324 Works

Data from: Is it possible to reconstruct an accurate cell lineage using CRISPR recorders?

Irepan Salvador-Martínez, Marco Grillo, Michalis Averof & Maximilian J. Telford
Cell lineages provide the framework for understanding how multicellular organisms are built and how cell fates are decided during development. Describing cell lineages in most organisms is challenging, given the number of cells involved; even a fruit fly larva has ~50,000 cells and a small mammal has more than 1 billion cells. Recently, the idea of using CRISPR to induce mutations during development as heritable markers for lineage reconstruction has been proposed and trialled by...

Data from: Decision and navigation in mouse parietal cortex

Michael Krumin, Julie J. Lee, Kenneth D. Harris & Matteo Carandini
Posterior parietal cortex (PPC) has been implicated in navigation, in the control of movement, and in visually-guided decisions. To relate these views, we measured activity in PPC while mice performed a virtual navigation task driven by visual decisions. PPC neurons were selective for specific combinations of the animal's spatial position and heading angle. This selectivity closely predicted both the activity of individual PPC neurons, and the arrangement of their collective firing patterns in choice-selective sequences....

Data from: An assessment of the role of the falx cerebri and tentorium cerebelli in the cranium of the cat (Felis silvestris catus)

Víctor Sellés De Lucas, Hugo Dutel, Susan E. Evans, Flora Gröning, Alana C. Sharp, Peter J. Watson & Michael J. Fagan
The falx cerebri and the tentorium cerebelli are two projections of the dura mater in the cranial cavity which ossify to varying degrees in some mammalian species. The idea that the ossification of these structures may be necessary to support the loads arising during feeding has been proposed and dismissed in the past, but never tested quantitatively. To address this, a biomechanical model of a domestic cat (Felis silvestris catus) skull was created and the...

Data from: Mental illness, poverty and stigma in India: a case control study

Jean-Francois Trani, Parul Bakhshi, Jill Kuhlberg, Sreelatha S. Venkataraman, Hemalatha Venkataraman, Nagendra N. Mishra, Nora E. Groce, Sushrut Jadhav & Smita Deshpande
Objective: To assess the effect of experienced stigma on depth of multidimensional poverty of persons with severe mental illness (PSMI) in Delhi, India, controlling for gender, age and caste. Design: Matching case (hospital)–control (population) study. Setting: University Hospital (cases) and National Capital Region (controls), India. Participants: A case–control study was conducted from November 2011 to June 2012. 647 cases diagnosed with schizophrenia or affective disorders were recruited and 647 individuals of same age, sex and...

Data from: A dynamic framework for the study of optimal birth intervals reveals the importance of sibling competition and mortality risks

Matthew G. Thomas, Daryl P. Shanley, Alasdair I. Houston, John M. McNamara, Ruth Mace & Tom B. L. Kirkwood
Human reproductive patterns have been well studied, but the mechanisms by which physiology, ecology and existing kin interact to affect the life history need quantification. Here, we create a model to investigate how age-specific interbirth intervals adapt to environmental and intrinsic mortality, and how birth patterns can be shaped by competition and help between siblings. The model provides a flexible framework for studying the processes underlying human reproductive scheduling. We developed a state-based optimality model...

Data from: A prioritised list of invasive alien species to assist the effective implementation of EU legislation

Carles Carboneras, Piero Genovesi, Montserrat Vila, Tim Blackburn, Martina Carrete, Miguel Clavero, Bram D'hondt, Jorge F. Orueta, Belinda Gallardo, Pedro Geraldes, Pablo González-Moreno, Richard D. Gregory, Wolfgang Nentwig, Jean-Yves Paquet, Petr Pysek, Wolfgang Rabitsch, Iván Ramírez, Riccardo Scalera, Jose Tella, Paul Walton, Robin Wynde & Tim M. Blackburn
1. Effective prevention and control of invasive species generally relies on a comprehensive, coherent and representative list of species that enables resources to be used optimally. European Union (EU) Regulation 1143/2014 on invasive alien species (IAS) aims to control or eradicate priority species, and to manage pathways to prevent the introduction and establishment of new IAS; it applies to species considered of Union concern and subject to formal risk assessment. So far, 49 species have...

