32 Works

Data from: Do rivers influence fine-scale population genetic structure of tigers in the Sundarbans?

M. Abdul Aziz, Olutolani Smith, Adam Barlow, Simon Tollington, & Jim J. Groombridge
Global tiger Panthera tigris populations mostly survive within the geographically fragmented forest patches, thereby limited genetic exchange between isolated populations. Assessing the genetic status of these populations can reveal the effects of dispersal barriers and provide critical insights to guide future conservation actions. Using non-invasively collected biological samples, we investigated fine-scale genetic structure of tigers in the Sundarbans mangrove forests intersected by the complex river systems, and which holds one of the largest global tiger...

Data from: Analysis of wild macaque stone tools used to crack oil palm nuts

Tomos Proffitt, V. Lydia Luncz, Suchinda Malaivijitnond, Michael Gumert, Magdalena S. Svensson & Micahel Haslam
The discovery of oil palm (Elaeis guineensis) nut-cracking by wild long-tailed macaques (Macaca fascicularis) is significant for the study of non-human primate and hominin percussive behaviour. Up until now, only West African chimpanzees (Pan troglodytes verus) and modern human populations were known to use stone hammers to crack open this particular hard-shelled palm nut. The addition of non-habituated, wild macaques increases our comparative dataset of primate lithic percussive behaviour focused on this one plant species....

Data from: Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes

Rebecca E. O'Connor, Marta Farre, Sunitha Jospeh, Joana Damas, Lucas Kiazim, Rebecca Jennings, Sophie Bennett, Eden A. Slack, Emily Allanson, Denis M. Larkin & Darren K. Griffin
The number of de novo genome sequence assemblies is increasing exponentially; however, relatively few contain one scaffold/contig per chromosome. Such assemblies are essential for studies of genotype-to-phenotype association, gross genomic evolution, and speciation. Inter-species differences can arise from chromosomal changes fixed during evolution, and we previously hypothesized that a higher fraction of elements under negative selection contributed to avian-specific phenotypes and avian genome organization stability. The objective of this study is to generate chromosome-level assemblies...

Data from: Masculinisation of gene expression is associated with male quality in Drosophila melanogaster

Rebecca Dean, Camille Hammer, Vanessa Higham & Damian K. Dowling
The signature of sexual selection has been revealed through the study of differences in patterns of genome-wide gene expression, both between the sexes and between alternative reproductive morphs within a single sex. What remains unclear, however, is whether differences in gene expression patterns between individuals of a given sex consistently map to variation in individual quality. Such a pattern, particularly if found in males, would provide unambiguous evidence that the phenotypic response to sexual selection...

Data from: Phylogeny, ecology and deep time: 2D outline analysis of anuran skulls from the Early Cretaceous to Recent

Carla Bardua, Susan E. Evans & Anjali Goswami
Anurans have a long fossil record, spanning from the Early Jurassic to Recent. However, specimens are often severely flattened, limiting their inclusion in quantitative analyses of morphological evolution. We perform a two-dimensional morphometric analysis of anuran skull outlines, incorporating 42 Early Cretaceous to Miocene species, as well as 93 extant species in 32 families. Outlines were traced in tpsDig2 and analysed with elliptical Fourier analysis. Fourier coefficients were used in MANOVAs, phylogenetic MANOVAs (as significant...

Data from: Clinical spectrum of STX1B-related epileptic disorders

Stefan Wolking, Patrick May, Davide Mei, Rikke S. Møller, Simona Balestrini, Katherine L. Helbig, Cecilia Desmettre Altuzarra, Nicolas Chatron, Charu Kaiwar, Katharina Stoehr, Peter Widdess-Walsh, Bryce A. Mendelsohn, Adam Numis, Maria R. Cilio, Wim Van Paesschen, Lene L. Svendsen, Stephanie Oates, Elaine Hughes, Sushma Goyal, Kathleen Brown, Margarita Sifuentes Saenz, Thomas Dorn, Hiltrud Muhle, Alistair T. Pagnamenta, Dimitris V. Vavoulis … & Julian Schubert
Objective: The aim of this study was to expand the spectrum of epilepsy syndromes related to STX1B, encoding the presynaptic protein syntaxin-1B, and establish genotype-phenotype correlations by identifying further disease-related variants. Methods: We used next generation sequencing in the framework of research projects and diagnostic testing. Clinical data and EEGs were reviewed, including already published cases. To estimate the pathogenicity of the variants, we used established and newly developed in silico prediction tools. Results: We...

