567 Works

Data from: Riparian reserves help protect forest bird communities in oil palm dominated landscapes

Simon L. Mitchell, David P. Edwards, Henry Bernard, David Coomes, Tommaso Jucker, Zoe G. Davies & Matthew J. Struebig
1. Conversion of forest to oil palm agriculture is a significant and continuing threat to tropical biodiversity. Despite this, little is known about the value of riparian reserves in oil palm and how these conservation set-asides might best be managed to maintain biodiversity. 2. We characterised bird communities of 28 sites in an oil palm-forest mosaic in Sabah, Malaysia using 6104 encounters from 840 point counts. Sites included oil palm riparian reserves of various vegetation...

Data from: Genome-wide evidence for speciation with gene flow in Heliconius butterflies

Simon H. Martin, Kanchon K. Dasmahapatra, Nicola J. Nadeau, Camilo Salazar, James R. Walters, Fraser Simpson, Mark Blaxter, Andrea Manica, James Mallet & Chris D. Jiggins
Most speciation events probably occur gradually, without complete and immediate reproductive isolation, but the full extent of gene flow between diverging species has rarely been characterized on a genome-wide scale. Documenting the extent and timing of admixture between diverging species can clarify the role of geographic isolation in speciation. Here we use new methodology to quantify admixture at different stages of divergence in Heliconius butterflies, based on whole genome sequences of 31 individuals. Comparisons between...

Spectrum of mutational signatures in T-cell lymphoma reveals a key role for UV radiation in mycosis fungoides and Sezary syndrome

Christine Jones, Andrea Degasperi, Vieri Grandi, Tracey Mitchell & Serena Nik-Zainal
T-cell non-Hodgkin’s lymphomas develop following transformation of tissue resident T-cells. We performed a meta-analysis of mutational catalogues derived from whole exome sequencing data from 403 patients with eight subtypes of T-cell non-Hodgkin’s lymphoma to identify mutational signatures and recurrent gene mutations associated with specific causal peaks within these signatures. Signature 1, indicative of age-related deamination, was prevalent across all T-cell lymphoma subtypes, reflecting the derivation of these malignancies from memory T-cell subsets. The majority of...

A genome-wide investigation of adaptations related to tool use behaviour in New Caledonian and Hawaiian crows

Nicolas Dussex, Verena E. Kutschera, R. Axel W. Wiberg, Darren Parker, Gavin Hunt, Russell D. Gray, Kim Rutherford, Abe Hideaki, Robert Fleischer, Christian Rutz, Michael G. Ritchie, Jochen B.W. Wolf & Neil J. Gemmell
GFF3 file with protein-coding gne predictions for the C. moneduloides de novo genome assembly (available at the National Center for Biotechnology Information (NCBI); assembly accession number: VRTO00000000), generated using the MAKER2 pipeline.

Drones and global navigation satellite systems: current evidence from polar scientists

Iain Sheridan
Aerial unmanned vehicles, so-called drones, present a paradigm shift away from the long term use by scientists of manned airplanes and helicopters. This is evident from the number of research articles that focus on data obtained with drones. This article examines the use of aerial drones for scientific research in cryospheric regions, especially Antarctica and the Arctic. Specifically it aims to provide insights into the choices and performance of Global Navigation Satellite Systems (GNSS) use...

Data from: Were the floods in the UK 2007 and Germany 2013 game-changers?

Stephen Platt
This dataset concerns recovery after major floods in the UK 2007 and Germany 2013. It contains two sheets. The first sheet contains data from a survey of residents and local businesses in Catcliffe, between Sheffield and Rotherham in South Yorkshire and in Dreiflüsse-Eck, the “Three Rivers Corner” in Passau in Bavaria conducted in late 2018 and early 2019. The second sheet conatisn data from a survey with flood experts in the UK and Germany. The...

Data from: Resegmentation is an ancestral feature of the gnathostome vertebral skeleton

Katharine E. Criswell & J. Andrew Gillis
The vertebral skeleton is a defining feature of vertebrate animals. However, the mode of vertebral segmentation varies considerably between major lineages. In tetrapods, adjacent somite halves recombine to form a single vertebra through the process of ‘resegmentation’. In teleost fishes, there is considerable mixing between cells of the anterior and posterior somite halves, without clear resegmentation. To determine whether resegmentation is a tetrapod novelty, or an ancestral feature of jawed vertebrates, we tested the relationship...

