167 Works

Estimating phylogenies from shape and similar multidimensional data: why it is not reliable

Ceferino Varón González, Simon Whelan & Christian Peter Klingenberg
In recent years, there has been controversy whether multidimensional data such as geometric morphometric data or information on gene expression can be used for estimating phylogenies. This study uses simulations of evolution in multidimensional phenotype spaces to address this question and to identify specific factors that are important for answering it. Most of the simulations use phylogenies with four taxa, so that there are just three possible unrooted trees and the effect of different combinations...

Data from: Repeated evidence that the accelerated evolution of sperm is associated with their fertilization function

John Fitzpatrick, Daisy Bridge & Rhonda Snook
Spermatozoa are the most morphologically diverse cell type, leading to the widespread assumption that they evolve rapidly. However, there is no direct evidence that sperm evolve faster than other male traits. Such a test requires comparing male traits that operate in the same selective environment, ideally produced from the same tissue, yet vary in function. Here we examine rates of phenotypic evolution in sperm morphology using two insect groups where males produce fertile and non-fertile...

Data from: Consistent size-independent harvest selection on fish body shape in two recreationally exploited marine species

Josep Alós, Miquel Palmer, Marta Linde-Medina & Robert Arlinghaus
Harvesting wild animals may exert size-independent selection pressures on a range of morphological, life history, and behavioral traits. Most work so far has focused on selection pressures on life history traits and body size as morphological trait. We studied here how recreational fishing selects for morphological traits related to body shape, which may correlate with underlying swimming behavior. Using landmark-based geometric morphometrics, we found consistent recreational fishing-induced selection pressures on body shape in two recreationally...

Data from: Downsizing a giant: re-evaluating Dreadnoughtus body mass

Karl T. Bates, Peter L. Falkingham, Sophie Macaulay, Charlotte Brassey & Susannah C. R. Maidment
Estimates of body mass often represent the founding assumption on which biomechanical and macroevolutionary hypotheses are based. Recently, a scaling equation was applied to a newly discovered titanosaurian sauropod dinosaur (Dreadnoughtus), yielding a 59 300 kg body mass estimate for this animal. Herein, we use a modelling approach to examine the plausibility of this mass estimate for Dreadnoughtus. We find that 59 300 kg for Dreadnoughtus is highly implausible and demonstrate that masses above 40...

Data from: Predation risk perception, food density and conspecific cues shape foraging decisions in a tropical lizard

Maximilian Drakeley, Oriol Lapiedra & Jason J. Kolbe
When foraging, animals can maximize their fitness if they are able to tailor their foraging decisions to current environmental conditions. When making foraging decisions, individuals need to assess the benefits of foraging while accounting for the potential risks of being captured by a predator. However, whether and how different factors interact to shape these decisions is not yet well understood, especially in individual foragers. Here we present a standardized set of manipulative field experiments in...

Data from: Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure

Petri Kemppainen, Christopher G. Knight, Devojit K. Sarma, Thaung Hlaing, Anil Prakash, Yan Naung Maung Maung, Pradya Somboon, Jagadish Mahanta & Catherine Walton
Recent advances in sequencing allow population-genomic data to be generated for virtually any species. However, approaches to analyse such data lag behind the ability to generate it, particularly in nonmodel species. Linkage disequilibrium (LD, the nonrandom association of alleles from different loci) is a highly sensitive indicator of many evolutionary phenomena including chromosomal inversions, local adaptation and geographical structure. Here, we present linkage disequilibrium network analysis (LDna), which accesses information on LD shared between multiple...

Data from: Learning to speciate: the biased learning of mate preferences promotes adaptive radiation

R. Tucker Gilman & Genevieve M. Kozak
Bursts of rapid repeated speciation called adaptive radiations have generated much of Earth’s biodiversity and fascinated biologists since Darwin, but we still do not know why some lineages radiate and others do not. Understanding what causes assortative mating to evolve rapidly and repeatedly in the same lineage is key to understanding adaptive radiation. Many species that have undergone adaptive radiations exhibit mate preference learning, where individuals acquire mate preferences by observing the phenotypes of other...