Data from: Weighing trees with lasers: advances, challenges and opportunities

Mathias Disney, M. Boni Vicari, A. Burt, K. Calders, S. L. Lewis, P. Raumonen & P. Wilkes
Terrestrial laser scanning (TLS) is providing exciting new ways to quantify tree and forest structure, particularly above-ground biomass (AGB). We show how TLS can address some of the key uncertainties and limitations of current approaches to estimating AGB based on empirical allometric scaling equations (ASEs) that underpin all large-scale estimates of AGB. TLS provides extremely detailed non-destructive measurements of tree form independent of tree size and shape. We show examples of three-dimensional (3D) TLS measurements...

Data from: Impact of person-centred care training and person-centred activities on quality of life, agitation, and antipsychotic use in people with dementia living in nursing homes: a cluster-randomised controlled trial

Clive Ballard, Anne Corbett, Martin Orrell, Gareth Williams, Esme Moniz-Cook, Renee Romeo, Bob Woods, Lucy Garrod, Ingelin Testad, Barbara Woodward-Carlton, Jennifer Wenborn, Martin Knapp & Jane Fossey
Background: Agitation is a common, challenging symptom affecting large numbers of people with dementia and impacting on quality of life (QoL). There is an urgent need for evidence-based, cost-effective psychosocial interventions to improve these outcomes, particularly in the absence of safe, effective pharmacological therapies. This study aimed evaluate the efficacy of a person-centered care and psychosocial intervention (WHELD) on QoL, agitation and antipsychotic use in people with dementia living in nursing homes, and to determine...

Data from: Mutation in the intracellular chloride channel CLCC1 associated with autosomal recessive retinitis pigmentosa

Lin Li, Xiaodong Jiao, Ilaria D’Atri, Fumihito Ono, Ralph Nelson, Chi-Chao Chan, Naoki Nakaya, Zhiwei Ma, Yan Ma, Xiaoying Cai, Longhua Zhang, Siying Lin, Abdul Hameed, Barry A. Chioza, Holly Hardy, Gavin Arno, Sarah Hull, Muhammad Imran Khan, James Fasham, V. Gaurav Harlalka, Michel Michaelides, Anthony T. Moore, Zeynep Hande Coban Akdemir, Shalini Jhangiani, James R. Lupski … & Frans P. M. Cremers
We identified a homozygous missense alteration (c.75C>A, p.D25E) in CLCC1, encoding a presumptive intracellular chloride channel highly expressed in the retina, associated with autosomal recessive retinitis pigmentosa (arRP) in eight consanguineous families of Pakistani descent. The p.D25E alteration decreased CLCC1 channel function accompanied by accumulation of mutant protein in granules within the ER lumen, while siRNA knockdown of CLCC1 mRNA induced apoptosis in cultured ARPE-19 cells. TALEN KO in zebrafish was lethal 11 days post...

Data from: The rice paradox: multiple origins but single domestication in Asian rice

Jae Young Choi, Adrian E Platts, Dorian Q Fuller, Yue-Ie Hsing, Rod A Wing & Michael D Purugganan
The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara. Coalescence-based modeling of demographic...

Data from: EPA-ng: massively parallel evolutionary placement of genetic sequences

Pierre Barbera, Alexey M. Kozlov, Lucas Czech, Benoit Morel, Diego Darriba, Tomas Flouri & Alexandros Stamatakis
Next Generation Sequencing (NGS) technologies have led to a ubiquity of molecular sequence data. This data avalanche is particularly challenging in metagenetics, which focuses on taxonomic identification of sequences obtained from diverse microbial environments. Phylogenetic placement methods determine how these sequences fit into anevolutionary context. Previous implementations of phylogenetic placement algorithms, such as the Evolutionary Placement Algorithm (EPA) included in RAxML, or pplacer, are being increasingly used for this purpose. However, due to the steady...

Data from: A novel approach to wildlife transcriptomics provides evidence of disease-mediated differential expression and changes to the microbiome of amphibian populations

Lewis J. Campbell, Stewart A. Hammond, Stephen J. Price, Manmohan D. Sharma, Trenton W.J. Garner, Inanc Birol, Caren C. Helbing, Lena Wilfert, Amber G.F. Griffiths & Trenton W. J. Garner
Ranaviruses are responsible for a lethal, emerging infectious disease in amphibians and threaten their populations throughout the world. Despite this, little is known about how amphibian populations respond to ranaviral infection. In the United Kingdom, ranaviruses impact the common frog (Rana temporaria). Extensive public engagement in the study of ranaviruses in the UK has led to the formation of a unique system of field sites containing frog populations of known ranaviral disease history. Within this...