Data from: Parental investment in a Tibetan population does not reflect stated cultural norms

Juan Du & Ruth Mace
In this paper, we examined both stated norms of gender preference and actual sex-biases in parental investment in a Tibetan pastoralist society. We collected detailed demographic data to examine how biased parental investment had an effect on infant mortality, infant feeding, the length of interbirth intervals and a decision when giving gifts. Our results indicate a mismatch between self-reported son preference and measures of actual parental investment that favour daughters. We interpret this female-biased parental...

Data from: Variation in the benefits of multiple mating on female fertility in wild stalk-eyed flies

Lara Meade, Elisabeth Harley, Alison Cotton, James Howie, Andrew Pomiankowski, Kevin Fowler & James M. Howie
Polyandry, female mating with multiple males, is widespread across many taxa and almost ubiquitous in insects. This conflicts with the traditional idea that females are constrained by their comparatively large investment in each offspring, and so should only need to mate once or a few times. Females may need to mate multiply to gain sufficient sperm supplies to maintain their fertility, especially in species in which male promiscuity results in division of their ejaculate amongst...

Data from: Shotgun mitogenomics across body size classes in a local assemblage of tropical Diptera: phylogeny, species diversity and mitochondrial abundance spectrum

Le Qin Choo, Alex Crampton-Platt & Alfried P. Vogler
Mitochondrial genomes can be assembled readily from shotgun-sequenced DNA mixtures of mass-trapped arthropods (“mitochondrial metagenomics”), speeding up the taxonomic characterization. Bulk sequencing was conducted on some 800 individuals of Diptera obtained by canopy fogging of a single tree in Borneo dominated by small (<1.5 mm) individuals. Specimens were split into five body size classes for DNA extraction, to equalize read numbers across specimens and to study how body size, a key ecological trait, interacts with...

Data from: Membrane proteins are dramatically less conserved than water-soluble proteins across the tree of life

Victor Sojo, Christophe Dessimoz, Andrew Pomiankowski & Nick Lane
Membrane proteins are crucial in transport, signaling, bioenergetics, catalysis, and as drug targets. Here we show that membrane proteins have dramatically fewer detectable orthologs than water-soluble proteins, less than half in most species analyzed. This sparse distribution could reflect rapid divergence or gene loss. We find that both mechanisms operate. First, membrane proteins evolve faster than water-soluble proteins, particularly in their exteriorfacing portions. Second, we demonstrate that predicted ancestral membrane proteins are preferentially lost compared...

Data from: Camp stability predicts patterns of hunter–gatherer cooperation

Daniel Smith, Mark Dyble, James Thompson, Katie Major, Abigail E. Page, Nikhil Chaudhary, Gul Deniz Salali, Lucio Vinicius, Andrea Bamberg Migliano & Ruth Mace
Humans regularly cooperate with non-kin, which has been theorized to require reciprocity between repeatedly interacting and trusting individuals. However, the role of repeated interactions has not previously been demonstrated in explaining real-world patterns of hunter–gatherer cooperation. Here we explore cooperation among the Agta, a population of Filipino hunter–gatherers, using data from both actual resource transfers and two experimental games across multiple camps. Patterns of cooperation vary greatly between camps and depend on socio-ecological context. Stable...

Data from: Natural history of limb girdle muscular dystrophy R9 over 6 years: searching for trial endpoints

Alexander P. Murphy, Jasper Morrow, Julia R. Dahlqvist, Tanya Stojkovic, Tracey A. Willis, Christopher D. J. Sinclair, Stephen Wastling, Tarek Yousry, Michael S. Hanna, Meredith K. James, Anna Mayhew, Michelle Eagle, Laurence E. Lee, Jean-Yves Hogrel, Pierre G. Carlier, John S. Thornton, John Vissing, Kieren G. Hollingsworth & Volker Straub
Objective: Limb girdle muscular dystrophy type R9 (LGMD R9) is an autosomal recessive muscle disease for which there is currently no causative treatment. The development of putative therapies requires sensitive outcome measures for clinical trials in this slowly progressing condition. This study extends functional assessments and MRI muscle fat fraction measurements in an LGMD R9 cohort across 6 years. Methods: Twenty‐three participants with LGMD R9, previously assessed over a 1‐year period, were re‐enrolled at 6...

