49 Works

Recognition of discrete export signals in flagellar subunits during bacterial Type III secretion

Owain Bryant, Paraminder Dhillon, Colin Hughes & Gillian Fraser
Type III Secretion Systems (T3SS) deliver subunits from the bacterial cytosol to nascent cell surface flagella. Early flagellar subunits that form the rod and hook substructures are unchaperoned and contain their own export signals. A gate recognition motif (GRM) docks them at the FlhBc component of the FlhAB-FliPQR export gate, but the gate must then be opened and subunits must be unfolded to pass through the flagellar channel. This induced us to seek further signals...

The impacts of host association and perturbation on symbiont fitness

Kim Hoang
Symbiosis benefits hosts in numerous ways, but much less is known about how host-association affects symbionts. While symbiont fitness can be mediated by host, symbiont, and/or environmental factors, recent works indicate that symbiont performance can depend on whether the symbiont is needed by the host, suggesting that symbiosis is not always beneficial for symbionts. To determine the impact of symbiosis on symbionts across the Tree of Life, we conducted a meta-analysis across 83 unique host-symbiont...

Genotype-phenotype association for mate choice in progeny of Drosophila simulans backcross

D.F. Erezyilmaz & K. Lu
The data resource contains Drosophila simulans backcross female mate choice (phenotype) aligned with whole-genome genotypes of 784 female backcross progeny. The data were generated in a laboratory at Stony Brook University, New York and each test was conducted in 28.5 x 95mm plastic vials. Phenotype data was collected in 2015 and the final analysis was completed in 2021. Illumina libraries were sequenced at University of Oregon G3 Genomics Center, and the multiplexed shotgun genotyping (MSG)...

Coevolution’s conflicting role in the establishment of beneficial associations

Kim Hoang, Heidi Choi, Nicole Gerardo & Levi Morran
Reciprocal adaptation between hosts and symbionts can drive the maintenance of symbioses, resulting in coevolution and beneficial genotypic interactions. Consequently, hosts may experience decreased fitness when paired with non-sympatric partners compared to sympatric symbionts. However, coevolution does not preclude conflict—host and symbiont can act to advance their own fitness interests, which do not necessarily align with those of their partner. Despite coevolution’s importance in extant symbioses, we know little about its role in shaping the...

Shearwaters sometimes take long homing detours when denied natural outward journey information

Oliver Padget, Natasha Gillies, Martyna Syposz, Emma Lockley & Tim Guilford
The cognitive processes (learning and processing of information) underpinning long-distance navigation of birds are poorly understood. Here, we utilised the homing motivation of the Manx shearwater to investigate navigational decision making in a wild bird by displacing them 294km to the far side of a large island (the Island of Ireland). Since shearwaters are reluctant to fly over land, the island blocked the direct route home, forcing a navigational decision. Further still, on the far...

Data from: Life histories as mosaics: plastic and genetic components differ among traits that underpin life-history strategies

Anja Felmy, David N. Reznick, Joseph Travis, Tomos Potter & Tim Coulson
Life-history phenotypes emerge from clusters of traits that are the product of genes and phenotypic plasticity. If the impact of the environment differs substantially between traits, then life histories might not evolve as a cohesive whole. We quantified the sensitivity of components of the life history to food availability, a key environmental difference in the habitat occupied by contrasting ecotypes, for 36 traits in fast-and slow-reproducing Trinidadian guppies. Our dataset included six putatively independent origins...

Modelling the genetic aetiology of complex disease: human-mouse conservation of noncoding features and disease-associated loci

George Powell, Helen Long, Lousia Zolkiewski, Rebecca Dumbell, Ann-Marie Mallon, Cecilia M. Lindgren & Michelle Simon
Understanding the genetic aetiology of loci associated with disease is crucial for developing preventative measures and effective treatments. Mouse models are used extensively to understand human pathobiology and mechanistic functions of disease-associated loci. However, the utility of mouse models is limited by evolutionary divergence in transcription regulation for pathways of interest. Here, we summarise the conservation of genomic (exonic and multi-cell regulatory) features and complex disease associated variant sites between humans and mice. Our results...