Long-term movements and home range changes: rapid territory shifts in meerkats

Bart Kranstauber, Tim Clutton-Brock & Marta Manser
1. Territoriality and stable home ranges are a common space use pattern among animals. These ranges provide its inhabitants with important resources and thus favourable territories are associated with an increased fitness. While the role of territory quality and changes of territory ownership have often been investigated, the changes of territorial boundaries have been less studied. 2. Here we investigated space use changes in a social mammal species, applying a novel analytical approach, calculating long-term...

Benefits of cooperation in captive Damaraland mole rats

Thomas Houslay, Philippe Vullioud, Markus Zöttl & Tim Clutton-Brock
Although the social mole rats are commonly classified as eusocial breeders on the grounds that groups include a single breeding female (the ‘queen’) and a number of non-breeding individuals (‘helpers’) of both sexes, alloparental care is not highly developed in these species and there is no direct evidence that the presence or number of non-breeders is associated with reductions in the workload of the ‘queen’. An alternative interpretation of mole rat groups is that the...

Tracking the Near East origins and European dispersal of the house mouse

Thomas CUCCHI, Katerina Papayianni, Sophie Cersoy, Laetitia Aznar-Cormano, Antoine Zazzo, Régis Debruyne, Rémi Berthon, Adrian Bălășescu, Alan Simmons, François Valla, Yannis Hamilakis, Fanis Mavridis, Marjan Mashkour, Jamshid Darvish, Roohollah Siahsarvi, Fereidoun Biglari, Cameron A. Petrie, Lloyd Weeks, Alireza Sardari, Sepideh Maziar, Christiane Denys, David Orton, Emma Jenkins, Melinda Zeder, Jeremy B. Searle … & Jean-Denis Vigne
The house mouse (Mus musculus) is one of the most invasive mammals and an evolutionary model. However, the timing and components of its origin and dispersal remain poorly documented. To track its synanthropisation and subsequent biological invasion during the develoment of complex human societies, we analyzed 829 Mus specimens from 43 archaeological contexts in Southwestern Asia and Southeastern Europe, dating between 40,000 and 3,000 cal. BP, combining geometric morphometris numerical taxonomy with ancient mitochondrial DNA...

Kinetic data, oligomer data and binding data

Sara Linse, Tom Scheidt, Katja Bernfur, Michele Vendruscolo, Christopher Dobson, Samuel Cohen, Eimantas Sileikis, Martin Lundqvist, Fang Qian, Tiernan O'Malley, Thierry Bussiere, Paul Weinreb, Catherine Xu, Georg Meisl, Sean Devenish, Tuomas Knowles & Oskar Hansson
The amyloid cascade hypothesis, according to which the self-assembly of amyloid-β peptide (Aβ) is a causative process in Alzheimer’s disease, has driven many therapeutic efforts for the past 20 years. Failures of clinical trials investigating Aβ-targeted therapies have been interpreted as evidence against this hypothesis, irrespective of the characteristics and mechanisms of action of the therapeutic agents, which are highly challenging to assess. Here, we combine kinetic analyses with quantitative binding measurements to address the...

Early-life effects on body size in each sex interact to determine reproductive success in the burying beetle Nicrophorus vespilloides

Eleanor Bladon, Sinead English, Sonia Pascoal & Rebecca Kilner
Early-life conditions have been shown to have a profound effect on an animal’s body size and fecundity across diverse taxa. However, less is known about how early-life effects on fecundity within each sex interact to determine reproductive success. We used experiments with burying beetles Nicrophorus vespilloides to analyse this problem. The nutritional conditions experienced by burying beetles in early life are a key determinant of adult body size in both sexes, and adult body size...

Raw data for: No reproductive benefits of dear enemy recognition in a territorial songbird

Michael Reichert, Jodie Crane, Gabrielle Davidson, Eileen Dillane, Ipek Kulahci, James O'Neill, Kees Van Oers, Ciara Sexton & John Quinn
Territorial animals often learn to distinguish their neighbors from unfamiliar conspecifics. This cognitive ability facilitates the dear enemy effect, where individuals respond less aggressively to neighbors than to other individuals, and is hypothesized to be adaptive by reducing unnecessary aggressive interactions with individuals that are not a threat to territory ownership. A key prediction of this hypothesis, that individuals with better ability to learn to recognize neighbors should have higher fitness, has never been tested....

