52 Works

Unravelling processes between phenotypic plasticity and population dynamics in migratory birds

Jin Liu, Weipan Lei, Xunqiang Mo, Chris Hassell, Zhengwang Zhang & Tim Coulson
Populations can rapidly respond to environmental change via adaptive phenotypic plasticity, which can also modify interactions between individuals and their environment, affecting population dynamics. Bird migration is a highly plastic resource-tracking tactic in seasonal environments. However, the link between the population dynamics of migratory birds and migration tactic plasticity is not well understood. The quality of staging habitats affects individuals’ migration timing and energy budgets in the course of migration, and can consequently affect individuals’...

Individual variation explains aging patterns in a cooperatively breeding bird, the long-tailed tit (Aegithalos caudatus)

Mark Roper
1. Alloparental care in cooperatively-breeding species may alter breeder age-specific survival and reproduction, and subsequently senescence. The helping behaviour itself might also undergo age-related change, and decisions to help in facultative cooperative breeders are likely to be affected by the individual condition. 2. Helpers in long-tailed tits (Aegithalos caudatus) assist relatives after failing to raise their own brood, with offspring from helped nests being more likely to recruit into the breeding population. 3. Using data...

Improving landscape-scale productivity estimates by integrating trait-based models and remotely-sensed foliar-trait and canopy-structural data

Daniel Wieczynski, Sandra Diaz, Sandra Duran, Nikolaos Fyllas, Norma Salinas, Roberta Martin, Alexander Shenkin, Miles Silman, Gregory Asner, Lisa Bentley, Yadvinder Malhi, Brian Enquist & Van Savage
Assessing the impacts of anthropogenic degradation and climate change on global carbon cycling is hindered by a lack of clear, flexible, and easy-to-use productivity models along with scarce trait and productivity data for parameterizing and testing those models. We provide a simple solution: a mechanistic framework (RS-CFM) that combines remotely-sensed foliar-trait and canopy-structural data with trait-based metabolic theory to efficiently map productivity at large spatial scales. We test this framework by quantifying net primary productivity...

First large-scale quantification study of DNA preservation in insects from natural history collections using genome-wide sequencing

Victoria Elizabeth Mullin, William Stephen, Andres Arce, Will Nash, Calum Raine, David Notton, Ashleigh Whiffin, Vladimir Blagoderov, Karim Gharbi, James Hogan, Tony Hunter, Naomi Irish, Simon Jackson, Steve Judd, Chris Watkins, Wilfried Haerty, Jeff Ollerton, Selina Brace, Richard Gill & Ian Barnes
Insect declines are a global issue with significant ecological and economic ramifications. Yet we have a poor understanding of the genomic impact these losses can have. Genome-wide data from historical specimens has the potential to provide baselines of population genetic measures to study population change, with natural history collections representing large repositories of such specimens. However, an initial challenge in conducting historical DNA data analyses, is to understand how molecular preservation varies between specimens. Here,...

Beagle kelp maps from: One of the least disturbed marine coastal ecosystems on Earth: Spatial and temporal persistence of Darwin’s sub-Antarctic giant kelp forests

Alejandra Mora-Soto
Aim: Marine habitats and their dynamics are difficult to systematically monitor, particularly those in remote locations. This is the case with the sub-Antarctic ecosystem of the giant kelp Macrocystis pyrifera, which was already noted by Charles Darwin in his accounts on the Voyage of the Beagle and recorded on the nautical charts made during that expedition. We combined these and other nautical charts from the 19th and early 20th centuries with surveys conducted in the...

Data on nest choices by long-tailed tit helpers

Nicole Sturrock, Ben Hatchwell, Josh Firth & Jonathan Green
Cooperative breeding sometimes occurs when adult breeders form groups following natal dispersal and mating. In such cases, individuals typically face a choice of potential social partner with whom to cooperate. Selection of appropriate social partners is crucial to maximising the fitness payoffs from cooperation, but our understanding of the criteria guiding social partner choice is limited. Here, we analyse helping decisions by long-tailed tits (Aegithalos caudatus), which may redirect their care to assist breeders in...

Resource allocation underlies parental decision-making during incubation in the Manx shearwater

Natasha Gillies, Oliver Padget, Martyna Syposz, Sarah Bond & Tim Guilford
Examining resource allocation is fundamental to understanding the relationships between a species’ behaviour and its life history. Furthermore, for biparentally-caring animals, examining the relative investment decisions made by members of a breeding pair can give insight into the extent and nature of cooperative care. As a key measure of resource availability, examining body mass changes can help elucidate the ways in which parents balance their allocation. In birds, these trade-offs become particularly stark during incubation,...

Cortical adaptation to sound reverberation

Aleksandar Ivanov, Andrew King, Ben Willmore, Kerry Walker & Nicol Harper
In almost every natural environment, sounds are reflected by nearby objects, producing many delayed and distorted copies of the original sound, known as reverberation. Our brains usually cope well with reverberation, allowing us to recognize sound sources regardless of their environments. In contrast, reverberation can cause severe difficulties for speech recognition algorithms and hearing-impaired people. The present study examines how the auditory system copes with reverberation. We trained a linear model to recover a rich...