Biodiversity-productivity relationships are key to nature-based climate solutions

Akira Mori, Laura Dee, Andrew Gonzalez, Haruka Ohashi, Jane Cowles, Alexandra Wright, Michel Loreau, Yann Hautier, Tim Newbold, Peter Reich, Tetsuya Matsui, Wataru Takeuchi, Kei-Ichi Okada, Rupert Seidl & Forest Isbell
The global impacts of biodiversity loss and climate change are interlinked but the feedbacks between them are rarely assessed. Areas with greater tree diversity tend to be more productive, providing a greater carbon sink, and biodiversity loss could reduce these natural C sinks. Here, we quantify how tree and shrub species richness could affect biomass production at biome, national and regional scales. We find that greenhouse gas mitigation could help maintain tree diversity and thereby...

A non-coding indel polymorphism in the fruitless gene of Drosophila melanogaster exhibits antagonistically pleiotropic fitness effects

Michael Jardine, Filip Ruzicka, Charlotte Diffley, Kevin Fowler & Max Reuter
The amount of genetic variation for fitness within populations tends to exceed that expected under mutation-selection-drift balance. Several mechanisms have been proposed to actively maintain polymorphism and account for this discrepancy, including antagonistic pleiotropy (AP), where allelic variants have opposing effects on different components of fitness. Here we identify a non-coding indel polymorphism in the fruitless gene of Drosophila melanogaster and measure survival and reproductive components of fitness in males and females of replicate lines...

Data associated with: Going round the twist – An empirical analysis of shell coiling in helicospiral gastropods

Katie S. Collins, Roman Klapaukh, James S. Crampton, Michael F. Gazley, C. Ian Schipper, Anton Maksimenko & Benjamin R. Hines
The logarithmic helicospiral has been the most widely accepted model of regularly coiled mollusc form since it was proposed by Moseley (1838) and popularised by Thompson (1942) and Raup (1966). It is based on an explicit assumption that shells are isometric and grow exponentially, and an implicit assumption that the external form of the shell follows the internal shape, which implies that the parameters of the spiral could, theoretically, be reconstructed from the external whorl...

Spatial modulation of visual responses arises in cortex with active navigation

, Charu Bai Reddy, Sylvia Schröder, Tomaso Muzzu, Kenneth D. Harris, Aman B. Saleem & Matteo Carandini
During navigation, the visual responses of neurons in mouse primary visual cortex (V1) are modulated by the animal’s spatial position. Here we show that this spatial modulation is similarly present across multiple higher visual areas but negligible in the main thalamic pathway into V1. Similar to hippocampus, spatial modulation in visual cortex strengthens with experience and with active behavior. Active navigation in a familiar environment, therefore, enhances the spatial modulation of visual signals starting in...

Cerebral small vessel disease and functional outcome prediction after intracerebral haemorrhage

David Werring, Ghil Schwarz & Isabel Hostettler
Background. It is unknown whether adding cerebral small vessel disease (SVD) biomarkers can improve the performance of intracerebral hemorrhage (ICH) outcome predictive scores. Purpose. To determine whether: (1) CT-based SVD biomarkers are associated with 6-month functional outcome after ICH and (2) whether these biomarkers improve the performance of pre-existing ICH score. Methods. We included 864 patients with acute ICH from a multicentre, hospital-based prospective cohort study. We evaluated CT-based SVD biomarkers (white matter hypodensities [WMH];...

Historical analysis of seagrass loss in the United Kingdom

Alix E. Green, Michael A. Chadwick, Richard K.F. Unsworth & Peter J.S. Jones
This dataset includes empirical and qualitative data from a multitude of sources using systematic review methods to provide analysis on seagrass occurrence and loss in the United Kingdom. We document 8,493 ha of recently mapped seagrass in the UK since 1998.

