108 Works

Data from: Bat species comparisons based on external morphology: a test of traditional versus geometric morphometric approaches

Daniela A. Schmieder, Hugo A. Benítez, Ivailo M. Borissov & Carmelo Fruciano
External morphology is commonly used to identify bats as well as to investigate flight and foraging behavior, typically relying on simple length and area measures or ratios. However, geometric morphometrics is increasingly used in the biological sciences to analyse variation in shape and discriminate among species and populations. Here we compare the ability of traditional versus geometric morphometric methods in discriminating between closely related bat species – in this case European horseshoe bats (Rhinolophidae, Chiroptera)...

Data from: Two new species of Ichthyosaurus from the lowermost Jurassic (Hettangian) of Somerset, England

Dean R. Lomax & Judy A. Massare
All specimens of Ichthyosaurus from the Lower Jurassic of Somerset were previously identified as I. communis, an abundant and extremely variable species. Here, two new species of Ichthyosaurus are recognized from multiple specimens. The species are assigned to Ichthyosaurus on the basis of the humerus, pectoral girdle and forefin morphologies. I. larkini sp. nov. is distinguished by a broad jugal with a blunt anterior end that extends as far forward as the middle of the...

Data from: Illness beliefs in end stage renal disease and associations with self-care modality choice

Anuradha Jayanti, Philip Foden, Alison Wearden & Sandip Mitra
Background: Interest in self-care haemodialysis (HD) has increased because it improves patients’clinical and quality-of-life outcomes. Patients who undertake self-management for haemodialysis may hold illness beliefs differently to those choosing institutional care at the time of making the modality choice or moulded by their illness and dialysis treatment experience. Illness perceptions amongst predialysis patients and in those undertaking fully-assisted and self-care haemodialysis are being investigated in a combined cross-sectional and longitudinal study. Study Design: The study...

Data from: Testing and quantifying phylogenetic signals and homoplasy in morphometric data

Christian Peter Klingenberg, Nelly A. Gidaszewski, Christian Peter Klingenberg & Nelly A. Gidaszewski
The relationship between morphometrics and phylogenetic analysis has long been controversial. Here we propose an approach that is based on mapping morphometric traits onto phylogenies derived from other data and thus avoids the pitfalls encountered by previous studies. This method treats shape as a single, multidimensional character. We propose a test for the presence of a phylogenetic signal in morphometric data, which simulates the null hypothesis of the complete absence of phylogenetic structure by permutation...

Data from: The interaction of Saccharomyces paradoxus with its natural competitors on oak bark

Vienna Kowallik, Eric Miller & Duncan Greig
The natural history of the model yeast Saccharomyces cerevisiae is poorly understood and confounded by domestication. In nature, S. cerevisiae and its undomesticated relative S. paradoxus are usually found on the bark of oak trees, a habitat very different from wine or other human fermentations. It is unclear whether the oak trees are really the primary habitat for wild yeast, or whether this apparent association is due to biased sampling. We use culturing and high-throughput...

Data from: The value of trophic interactions for ecosystem function: dung beetle communities influence seed burial and seedling recruitment in tropical forests

Hannah M. Griffiths, Richard D. Bardgett, Julio Louzada & Jos Barlow
Anthropogenic activities are causing species extinctions, raising concerns about the consequences of changing biological communities for ecosystem functioning. To address this, we investigated how dung beetle communities influence seed burial and seedling recruitment in the Brazilian Amazon. First, we conducted a burial and retrieval experiment using seed mimics. We found that dung beetle biomass had a stronger positive effect on the burial of large than small beads, suggesting that anthropogenic reductions in large-bodied beetles will...

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: 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: Colonization of the Mediterranean Basin by the vector biting midge species Culicoides imicola: an old story

Stephanie Jacquet, Claire Garros, Eric Lombaert, Catherine Walton, Johana Restrepo, Xavier Allene, Thierry Baldet, Catherine Cetre-Sossah, Alexandra Chaskopoulou, Jean-Claude Delecolle, Amelie Desvars, Mouloud Djerbal, Moussa Fall, Laetitia Gardes, Michel De Garine-Wichatitsky, Maria Goffredo, Yuval Gottlieb, Assane Gueye Fall, Muo Kasina, Karien Labuschagne, Youssef Lhor, Javier Lucientes, Thibaud Martin, Bruno Mathieu, Miguel Miranda … & Y. Gottlieb
Understanding the demographic history and genetic make-up of colonizing species is critical for inferring population sources and colonization routes. This is of main interest for designing accurate control measures in areas newly colonized by vector species of economically important pathogens. The biting midge Culicoides imicola is a major vector of orbiviruses to livestock. Historically, the distribution of this species was limited to the Afrotropical region. Entomological surveys first revealed the presence of C. imicola in...

Data from: Can long-range PCR be used to amplify genetically divergent mitochondrial genomes for comparative phylogenetics? A case study within spiders (Arthropoda: Araneae).

