338 Works

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

Data from: Autocorrelation structure at rest predicts value correlates of single neurons during reward-guided choice

Sean E. Cavanagh, Joni D. Wallis, Steven W. Kennerley & Laurence T. Hunt
Correlates of value are routinely observed in the prefrontal cortex (PFC) during reward-guided decision making. In previous work (Hunt et al., 2015), we argued that PFC correlates of chosen value are a consequence of varying rates of a dynamical evidence accumulation process. Yet within PFC, there is substantial variability in chosen value correlates across individual neurons. Here we show that this variability is explained by neurons having different temporal receptive fields of integration, indexed by...

Data from: Contrasting geographic structure in evolutionarily divergent Lake Tanganyika catfishes

Claire R. Peart, Kanchon K. Dasmahapatra & Julia J. Day
Geographic isolation is suggested to be among the most important processes in the generation of cichlid fish diversity in East Africa’s Great lakes, both through isolation by distance and fluctuating connectivity caused by changing lake levels. However, even broad scale phylogeographic patterns are currently unknown in many non-cichlid littoral taxa from these systems. To begin to address this we generated restriction-site associated DNA sequence (RADseq) data to investigate phylogeographic structure throughout Lake Tanganyika in two...

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: Hierarchical polygyny in multiparous lesser flat-headed bats

Panyu Hua, Libiao Zhang, Guangjian Zhu, Gareth Jones, Shuyi Zhang & Stephen James Rossiter
How males gain access to mates and the potential for female choice will determine whether polygyny can operate at several levels, from within litters and groups to the wider population. Female lesser flat-headed bats (Tylonycteris pachypus) form maternity groups in bamboo stems. Unusually for bats, they are multiparous, providing the opportunity to test whether multi-level polygyny differs among males depending on whether they roost with females, with males, or are solitary. We genotyped 662 individuals...

Data from: The complexity of mating decisions in stalk-eyed flies

Nadine C. Chapman, Penthai Siriwat, James Howie, Aaron Towlson, Lawrence Bellamy, Kevin Fowler & Andrew Pomiankowski
All too often, studies of sexual selection focus exclusively on the responses in one sex, on single traits, typically those that are exaggerated and strongly sexually dimorphic. They ignore a range of less obvious traits and behavior, in both sexes, involved in the interactions leading to mate choice. To remedy this imbalance, we analyze a textbook example of sexual selection in the stalk-eyed fly (Diasemopsis meigenii). We studied several traits in a novel, insightful, and...

Data from: Sex and genotype effects on nutrient-dependent fitness landscapes in Drosophila melanogaster

M. Florencia Camus, Kevin Fowler, Matthew W.D. Piper, Max Reuter & Matthew W. D. Piper
The sexes perform different reproductive roles and have evolved sometimes strikingly different phenotypes. One focal point of adaptive divergence occurs in the context of diet and metabolism, and males and females of a range of species have been shown to require different nutrients to maximize their fitness. Biochemical analyses in Drosophila melanogaster have confirmed that dimorphism in dietary requirements is associated with molecular sex differences in metabolite titres. In addition, they also showed significant within-sex...

Data from: High levels of genetic structure and striking phenotypic variability in a sexually dimorphic suckermouth catfish from the African Highveld

Jake Morris, Antonia G. P. Ford, Jarome R. Ali, Claire R. Peart, Roger Bills & Julia J. Day
Uncovering biological diversity to more accurately understand diversity patterns, and ultimately the processes driving diversification, is important not only from an evolutionary perspective but also a conservation perspective. This is particularly pertinent in Africa's rivers in which overall diversity, as well as how it arose, is poorly understood in comparison with lacustrine environments. Here we investigate population divergence in the sexually dimorphic suckermouth catfish species Chiloglanis anoterus (Crass, 1960) from the African Highveld, in which...