Data from: Mitochondrial genetic effects on reproductive success: signatures of positive intrasexual, but negative intersexual pleiotropy

M. Florencia Camus & Damian K. Dowling
Theory predicts that maternal inheritance of mitochondria will facilitate the accumulation of mtDNA mutations that are male biased, or even sexually antagonistic, in effect. While there are many reported cases of mtDNA mutations conferring cytoplasmic male sterility in plants, historically it was assumed such mutations would not persist in the streamlined mitochondrial genomes of bilaterian metazoans. Intriguingly, recent cases of mitochondrial variants exerting male-biases in effect have come to light in bilaterians. These cases aside,...

Data from: Kinship underlies costly cooperation in Mosuo villages

Matthew Gwynfryn Thomas, Ting Ji, JiaJia Wu, Qiao-Qiao He, Yi Tao, Ruth Mace & QiaoQiao He
The relative importance of social evolution theories such as kin selection, direct reciprocity and needs-based transfers in explaining real-world cooperation is the source of much debate. Previous field studies of cooperation in human communities have revealed variability in the extent to which each of these theories drive human sociality in different contexts. We conducted multivariate social network analyses predicting costly cooperation—labouring on another household’s farm—in 128,082 dyads of Mosuo farming households in southwest China. Through...

Data from: CSF biomarkers of neuroinflammation and cerebrovascular dysfunction in early Alzheimer's disease

Shorena Janelidze, Niklas Mattsson, Erik Stomrud, Olof Lindberg, Sebastian Palmqvist, Henrik Zetterberg, Kaj Blennow & Oskar Hansson
Objective: To measure cerebrospinal (CSF) levels of biomarkers reflecting microglia and astrocytes activation, neuroinflammation and cerebrovascular changes and study their associations with the core biomarkers of AD pathology (amyloid &[beta] (A&[beta]) and tau), structural imaging correlates and clinical disease progression over time. Methods: The study included cognitively unimpaired elderly (n=508), patients with mild cognitive impairment (MCI, n=256), and AD dementia (n=57) from the longitudinal Swedish BioFINDER cohort. CSF samples were analyzed for YKL-40, IL-6, IL-7,...

Data from: Postconvulsive central apnea as a biomarker for sudden unexpected death in epilepsy (SUDEP)

Laura Vilella, Nuria Lacuey, Johnson P. Hampson, M.R. Sandhya Rani, Rup K. Sanju, Daniel Friedman, Maromi Nei, Kingman Strohl, Catherine Scott, Brian K. Gehlbach, Bilal Zony, Norma J. Hupp, Anita Zaremba, Nassim Shafiabadi, Xihue Zhao, Victoria Reick-Mitrisin, Stephan Schuele, Jennifer Ogren, Ronald M. Harper, Beate Diehl, Lisa Bateman, Orrin Devinsky, George B. Richerson, Philippe Ryvlin & Samden D. Lhatoo
Objective: To characterize peri-ictal apnea and post-ictal asystole in generalized convulsive seizures (GCS) of intractable epilepsy. Methods: Prospective, multi-center epilepsy monitoring study of autonomic and breathing biomarkers of SUDEP in patient’s ≥18 years old with intractable epilepsy and monitored GCS. Video EEG, thoraco-abdominal excursions, nasal airflow, capillary oxygen saturation and electrocardiography were analyzed. Results: We studied 148 GCS in 87 patients. Nineteen patients had generalized epilepsy, 65 had focal, one had both and in two,...

Data from: Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events

Laurent A. F. Frantz, Anna Rudzinski, Abang Mansyursyah Surya Nugraha, Allowen Evin, James Burton, Ardern Hulme-Beaman, Anna Linderholm, Ross Barnett, Rodrigo Vega, Evan K. Irving-Pease, James Haile, Richard Allen, Kristin Leus, Jill Shephard, Mia Hillyer, Sarah Gillemot, Jeroen Van Den Hurk, Sharron Ogle, Cristina Atofanei, Mark G. Thomas, Friederike Johansson, Abdul Haris Mustari, John Williams, Kusdiantoro Mohamad, Chandramaya Siska Damayanti … & Greger Larson
The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back 40 Myr ago. Recent studies, however, suggest that much of Sulawesi’s fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification, and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions...

Data from: Lepidosaurian diversity in the Mesozoic–Paleogene: the potential roles of sampling biases and environmental drivers

Terri J. Cleary, Roger B.J. Benson, Susan E. Evans, Paul M. Barrett & Roger B. J. Benson
Lepidosauria is a speciose clade with a long evolutionary history, but there have been few attempts to explore its taxon-richness through time. Here we estimate patterns of terrestrial lepidosaur genus diversity for the Triassic–Paleogene (252–23 Ma), and compare observed and sampling-corrected richness curves generated using Shareholder Quorum Subsampling and classical rarefaction. Generalized least-squares regression (GLS) is used to investigate the relationships between richness, sampling and environmental proxies. We found low levels of richness from the...