Andrew G. Briscoe, Sarah Goodacre, Susan E. Masta, Martin I. Taylor, Miquel A. Arnedo, David Penney, John Kenny, Simon Creer & Sara Goodacre
The development of second generation sequencing technology has resulted in the rapid production of large volumes of sequence data for relatively little cost, thereby substantially increasing the quantity of data available for phylogenetic studies. Despite these technological advances, assembling longer sequences, such as that of entire mitochondrial genomes, has not been straightforward. Existing studies have been limited to using only incomplete or nominally intra-specific datasets resulting in a bottleneck between mitogenome amplification and downstream high-throughput...

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: Change and stability in a steep morph-frequency cline in the snail Cepaea nemoralis (L.) over 43 years.

Robert A. D. Cameron, Laurence M. Cook & Jeremy J. D. Greenwood
Populations of the polymorphic land snail Cepaea nemoralis (L.) from Deepdale, Derbyshire, UK, sampled in 1965-67, showed a pattern of area effects, with steep clines among groups of populations differing in shell colour and banding morph frequencies. In 2010 most of these populations were resampled. In particular a continuous transect made in 1967 of 42 18.34m x 18.34m quadrats across a steep cline in several morph frequencies was completely resampled. In the dale as a...

Data from: Interspecific variation in the structural properties of flight feathers in birds indicates adaptation to flight requirements and habitat

Peter L. Pap, Gergely Osvath, Krisztina Sandor, Orsolya Vincze, Lorinc Barbos, Attila Marton, Robert L. Nudds & Csongor I. Vagasi
1. The functional significance of intra- and interspecific structural variations in the flight feathers of birds is poorly understood. Here, a phylogenetic comparative analysis of four structural features (rachis width, barb and barbule density and porosity) of proximal and distal primary feathers of 137 European bird species was conducted. 2. Flight type (flapping and soaring, flapping and gliding, continuous flapping or passerine type), habitat (terrestrial, riparian or aquatic), wing characteristics (wing area, S and aspect...

Data from: Locomotory abilities and habitat of the Cretaceous bird Gansus yumenensis inferred from limb length proportions

Robert L. Nudds, Jessie Atterholt, Xia Wang, H. L. You, Gareth J. Dyke, J. Atterholt, R. L. Nudds, X. Wang & H.-L. You
The relative length proportions of the three bony elements of the pelvic (femur, tibiotarsus and tarsometatarsus) and pectoral (humerus, ulna and manus) limbs of the early Cretaceous bird Gansus yumenensis, a well-represented basal ornithuromorph from China are investigated and compared to those of extant taxa. Ternary plots show that the pectoral limb length proportions of Gansus are most similar to Apodiformes (swifts and hummingbirds), which plot away from all other extant birds. In contrast, the...

Data from: Phenotypic plasticity in response to environmental heterogeneity contributes to fluctuating asymmetry in plants: first empirical evidence

Branka Tucić, Sanja Budečević, Sanja Manitašević Jovanović, Ana Vuleta, Christian P. Klingenberg & Christian Peter Klingenberg
Fluctuating asymmetry (FA) is widely used to quantify developmental instability (DI) in ecological and evolutionary studies. It has long been recognized that FA may not exclusively originate from DI for sessile organisms such as plants, because phenotypic plasticity in response to heterogeneities in the environment might also produce FA. This study provides the first empirical evidence for this hypothesis. We reasoned that solar irradiation, which is greater on the southern side than on the northern...

Data from: A new family of Cambrian rhynchonelliformean brachiopods (Order Naukatida) with an aberrant coral-like morphology

Michael Streng, Aodhán D. Butler, John S. Peel, Russell J. Garwood & Jean-Bernard Caron
Tomteluva perturbata gen. et sp. nov. and Nasakia thulensis gen. et sp. nov., two new rhynchonelliformean brachiopod taxa, are described from carbonate beds from the lower middle Cambrian (Series 3, Stage 5) basinal Stephen Formation, Canada, and the upper lower Cambrian (Series 2, Stage 4) Henson Gletscher Formation, North Greenland, respectively. The two taxa are characterized by an unusual coral-like morphology typified by a high conical ventral valve with an anteriorly curved umbo and a...

Data from: Endoskeletal structure in Cheirolepis (Osteichthyes, Actinopterygii), an early ray-finned fish

Sam Giles, Michael I. Coates, Russell J. Garwood, Martin D. Brazeau, Robert Atwood, Zerina Johanson & Matt Friedman
As the sister lineage of all other actinopterygians, the Middle to Late Devonian (Eifelian–Frasnian) Cheirolepis occupies a pivotal position in vertebrate phylogeny. Although the dermal skeleton of this taxon has been exhaustively described, very little of its endoskeleton is known, leaving questions of neurocranial and fin evolution in early ray-finned fishes unresolved. The model for early actinopterygian anatomy has instead been based largely on the Late Devonian (Frasnian) Mimipiscis, preserved in stunning detail from the...

Data from: Sexual imprinting: What strategies should we expect to see in nature?