Data from: Temporal and phylogenetic evolution of the sauropod dinosaur body plan

Karl T. Bates, Philip D. Mannion, Peter L. Falkingham, Stephen L. Brusatte, John R. Hutchinson, Alexandros Otero, William I. Sellers, Corwin Sullivan, Kent A. Stevens & Vivian Allen
The colossal size and body plan of sauropod dinosaurs are unparalleled in terrestrial vertebrates. However, to date, there have been only limited attempts to examine temporal and phylogenetic patterns in the sauropod bauplan. Here, we combine three-dimensional computational models with phylogenetic reconstructions to quantify the evolution of whole-body shape and body segment properties across the sauropod radiation. Limitations associated with the absence of soft tissue preservation in fossils result in large error bars about mean...

Data from: Modelling and simulation of a thermally induced optical transparency in a dual micro-ring resonator

Joseph Lydiate
This paper introduces the simulation and modelling of a novel dual micro-ring resonator. The geometric configuration of the resonators, and the implementation of a simulated broadband excitation source, results in the realization of optical transparencies in the combined through port output spectrum. The 130 nm silicon on insulator rib fabrication process is adopted for the simulation of the dual-ring configuration. Two titanium nitride heaters are positioned over the coupling regions of the resonators, which can...

Data from: Estimating the prevalence of food risk increasing behaviours in UK kitchens

Anna K. Jones, Paul Cross, Michael Burton, Caroline Millman, Sarah J. O'Brien, Dan Rigby & Sarah J. O’Brien
Foodborne disease poses a serious threat to public health. In the UK, half a million cases are linked to known pathogens and more than half of all outbreaks are associated with catering establishments. The UK Food Standards Agency (FSA) has initiated the UK Food Hygiene Rating Scheme in which commercial food establishments are inspected and scored with the results made public. In this study we investigate the prevalence of food risk increasing behaviours among chefs,...

Data from: ‘Venus trapped, Mars transits’: Cu and Fe redox chemistry, cellular topography and in situ ligand binding in terrestrial isopod hepatopancreas

Peter Kille, A. John Morgan, Kate Powell, J. Frederick W. Mosselmans, Daniel Hart, Paul Gunning, Anthony Hayes, Derek Scarborough, Iain Mcdonald & John M. Charnock
Woodlice efficiently sequester copper (Cu) in ‘cuprosomes’ within hepatopancreatic ‘S’ cells. Binuclear ‘B’ cells in the hepatopancreas form iron (Fe) deposits; these cells apparently undergo an apocrine secretory diurnal cycle linked to nocturnal feeding. Synchrotron-based m-focus X-ray spectroscopy undertaken on thin sections was used to characterize the ligands binding Cu and Fe in S and B cells of Oniscus asellus (Isopoda). Main findings were: (i) morphometry confirmed a diurnal B-cell apocrine cycle; (ii) X-ray fluorescence...

Data from: The coevolution of sexual imprinting by males and females

Miguel Angel Gomez-Llano, Eva Maria Navarro-López & Robert Tucker Gilman
Sexual imprinting is the learning of a mate preference by direct observation of the phenotype of another member of the population. Sexual imprinting can be paternal, maternal, or oblique if individuals learn to prefer the phenotypes of their fathers, mothers, or other members of the population, respectively. Which phenotypes are learned can affect trait evolution and speciation rates. “Good genes” models of polygynous systems predict that females should evolve to imprint on their fathers, because...

Data from: First diagnosis of septic arthritis in a dinosaur

Jennifer Anné, Brandon P. Hedrick & Jason P. Schein
Identification and interpretation of pathologies in the fossil record allows for unique insights into the life histories of extinct organisms. However, the rarity of such finds limits not only the sample size for palaeopathologic studies, but also the types of analyses that may be performed. In this study, we present the first occurrence of a palaeopathology in a vertebrate from the Mesozoic of the East Coast of North America (Appalachia), a pathologic ulna and radius...