Data from: The influence of gene flow on species tree estimation: a simulation study

Adam D. Leaché, Rebecca B. Harris, Bruce Rannala & Ziheng Yang
Gene flow among populations or species and incomplete lineage sorting (ILS) are two evolutionary processes responsible for generating gene tree discordance and therefore hindering species tree estimation. Numerous studies have evaluated the impacts of ILS on species tree inference, yet the ramifications of gene flow on species trees remain less studied. Here, we simulate and analyze multilocus sequence data generated with ILS and gene flow to quantify their impacts on species tree inference. We characterize...

Data from: Hybridization facilitates evolutionary rescue

Rike B. Stelkens, Michael A. Brockhurst, Gregory D. D. Hurst & Duncan Greig
The resilience of populations to rapid environmental degradation is a major concern for biodiversity conservation. When environments deteriorate to lethal levels, species must evolve to adapt to the new conditions to avoid extinction. Here, we test the hypothesis that evolutionary rescue may be enabled by hybridization, because hybridization increases genetic variability. Using experimental evolution, we show that interspecific hybrid populations of Saccharomyces yeast adapt to grow in more highly degraded environments than intraspecific and parental...

Data from: Convergence and constraint in the cranial evolution of mosasaurid reptiles and early cetaceans

Rebecca Bennion, Jamie MacLaren, Ellen Coombs, Felix Marx, Olivier Lambert & Valentin Fischer
The repeated return of tetrapods to aquatic life provides some of the best-known examples of convergent evolution. One comparison which has received relatively little focus is that of mosasaurids (a group of Late Cretaceous squamates) and archaic cetaceans (the ancestors of modern whales and dolphins), both of which show high levels of craniodental disparity, similar initial trends in locomotory evolution, and global distributions. Here we investigate convergence in skull ecomorphology during the initial aquatic radiations...

Data from: Meiotic drive does not cause condition-dependent reduction of the sexual ornament in stalk-eyed flies

Sam Finnegan, Matteo Mondani, Kevin Fowler & Andrew Pomiankowski
Meiotic drive systems are associated with low frequency chromosomal inversions. These are expected to accumulate deleterious mutations due to reduced recombination and low effective population size. We test this prediction using the “sex-ratio” (SR) meiotic drive system of the Malaysian stalk-eyed fly Teleopsis dalmanni.SR is associated with a large inversion (or inversions) on the X chromosome. In particular, we study eyespan in males carrying the SR chromosome, as this trait is a highly exaggerated, sexually...

Flow cytometry data: healthy donor bone marrow taken during hip surgery

Jessica Timms, James Opzoomer, Kevin Blighe, Thanos Mourikis, Nicolas Chapuis, Richard Bekoe, Sedigeh Kareemaghay, Paola Nocerino, Benedetta Apollonio, Alan Ramsay, Mahvash Tavassoli, Claire Harrison, Francesca Ciccarelli, Peter Parker, Michaela Fontenay, Paul Barber, James Arnold & Shahram Kordasti
High dimensional cytometry is an innovative tool for immune monitoring in health and disease, it has provided novel insight into the underlying biology as well as biomarkers for a variety of diseases. However, the analysis of large multiparametric datasets usually requires specialist computational knowledge. Here we describe ImmunoCluster (https://github.com/kordastilab/ImmunoCluster) an R package for immune profiling cellular heterogeneity in high dimensional liquid and imaging mass cytometry, and flow cytometry data, designed to facilitate computational analysis by...

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...

Imaging mass cytometry data: Diffuse large B-cell lymphoma lymph node section

Jessica Timms, James Opzoomer, Kevin Blighe, Thanos Mourikis, Nicolas Chapuis, Richard Bekoe, Sedigeh Kareemaghay, Paola Nocerino, Benedetta Apollonio, Alan Ramsay, Mahvash Tavassoli, Claire Harrison, Francesca Ciccarelli, Peter Parker, Michaela Fontenay, Paul Barber, James Arnold & Shahram Kordasti
High dimensional cytometry is an innovative tool for immune monitoring in health and disease, it has provided novel insight into the underlying biology as well as biomarkers for a variety of diseases. However, the analysis of large multiparametric datasets usually requires specialist computational knowledge. Here we describe ImmunoCluster (https://github.com/kordastilab/ImmunoCluster) an R package for immune profiling cellular heterogeneity in high dimensional liquid and imaging mass cytometry, and flow cytometry data, designed to facilitate computational analysis by...