Recordings of the discovery of novel food patches in common woodland birds 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 the recordings of great tits, blue tits, marsh tits and nuthatches discovering novel food patches in relation to manipulated local population densities (see 1a4dcbb3-c4fb-4bd4-acb3-d03932de9323). Prior to and during the density manipulation experiment, novel feeders were placed at random locations and the discovery of these was 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...

Data for Trainable Segmentation for Transmission Electron Microscope Images of Inorganic Nanoparticles

Thomas Slater & Kevin Treder
The data are 3 sets of images that were used to investigate trainable segmentation using the open-source python package ParticleSpy (10.5281/zenodo.3763072). The images were obtained using either high-angle annular dark field (HAADF) scanning transmission electron microscopy (STEM) or high-resolution transmission electron microscopy (HRTEM). Specififcally, the 3 datasets are: 1: HAADF-STEM images of a mix of metallic nanoparticles, namely PtNi nanoparticles, Pd nanocubes and Au nanospheres. The images were obtained using a JEOL ARM 200 scanning...

Random forest modelling of multi-scale, multi-species habitat associations within KAZA transfrontier conservation area using spoor data

Charlotte E. Searle, Zaneta Kaszta, Dominik T. Bauer, M. Kristina Kesch, Jane E. Hunt, Roseline Mandisodza-Chikerema, Michael V. Flyman, David W. Macdonald, Amy J. Dickman, Andrew J. Loveridge & Samuel A. Cushman
As landscape-scale conservation models grow in prominence, assessments of how wildlife utilise multiple-use landscapes are required to inform effective conservation and management planning. Such efforts should strive to incorporate multi-species perspectives to maximise value for conservation, and should account for scale to accurately capture species-environment relationships. We show that the random forest machine learning algorithm can be used to model large-scale sign-based data in a multi-scale framework. We used this method to investigate scale-dependent habitat...

Termite diversity is resilient to land-use change

Gabriel Quansah, Gabriel Quansah, Stephen Adu-Bredu, Vincent Logah, Yadvinder Malhi, Paul Eggleton & Catherine Parr
Cocoa is an important crop for Ghana’s economy, contributing 25% of Gross Domestic Product (GDP). The crop, however, is mainly cultivated on forest-derived soils and is a major cause of land-use change. Termites are an important biological component of tropical ecosystems providing numerous ecosystem services. Previous studies have indicated that termites are sensitive to forest disturbance and decrease in richness and abundance across land-use intensification gradients, with consequences for the essential services that they provide....

Trait-mediated competition drives an ant invasion and alters functional diversity

Mark K L Wong
The assumption that differences in species’ traits reflect their different niches has long influenced how ecologists infer processes from assemblage patterns. For instance, many assess the importance of environmental filtering versus classical limiting-similarity competition in driving biological invasions by examining whether invaders’ traits are similar or dissimilar to those of residents, respectively. However, mounting evidence suggests that hierarchical differences between species’ trait values can distinguish their competitive abilities (e.g., for the same resource) instead of...

A Bismarckian Type of Fiscal Welfare? Insights on the Use of Social Tax Expenditures in French Social and Employment Policy ( LIEPP Working Paper, n° 65)

Nathalie Morel, Chloé Touzet & Michaël Zemmour
This article argues that situated approaches are necessary to reveal institu-tion-specific or regime specific structures, forms and uses of fiscal welfare instruments. We base our analysis on the French case, for which we have previously built an exhaustive database of social tax expenditures (STEs) for the year 2014. We find that France displays a specific structure of fiscal welfare. Most STEs are concentrated in the fields of employment, family and health policy; most STEs concern...

Using deep convolutional neural networks to forecast spatial patterns of Amazonian deforestation: supporting data and outputs

James Ball, Katerina Petrova, David Coomes & Seth Flaxman
1. Tropical forests are subject to diverse deforestation pressures while their conservation is essential to achieve global climate goals. Predicting the location of deforestation is challenging due to the complexity of the natural and human systems involved but accurate and timely forecasts could enable effective planning and on-the-ground enforcement practices to curb deforestation rates. New computer vision technologies based on deep learning can be applied to the increasing volume of Earth observation data to generate...

Assortative mating in Drosophila simulans and Drosophilia sechellia females

D.F. Erezyilmaz & K. Lu
The dataset presents data on female mate choice totals for different species pair combinations. Data are presented for wild types and inbred lines of Drosophila simulans and Drosophilia sechellia females. Most of the data was generated in a laboratory at Stony Brook University, with some at Oxford University. Each test was conducted in 28.5 x 95mm plastic vials. Data was collected at different points between 2014 and 2021 by the lead data author. The work...

Genotype-phenotype association for mate choice in a Drosophila simulans-sechellia backcross population

D.F. Erezyilmaz & K. Lu
The data resource contains Drosophila simulans-sechellia backcross female mate choice (phenotype) aligned with whole-genome genotypes of 692 female backcross progeny. The data was 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)...