Data from: Assessment of plasma proteomics biomarker’s ability to distinguish benign from malignant lung nodules

Gerard A. Silvestri, Nichole T. Tanner, Paul Kearney, Anil Vachani, Pierre P. Massion, Alexander Porter, Steven C. Springmeyer, Kenneth C. Fang, David Midthun, Peter J. Mazzone, D. Madtes, J. Landis, A. Levesque, K. Rothe, M. Balaan, B. Dimitt, B. Fortin, N. Ettinger, A. Pierre, L. Yarmus, K. Oakjones-Burgess, N. Desai, Z. Hammoud, A. Sorenson, R. Murali … & F. Allison
Background: Lung nodules are a diagnostic challenge, with an estimated yearly incidence of 1.6 million in the United States. This study evaluated the accuracy of an integrated proteomic classifier in identifying benign nodules in patients with a pretest probability of cancer (pCA) ≤ 50%. Methods: A prospective, multicenter observational trial of 685 patients with 8- to 30-mm lung nodules was conducted. Multiple reaction monitoring mass spectrometry was used to measure the relative abundance of two...

Data from: The nearshore cradle of early vertebrate diversification

Lauren Sallan, Matt Friedman, Robert S. Sansom, Charlotte M. Bird & Ivan J. Sansom
Ancestral vertebrate habitats are subject to controversy and obscured by limited, often contradictory paleontological data. We assembled fossil vertebrate occurrence and habitat datasets spanning the middle Paleozoic (480 million to 360 million years ago) and found that early vertebrate clades, both jawed and jawless, originated in restricted, shallow intertidal-subtidal environments. Nearshore divergences gave rise to body plans with different dispersal abilities: Robust fishes shifted shoreward, whereas gracile groups moved seaward. Fresh waters were invaded repeatedly,...

Data from: Quadrupedal locomotor simulation: producing more realistic gaits using dual-objective optimisation

William Irvin Sellers & Eishi Hirasaki
In evolutionary biomechanics it is often considered that gaits should evolve to minimise the energetic cost of travelling a given distance. In gait simulation this goal often leads to convincing gait generation. However, as the musculoskeletal models used get increasingly sophisticated, it becomes apparent that such a single goal can lead to extremely unrealistic gait patterns. In this paper we explore the effects of requiring adequate lateral stability and show how this both increases energetic...

Data from: Developmental plasticity, morphological variation and evolvability: a multilevel analysis of morphometric integration in the shape of compound leaves

Chris P. Klingenberg, Sascha Duttke, Simon Whelan & Minsung Kim
The structure of compound leaves provides flexibility for morphological change by variation in the shapes, sizes and arrangement of leaflets. Here we conduct a multilevel analysis of shape variation in compound leaves to explore the developmental plasticity and evolutionary potential that are the basis of diversification in leaf shape. We use the methods of geometric morphometrics to study the shapes of individual leaflets and whole leaves in 20 taxa of Potentilla (sensu lato). A newly...

Data from: Ventilatory mechanics from maniraptoran theropods to extant birds

Peter G. Tickle, Mark A. Norell & Jonathan R. Codd
Shared behavioural, morphological and physiological characteristics are indicative of the evolution of extant birds from non-avian maniraptoran dinosaurs. One such shared character is the presence of uncinate processes; respiratory structures in extant birds. Recent research has suggested a respiratory role for these processes found in oviraptorid and dromaeosaurid dinosaurs. By measuring the geometry of fossil rib cage morphology we demonstrate that the mechanical advantage, conferred by uncinate processes, for movements of the ribs in the...

Data from: A computational analysis of locomotor anatomy and body mass evolution in Allosauroidea (Dinosauria Theropoda)

Karl T. Bates, Roger B. J. Benson & Peter L. Falkingham
We investigate whether musculoskeletal anatomy and three-dimensional (3-D) body proportions were modified during the evolution of large (>6000 kg) body size in Allosauroidea (Dinosauria Theropoda). Three adaptations for maintaining locomotor performance at large body size, related to muscle leverage, mass, and body proportions, are tested and all are unsupported in this analysis. Predictions from 3-D musculoskeletal models of medium-sized (Allosaurus) and large-bodied (Acrocanthosaurus) allosauroids suggest that muscle leverage scaled close to isometry, well below the...