Data from: Genetic diversity maintained among fragmented populations of a tree undergoing range contraction

James S. Borrell, Nian Wang, Richard A. Nichols & Richard J. A. Buggs
Dwarf birch (Betula nana) has a widespread boreal distribution but has declined significantly in Britain where populations are now highly fragmented. We analysed the genetic diversity of these fragmented populations using markers that differ in mutation rate: conventional microsatellites markers (PCR-SSRs), RADseq generated transition and transversion SNPs (RAD-SNPs), and microsatellite markers mined from RADseq reads (RAD-SSRs). We estimated the current population sizes by census and indirectly, from the linkage disequilibrium found in the genetic surveys....

Data from: Negative biotic interactions drive predictions of distributions for species from a grassland community

Phillip P.A. Staniczenko, Kenwyn Blake Suttle, Richard G. Pearson & Phillip P. A. Staniczenko
Understanding the factors that determine species’ geographic distributions is important for addressing a wide range of biological questions, including where species will be able to maintain populations following environmental change. New methods for modelling species distributions include the effects of biotic interactions alongside more commonly used abiotic variables such as temperature and precipitation; however, it is not clear which types of interspecific relationship contribute to shaping species distributions and should therefore be prioritised in models....

Data from: Ejaculate sperm number compensation in stalk-eyed flies carrying a selfish meiotic drive element

Lara C. Meade, Deidre Dinneen, Ridhima Kad, Dominic Lynch, Kevin Fowler & Andrew Pomiankowski
Meiotic drive genes cause the degeneration of non-carrier sperm to bias transmission in their favour. Males carrying meiotic drive are expected to suffer reduced fertility due to the loss of sperm and associated harmful side-effects of the mechanisms causing segregation distortion. However, sexual selection should promote adaptive compensation to overcome these deleterious effects. We investigate this using SR, an X-linked meiotic drive system in the stalk-eyed fly, Teleopsis dalmanni. Despite sperm destruction caused by drive,...

Data from: Non-invasive imaging of CSF-mediated brain clearance pathways via assessment of perivascular fluid movement with DTI MRI

Ian F. Harrison, Bernard Siow, Aisha B. Akilo, Phoebe G. Evans, Ozama Ismail, Yolanda Ohene, Payam Nahavandi, David L. Thomas, Mark F. Lythgoe & Jack A. Wells
The glymphatics system describes a CSF-mediated clearance pathway for the removal of potentially harmful molecules, such as amyloid beta, from the brain. As such, its components may represent new therapeutic targets to alleviate aberrant protein accumulation that defines the most prevalent neurodegenerative conditions. Currently, however, the absence of any non-invasive measurement technique prohibits detailed understanding of glymphatic function in the human brain and in turn, it's role in pathology. Here, we present the first non-invasive...

Data from: The induction of the fibroblast extracellular senescence metabolome is a dynamic process

Emma N.L. James, Mark H. Bennett & Eric K. Parkinson
Cellular senescence is often associated with irreparable DNA double strand breaks (IrrDSBs) which accumulate with chronological age (IrrDSBsen). The removal of senescent cells ameliorates several age-related diseases in mice but the translation of these findings into a clinical setting would be aided by the characterisation of non-invasive biomarkers of senescent cells. Several serum metabolites are independent indicators of chronological age and some of these accumulate outside senescent fibroblasts independently of cell cycle arrest, repairable DNA...

Data from: The spectre of too many species

Adam D. Leache, Tianqi Zhu, Bruce Rannala & Ziheng Yang
Recent simulation studies examining the performance of Bayesian species delimitation as implemented in the BPP program have suggested that BPP may detect population splits but not species divergences and that it tends to over-split when data of many loci are analyzed. Here we confirm these results and provide the mathematical justifications. We point out that the distinction between population and species splits made in the protracted speciation model has no influence on the generation of...

Data from: Sporadic sampling not climatic forcing drives observed early hominin diversity

Simon J. Maxwell, Philip J. Hopley, Paul Upchurch & Christophe Soligo
The role of climate change in the origin and diversification of early hominins is hotly debated. Most accounts of early hominin evolution link observed fluctuations in species diversity to directional shifts in climate or periods of intense climatic instability. None of these hypotheses, however, have tested whether observed diversity patterns are distorted by variation in the quality of the hominin fossil record. Here, we present a detailed examination of early hominin diversity dynamics, including both...

Registration Year

  • 2018
    32

Resource Types

  • Dataset
    32

Affiliations

  • University College London
    32
  • New York University
    3
  • Duke University
    2
  • The Ohio State University
    2
  • University of Kent
    2
  • King's College London
    2
  • Zoological Society of London
    2
  • University of Oxford
    2
  • University of California, Davis
    2
  • Northwestern University
    1