temporal trends can also be predicted, as consequences of environmental change, and compared to those inferred from leaf-level measurements and/or remote-sensing methods, which are an increasingly important source of information on spatio-temporal variation in plant traits.Main conclusionsModel predictions evaluated against site-mean trait data from > 2,000 sites in the Plant Trait database yielded R2 = 73% for SLA, 38% for Nmass and 28% for Narea. Declining species-level Nmass, and increasing community-level SLA, have both been recently reported and were both correctly predicted. Leaf-trait mapping via optimality theory holds promise for macroecological applications, including an improved understanding of community leaf-trait responses to environmental change.
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Journal articleHunt ESE, Felice RN, Tobias JA, et al., 2023,
Ecological and life-history drivers of avian skull evolution
, EVOLUTION, Vol: 77, Pages: 1720-1729, ISSN: 0014-3820 -
OtherMengoli G, Harrison SP, Prentice IC, 2023,
Supplementary material to "A global function of climatic aridity accounts for soil moisture stress on carbon assimilation"
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Journal articleTan C, Trew J, Peacock T, et al., 2023,
Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential
, Nature Communications, Vol: 14, Pages: 1-13, ISSN: 2041-1723There has been limited characterisation of bat-borne coronaviruses in Europe. Here, we screened for coronaviruses in 48 faecal samples from 16 of the 17 bat species breeding in the UK, collected through a bat rehabilitation and conservationist network. We recovered nine (two novel) complete genomes across six bat species: four alphacoronaviruses, a MERS-related betacoronavirus, and four closely related sarbecoviruses. We demonstrate that at least one of these sarbecoviruses can bind and use the human ACE2 receptor for infecting human cells, albeit suboptimally. Additionally, the spike proteins of these sarbecoviruses possess an R-A-K-Q motif, which lies only one nucleotide mutation away from a furin cleavage site (FCS) that enhances infectivity in other coronaviruses, including SARS-CoV-2. However, mutating this motif to an FCS does not enable spike cleavage. Overall, while UK sarbecoviruses would require further molecular adaptations to infect humans, their zoonotic risk is unknown and warrants closer surveillance.
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