163 Works

Standardised site-level trends, mean productivity, and survival for migrant (arid and humid-zone) and resident species breeding across Europe

Catriona Morrison
Wildlife conservation policies directed at common and widespread, but declining, species are difficult to design and implement effectively, as multiple environmental changes are likely to contribute to population declines. Conservation actions ultimately aim to influence demographic rates, but targeting actions towards feasible improvements in these is challenging in widespread species with ranges that encompass a wide range of environmental conditions. Across Europe, sharp declines in the abundance of migratory landbirds have driven international calls for...

Data from: Transposable element annotation in non-model species - on the benefits of species specific repeat libraries using semi-automated EDTA and DeepTE de novo pipelines

Ellen Bell, Christopher Butler & Martin Taylor
Transposable elements (TEs) are significant genomic components which can be detected either through sequence homology against existing databases or de novo, with the latter potentially reducing underestimates of TE abundance. Here, we describe the semi-automated generation of a de-novo TE library which combines the newly described EDTA pipeline and DeepTE classifier in a non-model teleost (Corydoras sp. C115). We assess performance using both genomic and transcriptomic input by five metrics: (i) abundance (ii) composition (iii)...

Data from: Reconstructing paternal genotypes to infer patterns of sperm storage and sexual selection in the hawksbill turtle

Karl P. Phillips, Tove H. Jorgensen, Kevin G. Jolliffe, San-Marie Joliffe, Jock Henwood & David S. Richardson
Postcopulatory sperm storage can serve a range of functions, including ensuring fertility, allowing delayed fertilization and facilitating sexual selection. Sperm storage is likely to be particularly important in wide-ranging animals with low population densities, but its prevalence and importance in such taxa, and its role in promoting sexual selection, are poorly known. Here, we use a powerful microsatellite array and paternal genotype reconstruction to assess the prevalence of sperm storage and test sexual selection hypotheses...

Data from: Drift, not selection, shapes toll-like receptor variation among oceanic island populations

Catalina González-Quevedo, Lewis G. Spurgin, Juan Carlos Illera & David S. Richardson
Understanding the relative role of different evolutionary forces in shaping the level and distribution of functional genetic diversity among natural populations is a key issue in evolutionary and conservation biology. To do so accurately genetic data must be analyzed in conjunction with an unambiguous understanding of the historical processes that have acted upon the populations. Here we focused on diversity at toll-like receptor (TLR) loci, which play a key role in the vertebrate innate immune...

Data from: Wolbachia effects in natural populations of Chorthippus parallelus from the Pyrenean hybrid zone.

Jose L. Bella, Godfrey M. Hewitt, Mario Zabal-Aguirre, Francisca Arroyo, Javier Garcia-Hurtado & Joaquina De La Torre
We evaluate for the first time the effect of Wolbachia infection, involving two different supergoups, on the structure and dynamics of the hybrid zone between two subspecies of Chorthippus parallelus (Orthoptera) in the Pyrenees. Wolbachia infection showed no effects on female fecundity or a slight increment in females infected by F supergroup although in the last case it has to be well-established. Cytoplasmic incompatibility (CI) is confirmed in crosses carried out in the field between...

Data from: Cryptic haplotype-specific gamete selection yields offspring with optimal MHC immune genes

Tobias L. Lenz, Nina Hafer, Irene E. Samonte, Sarah E. Yeates & Manfred Milinski
Females choose specific mates in order to produce fitter offspring. However, several factors interfere with females' control over fertilization of their eggs, including sneaker males and phenotypically unpredictable allele segregation during meiosis. Mate choice at the individual level thus provides only a poor approximation for obtaining the best genetic match. Consequently, post-copulatory sperm selection by female oocytes has been proposed as a mechanism to achieve complementary combinations of parental haplotypes. Here, using controlled in vitro...