How to render species comparable taxonomic units through deep time: A case study on intraspecific osteological variability in extant and extinct Lacertid lizards

Emanuel Tschopp, James Napoli, Lukardis Wencker, Massimo Delfino & Paul Upchurch
Generally, the species is considered to be the only naturally occurring taxon. However, species recognised and defined using different species delimitation criteria cannot readily be compared, impacting studies of biodiversity through Deep Time. This comparability issue is particularly marked when comparing extant with extinct species, because the only available data for species delimitation in fossils is derived from their preserved morphology, which is generally restricted to osteology in vertebrates. Here, we quantify intraspecific, intrageneric, 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...

Middle Eocene terrestrial paleoweathering and climate evolution in the midlatitude Bohai Bay Basin of Eastern China

Di Chen, Xiongqi Pang, Kun Zhang, Guoyong Liu, Fujie Jiang, Liang Li, Youwei Wang, Min Li & Yang Liu
The middle Eocene is a key time period for understanding Cenozoic cooling of the global climate. In eastern Asia, this time period was marked by deposition of extensive mudstones, shales and interbedded siltstones, especially in the midlatitude Bohai Bay Basin. Still, midlatitude terrestrial records of climate evolution during the middle Eocene are rare. Here, we analyze a continuous, high-resolution record of this period using samples of the shales in the fourth submember of the third...

HemeLB input files for areteriovenous fistula simulation

Peter Coveney & Jon McCullough
This dataset contains the HemeLB input files used to run the blood flow simulations described in our manuscript "High fidelity physiological blood flow in patient-specific arteriovenous fistula for clinical applications". These work with the PressureCouplingBeds and ResistorCapacitorBeds branches of the source code available at https://github.com/UCL-CCS/HemePure_SelfCoupled. Provided in this dataset are four *.tar.gz files containing the necessary input files for the flow simulations through the arteries and veins of the left forearm discussed in our manuscript:...

Sudden Unexpected Death in Epilepsy: A Personalized Prediction Tool

Ashwani Jha, Cheongeun Oh, Dale Hesdorffer, Beate Diehl, Sasha Devore, Martin Brodie, Torbjörn Tomson, Josemir W. Sander, Thaddeus S. Walczak & Orrin Devinsky
Objective: To develop and validate a tool for individualised prediction of Sudden Unexpected Death in Epilepsy (SUDEP) risk, we re-analysed data from one cohort and three case-control studies undertaken 1980-2005. Methods: We entered 1273 epilepsy cases (287 SUDEP, 986 controls) and 22 clinical predictor variables into a Bayesian logistic regression model. Results: Cross-validated individualized model predictions were superior to baseline models developed from only average population risk or from generalised tonic-clonic seizure frequency (pairwise difference...

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...

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];...

Phase resolution of heterozygous sites in diploid genomes is important to phylogenomic analysis under the multispecies coalescent model

Ziheng Yang, Jun Huang, Tomas Flouri, Jeremy Bennett & Adam Leache
Genome sequencing projects routinely generate haploid consensus sequences from diploid genomes, which are effectively chimeric sequences with the phase at heterozygous sites resolved at random. The impact of phasing errors on phylogenomic analyses under the multispecies coalescent (MSC) model is largely unknown. Here we conduct a computer simulation to evaluate the performance of four phase-resolution strategies (the true phase resolution, the diploid analytical integration algorithm which averages over all phase resolutions, computational phase resolution using...

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...

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