No evidence for trade-offs between bird diversity, yield and water table depth on oil palm smallholdings: implications for tropical peatland landscape restoration

Eleanor Warren-Thomas, Fahmuddin Agus, Panji Akbar, Merry Crowson, Keith Hamer, Bambang Hariyadi, Jenny Hodgson, Winda Kartika, Mailys Lopes, Jennifer Lucey, Dedy Mustaqim, Nathalie Pettorelli, Asmadi Saad, Widia Sari, Gita Sukma, Lindsay Stringer, Caroline Ward & Jane Hill
Tropical peat swamp forests retain large carbon stocks and support unique biodiversity, but clearance and drainage for agriculture have resulted in fires, carbon emissions and biodiversity losses. Initiatives to re-wet cultivated peatlands may benefit biodiversity if this protects remaining forests from fire and agricultural encroachment, but there are concerns that re-wetting could reduce yields and damage livelihoods, as relationships between drainage, on-farm biodiversity, and crop yields have not been studied. We examined oil palm fruit...

Off-target integron activity leads to rapid plasmid compensatory evolution in response to antibiotic selection pressure

Célia Souque, Jose Escudero & R Craig MacLean
Integrons are mobile genetic elements that have played an important role in the dissemination of antibiotic resistance. As shown previously (Souque et al, 2021), the integron can generate under stress combinatorial variation in resistance cassette expression by cassette re-shuffling, accelerating the evolution of resistance. However, the flexibility of the integron integrase site recognition motif hints at potential off-target effects of the integrase on the rest of the genome that may have important evolutionary consequences. Here...

Local and moment magnitudes of Preston New Road seismicity, 2018-2019

Tom Kettlety & Antony Butcher
This is a combined microseismic catalogue of all of the seismic magnitudes recorded for microseismic events recorded during Cuadrilla's Preston New Road hydraulic fracturing operations. 5 magnitude types are given for each event: the downhole measured moment magnitude (Mw); the downhole measured local magnitude (ML); the surface measured ML; the surface measured Mw; and a combined/corrected Mw. This corrected Mw follows the procedure laid out in Kettlety et al. (2021, https://doi.org/10.1785/0220200187) and Baptie et al....

Design of free-space couplers for suspended triangular nano-beam waveguides - data

John Patrick Hadden, Cobi Maynard, Darly M Beggs, Robert A Taylor & Bennett Anthony J
These data are from a study involving the design and modelling of free-space couplers for suspended triangular nano-beam waveguides. We use Finite Element Analysis using Ansys Lumerical Mode, and Finite-Differece Time-Domain (FDTD) modelling to benchmark and optimise the performance of three types of designs: Type A - Grating coupler with mode converter, Type B - Wedge mirror with Bragg reflector, Type C - Wedge mirror with mode converter. The dataset includes 20 .CSV files with...

Seasonal dynamics of the wild rodent faecal virome

Jayna Raghwani, Christina Faust, Sarah Francois, Dung Nguyen, Kirsty Marsh, Aura Raulo, Sarah Hill, Kris Parag, Peter Simmonds, Sarah Knowles & Oliver Pybus
Viral discovery studies in wild animals often rely on cross-sectional surveys at a single time point. As a result, our understanding of the temporal stability of wild animal viromes remains poorly resolved. While studies of single host-virus systems indicate that host and environmental factors influence seasonal virus transmission dynamics, comparable insights for whole viral communities in multiple hosts are lacking. Leveraging non-invasive faecal samples from a long-term wild rodent study, we characterised viral communities of...

Long-term experimental drought alters floral scent and pollinator visits in a Mediterranean plant community despite overall limited impacts on plant phenotype and reproduction

Coline Jaworski, Benoît Geslin, Marie Zakardjian, Caroline Lecareux, Pauline Caillault, Gabriel Nève, Jean-Yves Meunier, Sylvie Dupouyet, Aoife Sweeney, Owen Lewis, Lynn Dicks & Catherine Fernandez
Pollinators are declining globally, with climate change implicated as an important driver. Climate change can induce phenological shifts and reduce floral resources for pollinators, but little is known about its effects on floral attractiveness and how this might cascade to affect pollinators, pollination functions and plant fitness. We used an in situ long-term drought experiment to investigate multiple impacts of reduced precipitation in a natural Mediterranean shrubland, a habitat where climate change is predicted to...