Data from: Is saltmarsh restoration success constrained by matching natural environments or altered succession? a test using niche models

Martin J. P. Sullivan, Anthony J. Davy, Alastair Grant & Hannah L. Mossman
1.Restored habitats, such as saltmarsh created through managed realignment, sometimes fail to meet targets for biological equivalence with natural reference sites. Understanding why this happens is important in order to improve restoration outcomes. 2.Elevation in the tidal frame and sediment redox potential are major controls on the distribution of saltmarsh plants. We use niche models to characterize ten species’ responses to these, and test whether differences in species occurrence between restored and natural saltmarshes in...

Data from: Assessing risks of invasion through gamete performance: farm Atlantic salmon sperm and eggs show equivalence in function, fertility, compatibility and competitiveness to wild Atlantic salmon

Sarah E. Yeates, Sigurd Einum, William V. Holt, Ian A. Fleming & Matthew J. G. Gage
Adaptations at the gamete level (a) evolve quickly, (b) appear sensitive to inbreeding and outbreeding and (c) have important influences on potential to reproduce. We apply this understanding to problems posed by escaped farm salmon and measure their potential to reproduce in the wild. Farm Atlantic salmon (Salmo salar) are a threat to biodiversity, because they escape in large numbers and can introgress, dilute or disrupt locally adapted wild gene pools. Experiments at the whole...

Structural equation modeling reveals determinants of fitness in a cooperatively breeding bird

Michela Busana, Franz J Weissing, Martijn Hammers, Joke Bakker, Hannah L Dugdale, Sara Raj Pant, David S Richardson, Terrence A Burke & Jan Komdeur
Even in well-studied organisms, it is often challenging to uncover the social and environmental determinants of fitness. Typically, fitness is determined by a variety of factors that act in concert, thus forming complex networks of causal relationships. Moreover, even strong correlations between social and environmental conditions and fitness components may not be indicative of direct causal links, as the measured variables may be driven by unmeasured (or unmeasurable) causal factors. Standard statistical approaches, like multiple...

Zooplankton abundance data derived from the Plankton Imager system from the Western English Channel and Eastern Irish Sea from 2016 to 2019

These data are abundances (in numbers per meters cubed) of zooplankton taxa, calculated from the analysis of images taken using the Plankton Imager system also included are station positions and sampling date / times. The images where collected using the PI (formerly known as Plankton Image Analyser (PIA)), during the PELTIC (Pelagic ecosystem in the western English Channel and eastern Celtic Sea) surveys from 2016 to 2019, on board the RV Cefas Endeavour. Zooplankton samples...

Ageing, Well-being and Development Project 2002, 2008

Armando Barrientos & Peter Lloyd-Sherlock

Multispectral airborne imagery and associated classifications, training data and validation data, for mapping nectar-rich floral resources for pollinators, Northamptonshire, UK 2020

S.B. Barnsley, A.A. Lovett & L.V. Dicks
Data presented here include imagery with ground-sampling distances of 3 cm and 7 cm for March 2019, May 2019 and July 2019. Also included are the corresponding ground-truth training and verification data presented as shapefiles, as well as the classification output and other data relevant to the project such as the width of floral units. The imagery was acquired by Spectrum Aviation using A6D-100c (50mm) Hasselblad cameras with bayer filters, mounted on a Sky Arrow...

Seasonal streambed carbon and nitrogen cycling (including greenhouse gases) in an agriculturally-impacted stream. Measured at Wood Brook UK, 2016-2017

S. Comer-Warner, S. Krause, D.C. Gooddy, S. Ullah & S.K. Wexler
The dataset contains chemistry data from streambed porewater (10 and 20 cm) and surface water, as well as nitrogen chemistry data at 2.5 cm resolution within the upper 15 cm of the streambed. The dataset includes concentrations of dissolved organic carbon (DOC), carbon dioxide, methane, ammonium, nitrate, nitrite and nitrous oxide, and isotopic ratios of δ13CCO2, δ15NNO3+NO2 and δ18ONO3+NO2. Also included are measurements of dissolved oxygen and temperature. Samples were collected from three reaches within...

