444 Works

Quantifying the structure and dynamics of fish shoals under predation threat in three-dimensions

Maksym Romenskyy, James Herbert-Read, Christol Ioannou, Alex Szorkovszky, Ashley Ward & David Sumpter
Detailed quantifications of how predators and their grouping prey interact in three dimensions (3D) remain rare. Here we record the structure and dynamics of fish shoals (Pseudomugil signifer) in 3D both with and without live predators (Philypnodon grandiceps) under controlled laboratory conditions. Shoals adopted two distinct types of shoal structure; ‘sphere-like’ geometries at depth, and flat ‘carpet-like’ structures at the water’s surface, with shoals becoming more compact in both horizontal and vertical planes in the...

Data from: Testing the limits of pheromone stigmergy in spatially constrained robotic swarms

Edmund Hunt, Simon Jones & Sabine Hauert
Area coverage and collective exploration are key challenges for swarm robotics. Previous research in this field has drawn inspiration from ant colonies, with real, or more commonly virtual, pheromones deposited into a shared environment to coordinate behaviour through stigmergy. Repellent pheromones can facilitate rapid dispersal of robotic agents, yet this has been demonstrated only for relatively small swarm sizes (N<30). Here, we report findings from swarms of real robots (Kilobots) an order of magnitude larger...

Supplementary data from: Decoupling of morphological disparity and taxonomic diversity during the end-Permian mass extinction

Junyu Wan, William Foster, Li Tian, Thomas Stubbs, Michael Benton, Xincheng Qiu & Aihua Yuan
An increasing number of unexpectedly diverse benthic communities are being reported from microbially-precipitated carbonate facies in shallow-marine platform settings after the end-Permian mass extinction. Ostracoda, which was one of the most diverse and abundant metazoan groups during this interval, recorded their greatest diversity and abundance associated with these facies. Previous studies, however, focused mainly on their taxonomic diversity and, therefore, left room for discussion of paleoecological significance. Here, we apply a morphometric method (semi-landmarks) to...

Cephalic biomechanics underpins the evolutionary success of trilobites

Jorge Esteve, Jordi Marcé-Nogué, Francesc Pérez-Peris & Emily Rayfield
Arthropods (i.e. insects, spiders, crustaceans, myriapods and others), are the most successful Phanerozoic animals. The group are characterised by the possession of a segmented body, jointed limbs and a hard cuticle that is episodically moulted. One highly successful, but now extinct, group of arthropods are the trilobites. Trilobites underwent episodic moulting (ecdysis), and most trilobites possess facial sutures, lines of weakness in the cephalon, via which the exuviae is shed and the animal emerges. However,...

The Camouflage Machine: Optimising protective colouration using deep learning with genetic algorithms

John Fennell, Laszlo Talas, Roland Baddeley, Innes Cuthill & Nicholas Scott-Samuel
Evolutionary biologists frequently wish to measure the fitness of alternative phenotypes using behavioural experiments. However, many phenotypes are complex. For example colouration: camouflage aims to make detection harder, while conspicuous signals (e.g. for warning or mate attraction) require the opposite. Identifying the hardest and easiest to find patterns is essential for understanding the evolutionary forces that shape protective colouration, but the parameter space of potential patterns (coloured visual textures) is vast, limiting previous empirical studies...

Corridor quality affects net movement, size of dispersers, and population growth in experimental microcosms

Dongbo Li, Christopher F. Clements, Isobel L.G. Shan & Jane Memmott
Corridors are expected to increase species dispersal in fragmented habitats. However, it remains unclear how the quality of corridors influences the dispersal process, and how it interacts with corridor length and width. Here we investigate these factors using a small-scale laboratory system where we track the dispersal of the model organism Collembola Folsomia candida. Using this system, we study the effects of corridor length, width, and quality on the probability of dispersal, net movement, body...

Bumblebee colony density on farmland is influenced by late-summer nectar supply and garden cover

Thomas Timberlake, Ian Vaughan, Mathilde Baude & Jane Memmott
1. Floral resources are important in limiting pollinator populations, but they are often highly variable across time and space and the effect of this variation on pollinator population dynamics is not well understood. The phenology (timing) of floral resources is thought to be important in structuring pollinator populations, but few studies have directly investigated this. 2. Our study quantifies the landscape composition, seasonal nectar and pollen supply, and Bombus terrestris colony density of 12 farms...

Data for: Neural divergence and hybrid disruption between ecologically isolated Heliconius butterflies

Stephen Montgomery, Matteo Rossi, W. Owen McMillan & Richard Merrill
The importance of behavioral evolution during speciation is well established, but we know little about how this is manifest in sensory and neural systems. A handful of studies have linked specific neural changes to divergence in host or mate preferences associated with speciation. However, the degree to which brains are adapted to local environmental conditions, and whether this contributes to reproductive isolation between close relatives that have diverged in ecology, remains unknown. Here, we examine...