Data from: Limited effects of the maternal rearing environment on the behaviour and fitness of an insect herbivore and its natural enemy

Alison J. Karley, Lucy Gilbert, Jennifer M. Slater & David Johnson
The maternal rearing environment can affect offspring fitness or phenotype indirectly via ‘maternal effects’ and can also influence a mother’s behaviour and fecundity directly. However, it remains uncertain how the effects of the maternal rearing environment cascade through multiple trophic levels, such as in plant-insect herbivore-natural enemy interactions. Pea aphids (Acyrthosiphon pisum) show differential fitness on host legume species, while generalist aphid parasitoids can show variable fitness on different host aphid species, suggesting that maternal...

Data from: Microglial activation in early Alzheimer trajectory is associated with higher grey matter volume

Grazia Daniela Femminella, Melanie Dani, Melanie Wood, Zhen Fan, Valeria Calsolaro, Rebecca Atkinson, Trudi Edginton, Rainer Hinz, David J. Brooks & Paul Edison
Objective: To investigate the influence of microglial activation in the early stages of Alzheimer’s disease trajectory, we assessed the relationship between microglial activation and grey matter volume and hippocampal volume in MCI patients. Methods: In this study, fifty-five participants (37 early stages MCI and 18 controls) underwent [11C]PBR28 PET, a marker of microglial activation; volumetric MRI to evaluate grey matter and hippocampal volumes as well as clinical and neuropsychometric evaluation. [11C]PBR28 VT (volume of distribution)...

Data from: Sampling diverse characters improves phylogenies: craniodental and postcranial characters of vertebrates often imply different trees

Ross C. P. Mounce, Robert Sansom & Matthew A. Wills
Morphological cladograms of vertebrates are often inferred from greater numbers of characters describing the skull and teeth than from postcranial characters. This is either because the skull is believed to yield characters with a stronger phylogenetic signal (i.e., contain less homoplasy), because morphological variation therein is more readily atomized, or because craniodental material is more widely available (particularly in the palaeontological case). An analysis of 85 vertebrate datasets published between 2000 and 2013 confirms that...

Data from: Uncovering genetic mechanisms of hypertension through multi-omic analysis of the kidney

James Eales
The kidney is an organ of key relevance to blood pressure (BP) regulation, hypertension and antihypertensive treatment. However, genetically mediated renal mechanisms underlying susceptibility to hypertension remain poorly understood. We integrated genotype, gene expression, alternative splicing and DNA methylation profiles of up to 430 human kidneys to characterise the effects of BP index variants from genome-wide association studies (GWAS) on renal transcriptome and epigenome. We uncovered kidney targets for 479 (58.3%) BP-GWAS variants and paired...

Plagioclase and clinopyroxene mineral chemical and Sr isotope data from Unit 10, Rum Layered Suite, NW Scotland

Brian O'Driscoll, Luke Hepworth & Stephen Daly
These plagioclase and clinopyroxene mineral chemical and Sr isotope data come from Unit 10, Rum Layered Suite, NW Scotland. They underpin a publication entitled 'Rapid crystallisation of precious metal-mineralised layers in mafic magmatic systems', to be published in Nature Geoscience in 2020.

Swallowtail butterfly wing and tail measurements

Robert Nudds & Lydia Koutrouditsou
The European swallowtail butterfly (Papilio machaon) is so named, because of the long and narrow prominences extending from the trailing edge of their hindwings and, although not a true tail, they are referred to as such. Despite being a defining feature, an unequivocal function for the tails is yet to be determined, with predator avoidance (diverting an attack from the rest of the body), and enhancement of aerodynamic performance suggested. The swallowtail, however, is sexually...

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