Location data of worker bumblebees across an agricultural landscape in Buckinghamshire, UK

C. Carvell, A.F.G. Bourke, S. Dreier, M.S. Heard, W.C. Jordan, S. Sumner, J. Wang & J.W. Redhead
This dataset contains locations of worker bumblebees of five species (Bombus terrestris, B. lapidarius, B. pascuorum, B. hortorum, B. ruderatus) across an agricultural landscape centred on the Hillesden Estate, Buckinghamshire, UK. Locations were recorded in the field using a handheld GPS unit. Workers were non-lethally DNA sampled between June and August 2011, and genetic analysis used to confirm species and assign individuals to full-sib groups (colonies). Data were collected as part of a project led...

Data from: Sexual conflict over remating interval is modulated by the sex peptide pathway

Damian T. Smith, Naomi V. E. Clarke, James M. Boone, Claudia Fricke & Tracey Chapman
Sexual conflict, in which the evolutionary interests of males and females diverge, shapes the evolution of reproductive systems across diverse taxa. Here, we used the fruit fly to study sexual conflict in natural, three-way interactions comprising a female, her current and previous mates. We manipulated the potential for sexual conflict by using sex peptide receptor (SPR) null females and by varying remating from 3 to 48 h, a period during which natural rematings frequently occur....

Data from: Local extinctions of obligate frugivores and patch size reduction disrupt the structure of seed dispersal networks

Jamille De Assis Bomfim, , Carlos A. Peres, Gustavo Carvalho & Eliana Cazetta
A central problem in ecology is to understand how human impacts affect plant-animal interactions that lead to effective seed dispersal services for plant communities. Seed dispersal services are the outcome of plant-frugivore interactions that often form local networks of interacting species. Recent work has shown that some frugivorous bird species are more critical to network organization than others. Here, we explore how patch size and the potential local extinctions of obligate frugivorous birds affect the...

Data from: Using DNA metabarcoding for simultaneous inference of common vampire bat diet and population structure

Kristine Bohmann, Shyam Gopalakrishnan, Martin Nielsen, Luisa Dos Santos Bay Nielsen, Gareth Jones, Daniel G. Streicker & M. Thomas P. Gilbert
Metabarcoding diet analysis has become a valuable tool in animal ecology; however, co-amplified predator sequences are not generally used for anything other than to validate predator identity. Exemplified by the common vampire bat we demonstrate the use of metabarcoding to infer predator population structure alongside diet assessments. Growing populations of common vampire bats impact human, livestock and wildlife health in Latin America through transmission of pathogens, such as lethal rabies infections. Techniques to determine large...

Data from: Managing Neotropical oil palm expansion to retain phylogenetic diversity

Graham W. Prescott, James J. Gilroy, Torbjørn Haugaasen, Claudia A. Medina Uribe, William A. Foster & David P. Edwards
The expansion of tropical agriculture is a major driver of the extinction crisis. A key question is whether biodiversity losses can be minimized by restricting future expansion to low-productivity farmland and retaining forest fragments, especially in rapidly changing Neotropical landscapes. We investigated these methods in the context of avian phylogenetic diversity, which summarizes the evolutionary history preserved within communities. Evidence suggests that phylogenetic diversity plays an important role in maintaining key ecosystem functions. We collected...

Data from: Museum DNA reveals the demographic history of the endangered Seychelles warbler

Lewis G. Spurgin, David J. Wright, Nigel J. Collar, Marco Van Der Velde, Jan Komdeur, Terry Burke & David S. Richardson
The importance of evolutionary conservation – how understanding evolutionary forces can help guide conservation decisions – is widely recognized. However, the historical demography of many endangered species is unknown, despite the fact that this can have important implications for contemporary ecological processes and for extinction risk. Here, we reconstruct the population history of the Seychelles warbler (Acrocephalus sechellensis) – an ecological model species. By the 1960s, this species was on the brink of extinction, but...