Hayes Griffin, Robert Tucker Gilman, Dalton W. Chaffee & R. Tucker Gilman
Sexual imprinting occurs when juveniles learn mate preferences by observing the phenotypes of other members of their populations, and it is ubiquitous in nature. Imprinting strategies, that is which individuals and phenotypes are observed and how strong preferences become, vary among species. Imprinting can affect trait evolution and the probability of speciation, and different imprinting strategies are expected to have different effects. However, little is known about how and why different imprinting strategies evolve, or...

Data from: A cross-lingual similarity measure for detecting biomedical term translations

Danushka Bollegala, Georgios Kontonatsios & Sophia Ananiadou
Bilingual dictionaries for technical terms such as biomedical terms are an important resource for machine translation systems as well as for humans who would like to understand a concept described in a foreign language. Often a biomedical term is first proposed in English and later it is manually translated to other languages. Despite the fact that there are large monolingual lexicons of biomedical terms, only a fraction of those term lexicons are translated to other...

Data from: A new titanosaurian braincase from the Cretaceous “Lo Hueco” locality in Spain sheds light on neuroanatomical evolution within Titanosauria

Fabien Knoll, Lawrence M. Witmer, Ryan C. Ridgely, Francisco Ortega & Jose Luis Sanz
Despite continuous improvements, our knowledge of the neurocranial anatomy of sauropod dinosaurs as a whole is still poor, which is especially true for titanosaurians even though their postcranial remains are common in many Upper Cretaceous sites worldwide. Here we describe a braincase from the uppermost Cretaceous locality of ‘‘Lo Hueco” in Spain that is one of the most complete titanosaurian braincases found so far in Europe. Although the titanosaurian Ampelosaurus sp. is known from the...

Data from: Almost a spider: a 305-million-year-old fossil arachnid and spider origins

Russell J. Garwood, Jason A. Dunlop, Paul A. Selden, Alan R. T. Spencer, Robert C. Atwood, Nghia T. Vo & Michael Drakopoulos
Spiders are an important animal group, with a long history. Details of their origins remain limited, with little knowledge of their stem group, and no insights into the sequence of character acquisition during spider evolution. We describe a new fossil arachnid, Idmonarachne brasieri gen. et sp. nov. from the late Carboniferous (Stephanian, ca. 305–299 Ma) of Montceau-les-Mines, France. It is three-dimensionally preserved within a siderite concretion, allowing both laboratory- and synchrotron-based phase-contrast computed tomography (CT)...

Data from: Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations

Alan McNally, Yaara Oren, Darren Kelly, Ben Pascoe, Steven Dunn, Tristan Seecharan, Minna Vehkala, Niko Välimäki, Michael B. Prentice, Amgad Ashour, Oren Avram, Tal Pupko, Ulrich Dobrindt, Ivan Literak, Sebastian Guenther, Katharina Schauffler, Lothar H. Wieler, Zong Zhiyong, Samuel K. Sheppard, James O. McInerney, Jukka Corander & Tristan Sreecharan
The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could...

Data from: The walking dead: blender as a tool for palaeontologists with a case study on extinct arachnids

Russell Garwood & Jason Dunlop
This paper serves two roles. First, it acts as an introduction to Blender, an open-source computer graphics program, which can be of utility to paleontologists. To lessen the software's otherwise steep learning curve, a step-by-step guide to create an idealized reconstruction of a fossil in the form of a three-dimensional model in Blender, or to use the software to render results from ‘virtual paleontology' techniques, is provided as an online supplemental data file. Second, here...

Data from: A population genomics insight into the Mediterranean origins of wine yeast domestication

Pedro Almeida, Raquel Barbosa, Polona Zalar, Yumi Imanishi, Kiminori Shimizu, Benedetta Turchetti, Jean-Luc Legras, Marta Serra, Sylvie Dequin, Arnaud Couloux, Julie Guy, Douda Bensasson, Paula Gonçalves & José Paulo Sampaio
The domestication of the wine yeast Saccharomyces cerevisiae is thought to be contemporary with the development and expansion of viticulture along the Mediterranean basin. Until now, the unavailability of wild lineages prevented the identification of the closest wild relatives of wine yeasts. Here, we enlarge the collection of natural lineages and employ whole-genome data of oak-associated wild isolates to study a balanced number of anthropic and natural S. cerevisiae strains. We identified industrial variants and...

Data from: An advanced shape-fitting algorithm applied to quadrupedal mammals: improving volumetric mass estimates

Charlotte A. Brassey & James D. Gardiner
Body mass is a fundamental physical property of an individual and has enormous bearing upon ecology and physiology. Generating reliable estimates for body mass is therefore a necessary step in many palaeontological studies. Whilst early reconstructions of mass in extinct species relied upon isolated skeletal elements, volumetric techniques are increasingly applied to fossils when skeletal completeness allows. We apply a new ‘alpha shapes’ (α-shapes) algorithm to volumetric mass estimation in quadrupedal mammals. α-shapes are defined...

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