A practical approach to measuring the biodiversity impacts of land conversion

América P. Durán, Jonathan M. H. Green, Christopher D. West, Piero Visconti, Neil Burgess, Malika Virah-Sawmy & Andrew Balmford
1. Further progress in reducing biodiversity loss relies on the improved quantification of the connections between drivers of habitat loss and subsequent biodiversity impacts. To this end, biodiversity impact metrics should be able to report linked trends in specific human activities and changes in biodiversity state, accounting for both the ecology of different species, and the cumulative effects of historical habitat losses. These characteristics are not currently captured within a single metric. 2. Here we...

Phenotypic plasticity in chemical defence allows butterflies to diversify host use strategies

Erika De Castro, Jamie Musgrove, Søren Bak, Owen McMillan & Chris Jiggins
Hostplant specialization is a major force driving ecological niche partitioning and diversification in insect herbivores. The cyanogenic defences of Passiflora plants keeps most herbivores at bay, but not larvae of Heliconius butterflies, which can both sequester and biosynthesize cyanogenic compounds. Here, we demonstrate that both Heliconius cydno chioneus, a host plant generalist, and H. melpomene rosina, a specialist, have remarkable plasticity in their chemical defence. When feeding on Passiflora species with cyanogenic compounds they can...

High temperatures drive offspring mortality in a cooperatively breeding bird

Amanda Bourne, Susan Cunningham, Claire Spottiswoode & Amanda Ridley
An improved understanding of life history responses to current environmental variability is required to predict species-specific responses to anthopogenic climate change. Previous research has suggested that cooperation in social groups may buffer individuals against some of the negative effects of unpredictable climates. We use a 15-year dataset on a cooperative-breeding arid-zone bird, the southern pied babbler Turdoides bicolor, to test i) whether environmental conditions and group size correlate with survival of young during three development...

Signalling adjustments to direct and indirect environmental effects on signal perception in meerkats

Gabriella Gall, Pauline Toni, Tim Clutton-Brock & Marta Manser
The efficiency of communication between animals is determined by the perception range of signals. With changes in the environment, signal transmission between a sender and a receiver can be affected both directly, where the signal’s propagation quality itself is affected, and indirectly, where for example the spacing between signaller and receiver is impacted. Here we investigated how meerkats (Suricata suricatta) in the Kalahari Desert adjust to these challenges in the context of maintaining group cohesion...

Hybridization and transgressive exploration of colour pattern and wing morphology in Heliconius butterflies

Claire Mérot, Vincent Debat, Yann Le Poul, Richard M Merrill, Russell E Naisbit, Adélie Tholance, Chris Jiggins & Mathieu Joron
Hybridization can generate novel phenotypes distinct from those of parental lineages, a phenomenon known as transgressive trait variation. Transgressive phenotypes might negatively or positively affect hybrid fitness, and increase available variation. Closely related species of Heliconius butterflies regularly produce hybrids in nature and hybridization is thought to play a role in the diversification of novel wing colour patterns despite strong stabilizing selection due to interspecific mimicry. Here, we studied wing phenotypes in first and second...

Data from: Genome-wide association analysis of type 2 diabetes in the EPIC-InterAct study

Lina Cai, Eleanor Wheeler, Nicola D. Kerrison, Jian'an Luan, Panos Deloukas, Paul W. Franks, Pilar Amiano, Eva Ardanaz, Catalina Bonet, Guy Fagherazzi, Leif C. Groop, Rudolf Kaaks, José María Huerta, Giovanna Masala, Peter M. Nilsson, Kim Overvad, Valeria Pala, Salvatore Panico, Miguel Rodriguez-Barranco, Olov Rolandsson, Carlotta Sacerdote, Matthias B. Schulze, Annemieke M.W. Spijkeman, Anne Tjonneland, Rosario Tumino … & Nicholas J. Wareham
Type 2 diabetes (T2D) is a global public health challenge. Whilst the advent of genome-wide association studies has identified >400 genetic variants associated with T2D, our understanding of its biological mechanisms and translational insights is still limited. The EPIC-InterAct project, centred in 8 countries in the European Prospective Investigations into Cancer and Nutrition study, is one of the largest prospective studies of T2D. Established as a nested case-cohort study to investigate the interplay between genetic...

