307 Works

The asymptotic behavior of bootstrap support values in molecular phylogenetics

Jun Huang, Yuting Liu, Tianqi Zhu & Ziheng Yang
The phylogenetic bootstrap is the most commonly used method for assessing statistical confidence in estimated phylogenies by non-Bayesian methods such as maximum parsimony and maximum likelihood (ML). It is observed that bootstrap support tends to be high in large genomic datasets whether or not the inferred trees and clades are correct. Here we study the asymptotic behavior of bootstrap support for the ML tree in large datasets when the competing phylogenetic trees are equally right...

Coexistence of predators in time: effects of season and prey availability on species activity within a Mediterranean carnivore guild

Marc Vilella, Mariona Ferrandiz-Rovira & Ferran Sayol
1. The degree of coexistence among predators can determine the structure of ecological communities. Niche partitioning is a common strategy applied by species to enhance their coexistence. Diet, habitat or time use can be responsible for segregation among carnivore species, the latter factor being the least studied in Mediterranean ecosystems. Terrestrial medium-sized carnivores (i.e. mesocarnivores) carry out important functions in ecosystems and identifying their interactions is essential for their conservation. 2. In this study, we...

Climate drives community-wide divergence within species over a limited spatial scale: evidence from an oceanic island

Antonia Salces-Castellano, Jairo Patiño, Nadir Alvarez, Carmelo Andújar, Paula Arribas, Juan J. Braojos-Ruiz, Marcelino Del Arco-Aguilar, Víctor García-Olivares, Dirk Karger, Heriberto López, Ioanna Manolopoulou, Pedro Oromí, Antonio J. Pérez-Delgado, William W. Peterman, Kenneth F. Rijsdijk & Brent C. Emerson
Geographic isolation substantially contributes to species endemism on oceanic islands when speciation involves the colonisation of a new island. However, less is understood about the drivers of speciation within islands. What is lacking is a general understanding of the geographic scale of gene flow limitation within islands, and thus the geographic scale and drivers of geographical speciation within insular contexts. Using a community of beetle species, we show that when dispersal ability and climate tolerance...

Intergroup aggression in meerkats

Mark Dyble, Thomas Houslay, Marta Manser & Tim Clutton-Brock
Violent conflicts between groups have been observed among many species of group living mammals and can have important fitness consequences, with individuals being injured or killed and with losing groups surrendering territory. Here, we explore between-group conflict among meerkats (Suricata suricatta), a highly social and cooperatively breeding mongoose. We show that interactions between meerkat groups are frequently 18 aggressive and sometimes escalate to fighting and lethal violence and that these interactions have consequences for group...

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.

Natural history, phenotypic spectrum, and discriminative features of multisystemic RFC1-disease

Andreas Traschütz, Andrea Cortese, Selina Reich, Natalia Dominik, Jennifer Faber, Heike Jacobi, Annette Hartmann, Dan Rujescu, Solveig Montaut, Andoni Echaniz-Laguna, Sevda Erer, Valerie Cornelia Schütz, Alexander Tarnutzer, Marc Sturm, Tobias Haack, Nadège Vaucamps-Diedhiou, Helene Puccio, Ludger Schöls, Thomas Klockgether, Bart P. Van De Warrenburg, Martin Paucar, Dagmar Timmann, Ralf-Dieter Hilgers, Jose Gazulla, Michael Strupp … & Matthis Synofzik
Objective: To delineate the full phenotypic spectrum, discriminative features, piloting longitudinal progression data, and sample size calculations of RFC1-repeat expansions, recently identified as causing cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS). Methods: Multimodal RFC1 repeat screening (PCR, southern blot, whole-exome/genome (WES/WGS)-based approaches) combined with cross-sectional and longitudinal deep-phenotyping in (i) cross-European cohort A (70 families) with ≥2 features of CANVAS and/or ataxia-with-chronic-cough (ACC); and (ii) Turkish cohort B (105 families) with unselected late-onset ataxia. Results:...

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...

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...

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];...

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...

Data from: Taxonomic structure of the fossil record is shaped by sampling bias

Graeme T. Lloyd, Jeremy R. Young & Andrew B. Smith
Understanding biases that affect how species are partitioned into higher taxa is critical for much of palaeobiology, as higher taxa are commonly used to estimate species diversity through time. Using the deep-sea record of coccolithophorid microfossils over the last 150 million years (myr), we demonstrate that sampling and taxonomic effort are important drivers of the species/genus ratio. An unexpected two-stepped change in the ratio of species to genera over the last 150 myr correlates strongly...

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: Environmental drivers of crocodyliform extinction across the Jurassic/Cretaceous transition

Jonathan P. Tennant, Philip D. Mannion & Paul Upchurch
Crocodyliforms have a much richer evolutionary history than represented by their extant descendants, including several independent marine and terrestrial radiations during the Mesozoic. However, heterogeneous sampling of their fossil record has obscured their macroevolutionary dynamics, and obfuscated attempts to reconcile external drivers of these patterns. Here, we present a comprehensive analysis of crocodyliform biodiversity through the Jurassic/Cretaceous (J/K) transition using subsampling and phylogenetic approaches and apply maximum-likelihood methods to fit models of extrinsic variables to...

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: The impact of HCV infection duration on HIV disease progression and response to cART amongst HIV seroconverters in the UK

Jamie Inshaw, Clifford Leen, Martin Fisher, Richard Gilson, David Hawkins, Simon Collins, Julie Fox, Ken McLean, Sarah Fidler, Andrew Phillips, Sam Lattimore, Abdel Babiker & Kholoud Porter
Introduction: The effect of HCV infection on HIV disease progression remains unclear; the effect of HCV infection duration on HIV disease progression is unknown. Methods: We used data from a cohort of HIV seroconverters to investigate the effect of HCV infection duration on time from HIV seroconversion to CD4 <350cells/mm3, AIDS or death, censoring at the earlier of cART initiation or last clinic visit, adjusting for confounders and splitting data into follow up periods from...

Data from: Early consequences of allopolyploidy alter floral evolution in Nicotiana (Solanaceae)

Elizabeth W. McCarthy, Jacob B. Landis, Amelda Kurti, Amber J. Lawhorn, Mark W. Chase, Sandra Knapp, Steven C. Le Comber, Andrew R. Leitch & Amy Litt
Background: Polyploidy has played a major role in angiosperm evolution. Previous studies have examined polyploid phenotypes in comparison to their extant progenitors, but not in context of predicted progenitor phenotypes at allopolyploid origin. In addition, differences in the trends of polyploid versus diploid evolution have not been investigated. We use ancestral character-state reconstructions to estimate progenitor phenotype at allopolyploid origin to determine patterns of polyploid evolution leading to morphology of the extant species. We also...

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...

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...

Evidence for ecological processes driving speciation among endemic lizards of Madagascar

Laura A. Nunes, Christopher J. Raxworthy & Richard G. Pearson
Although genetic patterns produced by population isolation during speciation are well documented, the biogeographic and ecological processes that trigger speciation remain poorly understood. Alternative hypotheses for the biogeography and ecology of speciation include geographic isolation combined with niche conservation (soft allopatry), or parapatric distribution on an environmental gradient with niche divergence (ecological speciation). Here we utilize species’ distributions, environmental data and two null models (Random Translation and Rotation, RTR, and the Background Similarity Test, BST)...

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...

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 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...

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...

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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