Shear wave splitting catalogue, Rutford Ice Stream (West Antarctica), November 2018 to February 2019

Sofia-Katerina Kufner, Alex Brisbourne, Andrew Smith, James Wookey, Carlos Martin, Thomas Hudson & John Michael Kendall
This dataset contains an ASCII file with shear wave splitting results for 202,652 station-event pairs from glacial micro-seismicity, recorded from a 35-station seismic network located ~40 km upstream of the grounding line of Rutford Ice Stream, West Antarctica. Microseismicity is located at the base of the ice stream at ~2.2 km depth (relative to the ice surface). Seismic waveform data, which was used to calculate shear wave splitting parameters is provided in miniseed format. Event...

Local population density of woodland birds from a manipulation experiment in Wytham Woods, Oxfordshire, UK 2021

K.B. Beck, J.A. Firth, K. McMahon, S. Croft, E.F. Cole & B. Sheldon
This dataset contains information about local population densities of great tits, blue tits, marsh tits and nuthatches from a manipulation experiment. The time, location and bird species were recorded using a Passive Integrated Transponder (PIT) tag attached to each bird and the information recorded using a Radio Frequency Identification (RFID) antenna within the feeder. Population density was manipulated by programming automated feeders to only open for a specific set of individuals (creating low- and high-density...

Structure-from-motion-generated imagery, nest location coordinates and counts for Adelie, chinstrap, gentoo and macaroni penguins on the South Sandwich Islands, from December to February, 2019-2020.

Tom Hart, Sarah Manthorpe, Gemma Clucas & Heather Lynch
This dataset contains penguin survey data and imagery from unmanned aerial vehicles (UAV) across the South Sandwich Islands, from December 2019 to February 2020. It comprises orthotiff images (orthotiffs) and digital elevation models (DEMS) of surveyed sites, geographic penguin colony outlines, nest coordinates for individual species, mixed species' sub-colonies and groups where species-level identification was not possible. Finally, it also includes the total count for these different categories for each individual site, alongside an estimate...

Data from: Reis et al. (2022). Climate and crown damage drive tree mortality in Southern Amazonian edge Forests. Journal of Ecology. DOI: 10.1111/1365-2745.13849

Simone Matias Reis, Beatriz Schwantes Marimon, Adriane Esquivel-Muelbert, Ben Hur Marimon Junior, Paulo Sérgio Morandi, Fernando Elias, Edmar Almeida de Oliveira, David Galbraith, Ted R. Feldpausch, Imma Oliveras Menor, Yadvinder Malhi & Oliver L. Phillips

Incorporating effects of age on energy dynamics predicts non-linear maternal allocation patterns in iteroparous animals

Antoine Barreaux, Andrew Higginson, Michael Bonsall & Sinead English
Iteroparous parents face a trade-off between allocating current resources to reproduction versus maximizing survival to produce further offspring. Optimal allocation varies across age, and follows a hump-shaped pattern across diverse taxa, including mammals, birds and invertebrates. This non-linear allocation pattern lacks a general theoretical explanation, potentially because most studies focus on offspring number rather than quality and do not incorporate uncertainty or age-dependence in energy intake or costs. Here, we develop a life history model...

Data from: SARS-CoV-2 antibody dynamics in blood donors and COVID-19 epidemiology in eight Brazilian state capitals

, Lewis F. Buss, Charles Whittaker, Tassila Salomon, Marcio K. Oikawa, Rafael H. M. Pereira, Isabel C. G. Moura, Lucas Delerino, Manoel Barral-Netto, Natalia M. Tavares, Rafael F. O. França, Viviane S. Boaventura, Fabio Miyajima, Alfredo Mendrone-Junior, César De Almeida Neto, Nanci A. Salles, Suzete C. Ferreira, Karine A. Fladzinski, Luana M. De Souza, Luciane K. Schier, Patricia M. Inoue, Lilyane A. Xabregas, Myuki A. E. Crispim, Nelson Fraiji, Fernando L. V. Araujo … & Ester C. Sabino
The COVID-19 situation in Brazil is complex due to large differences in the shape and size of regional epidemics. Here we tested monthly blood donation samples for IgG antibodies from March 2020 to March 2021 in eight of Brazil’s most populous cities. The inferred attack rate of SARS-CoV-2 adjusted for seroreversion in December 2020, before the Gamma VOC was dominant, ranged from 19.3% (95% CrI 17.5% - 21.2%) in Curitiba to 75.0% (95% CrI 70.8%...