Oxidative costs of cooperation in cooperatively breeding Damaraland mole-rats

Rute Mendonça, Philippe Vullioud, Nathan Katlein, Armelle Vallat, Gaetan Glauser, Nigel Bennett & Fabrice Helfenstein
Within cooperatively breeding societies, individuals adjust cooperative contributions to maximise indirect fitness and minimize direct fitness costs. Yet, little is known about the physiological costs of cooperation, which may be detrimental to direct fitness. Oxidative stress, the imbalance between reactive oxygen species (by-products of energy production) and antioxidant protection, may represent such a cost when cooperative behaviours are energetically demanding. Oxidative stress can lead to the accumulation of cellular damage, compromising survival and reproduction, thus...

A possible Cambrian stem-group gnathiferan-chaetognath from the Weeks Formation (Miaolingian) of Utah

Simon Conway Morris, Ru Smith, Jennifer Hoyal Cuthill, Enrico Bonino & Rudy Lerosey-Aubril
In recent years the plethora of “weird wonders”, the vernacular for the apparently extinct major bodyplans documented in many of the Cambrian Lagerstätten, has been dramatically trimmed. This is because various taxa have either been assigned to known phyla or at least accommodated in larger monophyletic assemblages. Nevertheless, a number of Cambrian taxa retain their enigmatic status. To this intriguing roster we add Dakorhachis thambus n. gen. n. sp., from the Miaolingian (Guzhangian) Weeks Formation...

Cuttlefish show flexible and future-dependent foraging cognition

Pauline Billard, Alexandra Schnell, Nicola Clayton & Christelle Jozet-Alves
Some animals optimise their foraging activity by learning and memorising food availability, in terms of quantity and quality, and adapt their feeding behaviour accordingly. Here we investigated whether cuttlefish flexibly adapt their foraging behaviour according to the availability of their preferred prey. In Experiment 1, cuttlefish switched from a selective to an opportunistic foraging strategy (or vice versa) when the availability of their preferred prey at night was predictable versus unpredictable. In Experiment 2, cuttlefish...

Weight loss, insulin resistance, and study design confound results in a meta-analysis of animal models of fatty liver

Harriet Hunter, Dana De Gracia Hahn, Amedine Duret, Yu Ri Im, Qinrong Cheah, Jiawen Dong, Madison Fairey, Clarissa Hjalmarsson, Alice Li, Hong Kai Lim, Lorcan McKeown, Claudia-Gabriela Mitrofan, Raunak Rao, Mrudula Utukuri, Ian A Rowe & Jake Mann
The classical drug development pipeline necessitates studies using animal models of human disease to gauge future efficacy in humans, however there is a low conversion rate from success in animals to humans. Non-alcoholic fatty liver disease (NAFLD) is a complex chronic disease without any established therapies and a major field of animal research. We performed a meta-analysis with meta-regression of 603 interventional rodent studies (10,364 animals) in NAFLD to assess which variables influenced treatment response....

The evolutionary dynamics and fitness landscape of clonal hematopoiesis

Caroline J. Watson, A.L. Papula, Gladys Y.P. Poon, Wing H. Wong, Andrew L. Young, Todd E. Druley, Daniel S. Fisher & Jamie R. Blundell
Somatic mutations acquired in healthy tissues as we age are major determinants of cancer risk. Whether variants confer a fitness advantage or rise to detectable frequencies by change remains largely unknown. Blood sequencing data from ∼50,000 individuals reveals how mutation, genetic drift and fitness shape the genetic diversity of healthy blood (clonal hematopoiesis). We show that positive selection, not drift, is the major force shaping clonal hematopoiesis, provide bounds on the number of hematopoietic stem...

Data from: Improving the resolution of canine genome-wide association studies using genotype imputation: a study of two breeds

Christopher Jenkins, Sally Ricketts, Cathryn Mellersh, Ellen Schofield & Luisa De Risio
Genotype imputation using a reference panel that combines high-density array data and publicly available whole genome sequence consortium variant data is potentially a cost-effective method to increase the density of extant lower-density array datasets. In this study three datasets (two Border Collie; one Italian Spinone) generated using a legacy array (Illumina CanineHD, 173,662 SNPs) were utilised to assess the feasibility and accuracy of this approach and to gather additional evidence for the efficacy of canine...

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