Data from: Experimental sexual selection and sex comb evolution in Drosophila

Rhonda R. Snook, Nelly A. Gidaszewski, Tracey Chapman & Leigh W. Simmons
Sexual selection can drive rapid evolutionary change in reproductive behaviour, morphology and physiology. This often leads to the evolution of sexual dimorphism, and continued exaggerated expression of dimorphic sexual characteristics, although a variety of other alternative selection scenarios exist. Here, we examined the evolutionary significance of a rapidly evolving, sexually dimorphic trait, sex comb tooth number, in two Drosophila species. The presence of the sex comb in both D. melanogaster and D. pseudoobscura is known...

Data from: Low migratory connectivity is common in long-distance migrant birds

Tom Finch, Simon Butler, Aldina Franco, Will Cresswell, Simon J. Butler & Aldina M. A. Franco
1. Estimating how much long-distance migrant populations spread out and mix during the non-breeding season (migratory connectivity) is essential for understanding and predicting population dynamics in the face of global change. 2. We quantify variation in population spread and inter-population mixing in long-distance, terrestrial migrant land-bird populations (712 individuals from 98 populations of 45 species, from tagging studies in the Neotropic and Afro-Palearctic flyways). We evaluate the Mantel test as a metric of migratory connectivity,...

Data from: The genetics of mate preferences in hybrids between two young and sympatric Lake Victoria cichlid species

Ola Svensson, Katie Woodhouse, Cock Van Oosterhout, Alan Smith, George F. Turner & Ole Seehausen
The genetic architecture of mate preferences is likely to affect significant evolutionary processes, including speciation and hybridization. Here, we investigate laboratory hybrids between a pair of sympatric Lake Victoria cichlid fish species that appear to have recently evolved from a hybrid population between similar predecessor species. The species demonstrate strong assortative mating in the laboratory, associated with divergent male breeding coloration (red dorsum versus blue). We show in a common garden experiment, using DNA-based paternity...

Data from: Winter wren populations show adaptation to local climate

Catriona A. Morrison, Robert A. Robinson & James W. Pearce-Higgins
Most studies of evolutionary responses to climate change have focused on phenological responses to warming, and provide only weak evidence for evolutionary adaptation. This could be because phenological changes are more weakly linked to fitness than more direct mechanisms of climate change impacts, such as selective mortality during extreme weather events which have immediate fitness consequences for the individuals involved. Studies examining these other mechanisms may be more likely to show evidence for evolutionary adaptation....

Data from: Telomere length reveals cumulative individual and transgenerational inbreeding effects in a passerine bird

Kat Bebbington, Lewis G. Spurgin, Eleanor A. Fairfield, Hannah L. Dugdale, Jan Komdeur, Terry Burke & David S. Richardson
Inbreeding results in more homozygous offspring that should suffer reduced fitness, but it can be difficult to quantify these costs for several reasons. First, inbreeding depression may vary with ecological or physiological stress and only be detectable over long time periods. Second, parental homozygosity may indirectly affect offspring fitness, thus confounding analyses that consider offspring homozygosity alone. Finally, measurement of inbreeding coefficients, survival and reproductive success may often be too crude to detect inbreeding costs...

Data from: PyroClean: Denoising pyrosequences from protein-coding amplicons for the recovery of interspecific and intraspecific genetic variation

Ricardo Ramirez-Gonzalez, Douglas W. Yu, Catharine Bruce, Darren Heavens, Mario Caccamo & Brent C. Emerson
DatasetsThis .zip files contains two folders. The folder "Control" contains the 15 raw 454 sequence files generated from the "Test Pools" analysis detailed in Table 2 of the manuscript, and a file of 27 Sanger sequences listed in Table S1. The folder "Tenerife" contains the 6 raw 454 sequence files associated generated from the "Tenerife Forest Samples" analysis detailed in Table 3 of the manuscript.

Registration Year

  • 2021
  • 2020
  • 2019
  • 2018
  • 2017
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  • 2015
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  • 2013
  • 2012

Resource Types

  • Dataset


  • University of East Anglia
  • University of Groningen
  • University of Sheffield
  • University of Leeds
  • Uppsala University
  • Bangor University
  • University of Cambridge
  • Earlham Institute
  • University of Oxford
  • Swiss Federal Institute of Technology in Zurich