Groundwater recharge in Africa from ground based measurements

Alan MacDonald, Murray Lark, Richard Taylor, Tamiru Abiye, Helen Fallas, Guillaume Favreau, Ibrahim Goni, Seifu Kebede, Bridget Scanlon, James Sorenson, Moshood Tijani, Kirsty Upton & Charles West
This dataset comprises a map of groundwater recharge for Africa and a database of the 134 observations used to generate the map. The map shows long term average annual groundwater recharge in mm per annum relevant to the period 1970 to 2020. It is in the form of a GIS shapefile and is available as a layer package for ESRI and also as a georeferenced TIFF and BIL file for easy exchange with other software....

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...

CT slices of three Protoceratopsian skulls and example slices of other Gobi Desert vertebrates

Congyu Yu, Fangbo Qin, Yin Li, Zichuan Qin & Mark Norell
This is a image dataset for deep learning studies. The main dataset comprises labeled CT slices from 3 protoceratopsian dinosaur skulls discovered from the Gobi Desert, Mongolia. The fossil specimens are now in the Division of Paleontology, American Museum of Natural History, New York, NY, USA. Inside the folders named after specimen number (i.e. IGM100-1021), there are six sub-folders comprising labeled or unlabled CT slice images of the specimen from three directions: axial, coronal, and...

Environmental variation and biotic interactions limit adaptation at ecological margins: lessons from rainforest Drosophila and European butterflies

Eleanor K. O'Brien, Greg M. Walter & Jon Bridle
Models of local adaptation to spatially varying selection predict that maximum rates of evolution are determined by the interaction between increased adaptive potential owing to increased genetic variation, and the cost genetic variation brings by reducing population fitness. We discuss existing and new results from our laboratory assays and field transplants of rainforest Drosophila and UK butterflies along environmental gradients, which try to test these predictions in natural populations. Our data suggest that: (i) local...

Dataset for quantifying avian inertial properties using calibrated computed tomography

Shane Windsor, Yusuf Mahadik & Nicholas Durston
Estimating centre of mass and mass moments of inertia is an important aspect of many studies in biomechanics. Characterising these parameters accurately in three dimensions is challenging with traditional methods requiring dissection or suspension of cadavers. Here, we present a method to quantify the three-dimensional centre of mass and inertia tensor of birds of prey using calibrated computed-tomography (CT) scans. The technique was validated using several independent methods, providing body segment mass estimates within approximately...

Year-round Arctic sea ice thickness from CryoSat-2 Baseline-D Level 1b observations 2010-2020

Jack Landy & Geoffrey Dawson
This dataset presents biweekly gridded sea ice thickness and uncertainty for the Arctic derived from the European Space Agency's satellite CryoSat-2. An associated 'developer's product' also includes intermediate parameters used or output in the sea ice thickness processing chain. Data are provided as biweekly grids with a resolution of 80 km, mapped onto a Northern Polar Stereographic Grid, covering the Arctic region north of 50 degrees latitude, for all months of the year between October...

Data from: Turnover in floral composition explains species diversity and temporal stability in the nectar supply of urban residential gardens

Nicholas Tew, Katherine Baldock, Ian Vaughan, Stephanie Bird & Jane Memmott
Residential gardens are a valuable habitat for insect pollinators worldwide, but differences in individual gardening practices substantially affect their floral composition. It is important to understand how the floral resource supply of gardens varies in both space and time so we can develop evidence-based management recommendations to support pollinator conservation in towns and cities. We surveyed 59 residential gardens in the city of Bristol, UK, at monthly intervals from March to October. For each of...

The functional diversity of marsupial limbs is influenced by both ecology and developmental constraint

Spencer Pevsner, David Grossnickle & Zhe-Xi Luo
Extant marsupials are less ecologically diverse than placentals, and this is reflected by placentals exhibiting a greater diversity of locomotor modes, including powered flight and fully aquatic swimming. One proposed explanation for this discrepancy is that the development of more disparate marsupial forelimbs is prevented by the neonate’s crawl to the pouch, which requires precocious forelimb development for climbing adaptations. To test predictions of this Developmental Constraint Hypothesis, we pursue a comparative morphometric study on...

Geographic and temporal morphological stasis in the latest Cretaceous ammonoid Discoscaphites iris from the U.S. Gulf and Atlantic Coastal Plains

James Witts, Corinne Myers, Matthew Garb, Kayla Irizarry, Ekaterina Larina, Anastasia Rashkova & Neil Landman
We examine temporal and spatial variation in morphology of the ammonoid cephalopod Discoscaphites iris using a large dataset from multiple localities in the Late Cretaceous (Maastrichtian) of the United States Gulf and Atlantic Coastal Plains, spanning a distance of 2000 km along the paleoshoreline. Our results suggest that the fossil record of D. iris is consistent with no within species net accumulation of phyletic evolutionary change across morphological traits or the lifetime of this species....