Data from: Environmental controls on African herbivore responses to landscapes of fear

Andrew Davies, Joris Cromsigt, Craig Tambling, Elizabeth Le Roux, Nicholas Vaughn, Dave Druce, David Marneweck & Gregory Asner
Herbivores balance forage acquisition with the need to avoid predation, often leading to tradeoffs between forgoing resources to avoid areas of high predation risk, or tolerating increased risk in exchange for improved forage. The outcome of these decisions is likely to change with varying resource levels, with herbivores altering their response to predation risk across heterogeneous landscapes. Such contrasting responses will alter the strength of non-consumptive predation effects, but are poorly understood in multiple- predator/multiple-prey...

Carbon dioxide flux and isotopic composition from sedimentary rock weathering, Waiapu River catchment, New Zealand

Tobias Roylands, Robert G Hilton, Mark H Garnett & Guillaume Soulet Soulet
These data were collected to study oxidative weathering processes in the Waiapu River catchment, New Zealand, with potential carbon release sourced from the oxidation of petrogenic organic carbon or carbonate dissolution coupled to the oxidation of sulfide minerals. There, in mudstones exposed in a highly erosive gully complex, in situ CO2 emissions were measured with drilled gas accumulation chambers following the design by Soulet et al. (2018, Biogeosciences 15, 4087-4102, https://doi.org/10.5194/bg-15-4087-2018). Temporal and spatial variability...

Transient amplification enhances the persistence of tropicalising coral assemblages in marginal high latitude environments

James Cant, Katie Cook, James Reimer, Takuma Mezaki, Masako Nakamura, Cliodhna O'Flaherty, Rob Salguero-Gomez & Maria Beger
Predicting the viability of species exposed to increasing climatic stress requires an appreciation for the mechanisms underpinning the success or failure of marginal populations. Rather than traditional metrics of long-term population performance, here we illustrate that short-term (i.e., transient) demographic characteristics, including measures of resistance, recovery, and compensation, are fundamental in the poleward range expansion of hard corals, facilitating the establishment of coral populations at higher latitudes. Through the annual census of tropical and subtropical...

Raw data and alignments for: Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone

Kerry Walton, Lachie Scarsbrook, Kieren Mitchell, Alexander Verry, Bruce Marshall, Nicolas Rawlence & Hamish Spencer
Natural history collections worldwide contain a plethora of mollusc shells. Recent studies have detailed the sequencing of DNA extracted from shells up to thousands of years old and from various taphonomic and preservational contexts. However, previous approaches have largely addressed methodological rather than evolutionary research questions. Here we report the generation of DNA sequence data from mollusc shells using such techniques, applied to Haliotis virginea Gmelin, 1791, a New Zealand abalone, in which morphological variation...

Data on: Climate drives the spatiotemporal dynamics of scrub typhus in China

Fangyu Ding, Qian Wang, Mengmeng Hao, Richard James Maude, Nicholas Philip John Day, Shengjie Lai, Shuai Chen, Liqun Fang, Tian Ma, Canjun Zheng & Dong Jiang
This dataset is the data used in the paper of Global change biology entitled "Climate drives the spatiotemporal dynamics of scrub typhus in China". We incorporate Chinese national surveillance data on scrub typhus from 2010 to 2019 into a climate-driven generalized additive mixed model to explain the spatiotemporal dynamics of this disease and predict how it may be affected by climate change under various representative concentration pathways (RCPs) for three future time periods (the 2030s,...

Registration Year

  • 2022
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  • Dataset
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Affiliations

  • University of Oxford
    46
  • University of Cambridge
    3
  • University of Leeds
    3
  • Harvard University
    3
  • University of Exeter
    3
  • Imperial College London
    3
  • University of Bristol
    3
  • State University of New York Downstate
    2
  • British Antarctic Survey
    2
  • Natural Environment Research Council
    2