The closure of the Neotethys in two episodes: first. as a result of Jurassic to Early Cretaceous obduction and second, as a result of Early Palaeocene collision; a comparison of surface geology and tomography (Central Internal Hellenides, Greece)

Rudolph Scherreiks & Camille BouDagher-Fadel
This contribution concerns Neotethys palaeogeography in the Central Internal Hellenides. Neotethys oceanic crust is represented in the Vardar zone of the Hellenides by the ophiolites of the Almopias sub-zone. Contrary to numerous tectonic models in the literature, we show that the Almopias ocean closed in two episodes.

A 5.3-million-year history of monsoonal precipitation in northwestern Australia

Jan-Berend Willem Stuut , Patrick De Deckker , Mariem Saavedra-Pellitero , Franck Bassinot , Anna Joy Drury , Maureen Walczak & Kana Nagashima
NIOZ - Royal Netherlands Institute for Sea Research, and Utrecht University, Texel, the Netherlands (1); MARUM – Center for Marine Environmental Sciences, Bremen University, Bremen, Germany (2); Department of Earth Sciences, Faculty of Science, Vrije Universiteit Amsterdam, The Netherlands (3); ANU – Australian National University, Research School of Earth Sciences, Canberra, Australia (4); School of Geography, Earth and Environmental Sciences at University of Birmingham, Edgbaston Birmingham, United Kingdom (5); LSCE - Laboratoire des Sciences du...

Data package from 'Pantropical variability in tree crown allometry' Global Ecology and Biogeography 2021. DOI: 10.1111/geb.13231

Grace Jopaul Loubota Panzou, Adeline Fayolle, Tommaso Jucker, Oliver Phillips, Stephanie Bohlman, Lindsay F. Banin, Simon L. Lewis, Kofi Affum-Baffoe, Luciana F. Alves, Cécile Antin, Eric Arets, Luzmila Arroyo, Timothy R. Baker, Nicolas Barbier, Hans Beeckman, Uta Berger, Yannick Enock Bocko, Frans Bongers, Sam Bowers, Thom Brade, Eduardo S. Brondizio, Arthur Chantrain, Jerome Chave, Halidou Compaore & David Coomes

Improving assessments of data-limited populations using life-history theory

Cat Horswill, Andrea Manica, Francis Daunt, Mark Newell, Sarah Wanless, Matthew Wood & Jason Matthiopoulos
1. Predicting how populations may respond to climate change and anthropogenic pressures requires detailed knowledge of demographic traits, such as survival and reproduction. However, the availability of these data varies greatly across space and taxa. Therefore, it is common practice to conduct population assessments by filling in missing values from surrogate species or other populations of the same species. Using these independent surrogate values concurrently with observed data neglects the life‐history trade‐offs that connect the...

Forecasts, neural networks, and results from the paper: 'Seasonal Arctic sea ice forecasting with probabilistic deep learning'

Tom R. Andersson & J. Scott Hosking
This dataset encompasses data produced in the study 'Seasonal Arctic sea ice forecasting with probabilistic deep learning', published in Nature Communications. The study introduces a new Arctic sea ice forecasting AI system, IceNet, which predicts monthly-averaged sea ice probability (SIP; probability of sea ice concentration > 15%) up to 6 months ahead at 25 km resolution. The study demonstrated IceNet's superior seasonal forecasting skill over a state-of-the-art physics-based sea ice forecasting system, ECMWF SEAS5, and...

Breaking a species barrier by enabling hybrid recombination

G. Ozan Bozdag, Jasmine Ono, Jai A. Denton, Emre Karakoc, Neil Hunter, Jun-Yi Leu & Duncan Greig
Hybrid sterility maintains reproductive isolation between species by preventing them from exchanging genetic material. Anti-recombination can contribute to hybrid sterility when different species’ chromosome sequences are too diverged to cross-over efficiently during hybrid meiosis, resulting in chromosome mis-segregation and aneuploidy. The genome sequences of the yeasts Saccharomyces cerevisiae and Saccharomyces paradoxus have diverged by about 12% and their hybrids are sexually sterile: nearly all of their gametes are aneuploid and inviable. Previous methods to increase...

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