Data from: Phylogenomics of elongate-bodied Springtails reveals independent transitions from aboveground to belowground habitats in deep time

Daoyuan Yu, Yinhuan Ding, Erik Tihelka, Chenyang Cai, Feng Hu, Manqiang Liu & Feng Zhang
Soil has become a major hotspot of biodiversity studies, yet the pattern and timing of the evolution of soil organisms are poorly known because of the scarcity of palaeontological data. To overcome this limitation, we conducted a genome-based macroevolutionary study of an ancient, diversified, and widespread lineage of soil fauna, the elongate-bodied springtails (class Collembola, order Entomobryomorpha). To build the first robust backbone phylogeny of this previously refractory group, we sampled representatives of major higher...

Accelerating ice loss from peripheral glaciers in North Greenland

Shfaqat Abbas Khan, William Colgan, Thomas A. Neumann, Michiel R. Van Den Broeke, Kelly M. Brunt, Brice Noël, Jonathan L. Bamber, Javed Hassan & Anders A. Bjørk
In recent decades, Greenland’s peripheral glaciers have experienced large-scale mass loss, resulting in a substantial contribution to sea-level rise. Only 4% of Greenland’s ice cover are small peripheral glaciers that are distinct from the ice sheet proper. Despite comprising this relatively small area, these small peripheral glaciers are responsible for 11% of the ice loss associated with Greenland’s recent sea-level rise contribution. Using the satellite laser platforms ICESat and ICESat-2, we estimate that ice loss...

Shifting balances in the weighting of sensory modalities are predicted by divergence in brain morphology in incipient species of Heliconius butterflies

Denise Dalbosco Dell'Aglio, W. Owen McMillan & Stephen Montgomery
Integrating and weighting sensory perception across modalities is crucial to how animals adapt to their environment. Divergence in brain structure is often in sensory processing regions, suggesting that investment reflects ecological needs. Here, we use two parapatric closely related species, Heliconius erato cyrbia and Heliconius himera, to test the hypothesis that divergence in sensory brain regions affects foraging decisions. These butterflies are isolated across an ecological gradient, which is linked to differences in brain morphology,...

Data from: Low fossilization potential of keratin protein revealed by experimental taphonomy

Evan T. Saitta, Chris Rogers, Richard A. Brooker, Geoffrey D. Abbott, Sumit Kumar, Shane S. O'Reilly, Paul Donohoe, Suryendu Dutta, Roger E. Summons & Jakob Vinther
Recent studies have suggested the presence of keratin in fossils dating back to the Mesozoic. However, ultrastructural studies revealing exposed melanosomes in many fossil keratinous tissues suggest that keratin should rarely, if ever, be preserved. In this study, keratin's stability through diagenesis was tested using microbial decay and maturation experiments on various keratinous structures. The residues were analysed using pyrolysis-gas chromatography-mass spectrometry and compared to unpublished feather and hair fossils and published fresh and fossil...

Data from: A Triassic crown squamate

Michael Benton, David Whiteside & Sophie Chambi-Trowell
Here we report a modern-type lizard from the Late Triassic of England (202 Ma), comprising a partial skeleton, skull, and mandibles. It displays at least 15 unique squamate traits, and further, shares unidentatan and anguimorph apomorphies. The new find fixes the origin of crown Squamata as much older than had been thought, and the revised dating shows substantial diversification of modern-type squamates following the Carnian Pluvial Episode, 232 million years ago. The data set comprises...

Additional file 4 of A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology

Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng … & Barry Smith
Additional file 4: Supplemental Table 3. Protein Ontology representation of SARS-CoV-2 proteins. Comparative information in RefSeq and UniProtKB is also provided.

Additional file 1 of Mendelian randomization analysis of factors related to ovulation and reproductive function and endometrial cancer risk

Shannon D’Urso, Pooja Arumugam, Therese Weider, Liang-Dar Hwang, Tom A. Bond, John P. Kemp, Nicole M. Warrington, David M. Evans, Tracy A. O’Mara & Gunn-Helen Moen
Additional file 1: Table S1. Genome-wide significant independent SNPs for Body Mass Index in women (Pulit 2018). Table S2. Genome-wide significant independent SNPs for Years Ovulating (Hg19). Table S3. Genome-wide significant independent SNPs for age at menarche downloaded from the ReproGen Consortium Website (Perry et al., 2014; Hg19). Table S4. Genome-wide significant independent SNPs for age at menopause downloaded from the ReproGen Consortium Website (Hg19; Day et al., 2015). Table S5. Genome-wide significant independent SNPs...

In vitro study on the effect of peucedanol on the activity of cytochrome P450 enzymes

Cun Zhang, Yongwei Li, Changlong Yin, Jie Zheng & Guozhi Liu
Peucedanol is a major extract of Peucedanum japonicum Thunb. (Apiaceae) roots, which is a commonly used herb in paediatrics. Its interaction with cytochrome P450 enzymes (CYP450s) would lead to adverse effects or even failure of therapy. The interaction between peucedanol and CYP450s was investigated. Peucedanol (0, 2.5, 5, 10, 25, 50, and 100 μM) was incubated with eight human liver CYP isoforms (CYP1A2, 2A6, 3A4, 2C8, 2C9, 2C19, 2D6, and 2E1), in pooled human liver...

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