Bird breeding data for Wytham Woods, Oxfordshire, UK, 2020 and 2021

K.B. Beck, J.A. Firth, K. McMahon, S. Croft, E.F. Cole & B. Sheldon
This dataset contains information on the following: nest building, identity of breeding pairs, date when the first egg is laid, number of eggs, hatch date and the number and condition of fledglings for great tits, blue tits, marsh tits and coal tits. The data presented were collected in Wytham Woods, Oxfordshire, UK during April and June in 2020 and 2021 by Keith McMahon, Sam Croft and Kristina Beck, as part of a long-term nestbox project...

Bird ringing records from Wytham Woods, Oxfordshire, UK during 2020 and 2021

K.B. Beck, J.A. Firth, K. McMahon, S. Croft, E.F. Cole & B. Sheldon
This dataset contains information about the ringing records of mainly great tits, blue tits, marsh tits and coal tits, and a few other bird species. The data were collected in Wytham woods, Oxfordshire, UK during 2020 and 2021, as part of a long-term population monitoring project on the breeding biology and behaviour of birds.

Pilgrimage During Covid-19: Impacts, Adaptations, and Recovery

Anne Bailey

Lifetime reproductive success and fitness estimates of long-tailed tits in the Rivelin Valley, Sheffield, UK, from 1994-2019

B.J. Hatchwell & J.P. Green
Dataset comprising data on the lifetime reproductive success (LRS) of 879 individually marked long-tailed tits Aegithalos caudatus, a cooperatively breeding passerine. LRS is measured in terms of the number of local recruits into the breeding population in the study area, controlling for fledgling sex and extra-pair paternity. LRS data are then partitioned into direct and indirect fitness components, quantified as genetic equivalents. Partitioning of fitness follows Hamilton’s definition of inclusive fitness: (a) direct fitness is...

Submerged aquatic vegetation, water quality (pH, salinity, and turbidity) and waterfowl abundance data from 1991-2017 in Back Bay, Virginia

Carly Sibilia, Jesús Aguirre-Gutiérrez, Lauren Mowbray & Yadvinder Malhi
Back Bay, Virginia, has been documented as an important foraging area for waterfowl since at least the mid-1800s. Expansive submerged plant beds historically supported diverse assemblages of non-breeding waterfowl, however coastal development and other anthropogenic influences have since led to fluctuations in submerged aquatic vegetation (SAV) and an associated decline in waterfowl abundance in the bay. To gain insight into the effects of environmental drivers on waterfowl foraging guilds, our study explores the effects of...

The life and times of Pteridinium simplex

Simon Darroch, Brandt Gibson, Maggie Syversen, Imran Rahman, Rachel Racicot, Frances Dunn, Susana Gutarra-Diaz, Eberhard Schindler, Achim Wehrmann & Marc Laflamme
Pteridinium simplex is an iconic erniettomorph taxon best known from late Ediacaran successions in South Australia, Russia, and Namibia. Despite nearly 100 years of study, there remain fundamental questions surrounding the paleobiology and -ecology of this organism, including it’s life position relative the sediment-water interface, and how it fed and functioned within benthic communities. Here, we combine a re-description of specimens housed at the Senckenberg Forschungsinstitut und Naturmuseum Frankfurt with field observations of fossiliferous surfaces...

A song of wind and ice: increased frequency of marine cold-spells in southwestern Patagonia and their possible effects on giant kelp forests

Alejandra Mora-Soto, Catalina Aguirre, Jose Luis Iriarte, Mauricio Palacios, Erasmo C. Macaya & Marc Macias-Fauria
In contrast to other coastal regions of the world, the giant kelp (Macrocystis pyrifera) ecosystem in southwestern Patagonia has been persistent in area and associated biodiversity in the last decades. In this ecoregion, Sea Surface Temperature (SST) records have consistently remained below the upper thermal threshold for kelp survival, however no studies have analysed the spatiotemporal variability of SSTs and their anomalies across the geographical diversity of the southwestern Patagonian coastline. We explored the geographical...

Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial – BCPP/ Ya Tsie trial

Lerato Magosi, Yinfeng Zhang, Tanya Golubchik, Victor DeGruttola, Eric Tchetgen Tchetgen, Vladimir Novitsky, Janet Moore, Pam Bachanas, Tebogo Segolodi, Refeletswe Lebelonyane, Molly Pretorius Holme, Sikhulile Moyo, Joseph Makhema, Shahin Lockman, Christophe Fraser, Myron Essex & Marc Lipsitch
Background: Mathematical models predict that community-wide access to HIV testing-and-treatment can rapidly and substantially reduce new HIV infections. Yet several large universal test-and-treat HIV prevention trials in high-prevalence epidemics demonstrated variable reduction in population-level incidence. Methods: To elucidate patterns of HIV spread in universal test-and-treat trials we quantified the contribution of geographic-location, gender, age and randomized-HIV-intervention to HIV transmissions in the 30-community Ya Tsie trial in Botswana (estimated trial population: 175,664). Results: Deep-sequence phylogenetic analysis...

Registration Year

  • 2022

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  • University of Oxford
  • University of Bristol
  • University of Cambridge
  • University of Leeds
  • Harvard University
  • University of Exeter
  • Imperial College London
  • University of Glasgow
  • State University of New York Downstate
  • British Antarctic Survey