30 Works

Response to the Government’s ‘Data: A New Direction’ Consultation

Jiahong Chen, Edward Dove, Lilian Edwards, Ansgar Koene, Derek McAuley , Anna-Maria Piskopani & Lachlan Urquhart

A high-throughput assay for quantifying phenotypic traits of microalgae

Phoebe Argyle, Jana Hinners, Nathan G. Walworth, Sinead Collins, Naomi M. Levine & Martina A. Doblin
High-throughput methods for phenotyping microalgae are in demand across a variety of research and commercial purposes. Many microalgae can be readily cultivated in multi-well plates for experimental studies which can reduce overall costs, while measuring traits from low volume samples can reduce handling. Here we develop a high-throughput quantitative phenotypic assay (QPA) that can be used to phenotype microalgae grown in multi-well plates. The QPA integrates 10 low-volume, relatively high-throughput trait measurements (growth rate, cell...

Multivariate trait analysis reveals diatom plasticity constrained to a reduced set of biological axes

Phoebe Argyle, Nathan G. Walworth, Jana Hinners, Sinéad Collins, Naomi M. Levine & Martina A. Doblin
Trait-based approaches to phytoplankton ecology have gained traction in recent decades as phenotypic traits are incorporated into ecological and biogeochemical models. Here, we use high-throughput phenotyping to explore both intra- and interspecific constraints on trait combinations that are expressed in the cosmopolitan marine diatom genus Thalassiosira. We demonstrate that within Thalassiosira, phenotypic diversity cannot be predicted from genotypic diversity, and moreover, plasticity can create highly divergent phenotypes that are incongruent with taxonomic grouping. Significantly, multivariate...

Isoprene concentration and flux measurements and associated meteorological parameters from Auchencorth Moss, Scotland, June and July, 2015

B. Langford, J. Cash, M. Vieno, M.R. Heal, J. Drewer, M.R. Jones, S.R. Leeson, I. Simmons, C.F. Braban & E. Nemitz
Isoprene flux and concentration measurements made from Auchencorth Moss during the summer of 2015. Isoprene concentrations were measured using a proton transfer reaction mass spectrometer (PTR-MS) and fluxes were calculated using the eddy covariance technique. The dataset includes the supporting meteorology including air temperature, photosynthetically active radiation, wind speed, wind direction, friction velocity, sensible heat flux.

Data from: A Miopetaurista (Sciuridae, Rodentia) cranium from the middle Miocene of Bavaria (Germany) and brain evolution in flying squirrels

Isaac Casanovas-Vilar, Montserrat Grau-Camats, Ornella C. Bertrand, Jérôme Prieto, Sergi López-Torres & Mary Silcox
Flying squirrels (Sciurinae, Pteromyini) are the most successful group of gliding mammals. However, their fossil record mostly consists of isolated dental remains which provide very limited insights into their paleobiology and evolution. Only recently, the first skeleton of a fossil flying squirrel, belonging to the species Miopetaurista neogrivensis, has been described. It presents all the diagnostic gliding-related postcranial features of its extant relatives and shows that this group has undergone very little morphological change for...

Transcript- and annotation-guided genome assembly of the European starling

Katarina Stuart, Richard Edwards, Yuanyuan Cheng, Wes Warren, Dave Burt, William Sherwin, Natalie Hofmeister, Scott Werner, Gregory Ball, Melissa Bateson, Matthew Brandley, Katherine Buchanan, Phillip Cassey, David Clayton, Tim De Meyer, Simone Meddle & Lee Rollins
The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long-read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second North American genome (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterisation. S. vulgaris vAU combined 10x Genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length...

Susceptibility to a sexually transmitted disease in a wild koala population shows heritable genetic variance but no inbreeding depression

Kasha Strickland, Romane Cristescu, Anthony Schultz, Loeske Kruuk, Deirdre De Villiers & Celine Frere
The koala, one of the most iconic Australian wildlife species, is facing several concomitant threats that are driving population declines. Some threats are well known and have clear methods of prevention (e.g., habitat loss can be reduced with stronger land-clearing control), whereas others are less easily addressed. One of the major current threats to koalas is chlamydial disease, which can have major impacts on individual survival and reproduction rates and can translate into population declines....

Mosquito saliva enhances virus infection through sialokinin-dependent vascular leakage

Daniella Lefteri, Steven Bryden, Marieke Pingen, Sandra Terry, Ailish McCafferty, Emily Beswick, Georgi Georgiev, Marleen Van der Laan, Valeria Mastrullo, Paola Campagnolo, Robert Waterhouse, Margus Varjak, Andres Merits, Rennos Fragkoudis, Stephen Griffin, Kave Shams, Emilie Pondeville & Clive McKimmie
Viruses transmitted by Aedes mosquitoes are an increasingly important global cause of disease. Defining common determinants of host susceptibility to this large group of het- erogenous pathogens is key for informing the rational design of panviral medicines. Infection of the vertebrate host with these viruses is enhanced by mosquito saliva, a complex mixture of salivary-gland-derived factors and microbiota. We show that the enhancement of infection by saliva was dependent on vascular function and was inde-...

Data from: Within-trio tests provide little support for post-copulatory selection on MHC haplotypes in a free-living population

Wei Huang & Josephine Pemberton
Sexual selection has been proposed as a force that could maintain the diversity of major histocompatibility complex (MHC) genes in vertebrates. Potential selective mechanisms can be divided into pre-copulatory and post-copulatory, and in both cases the evidence for occurrence is mixed, especially in natural populations. In this study, we used a large number of parent-offspring trios that were diplotyped for MHC class II genes in a wild population of Soay sheep (Ovis aries) to examine...

Thoroughbred horse inbreeding measures and racing phenotypes

Emmeline Hill, Martin Stoffel, Beatrice McGivney, David MacHugh & Josephine Pemberton
We quantified inbreeding based on runs of homozygosity (ROH) using 297K SNP genotypes from 6,128 horses born in Europe and Australia, of which 13.2% were unraced.

Humans of AI3SD: Dr James Cumby

Michelle Pauli & James Cumby
This interview forms part of our Humans of AI3SD Series.

Universal Dependencies and Semantics for English and Hebrew Child-directed Speech

Ida Szubert, Omri Abend, Nathan Schneider, Samuel Gibbon, Sharon Goldwater & Mark Steedman

DCMS Response To Call Connected Tech Smart Or Sinister Horizon

Derek McAuley, Andy Crabtree, Anna-Maria Piskopani, Jiahong Chen & Lachlan Arquhart

Data from: Stepwise evolution of a butterfly supergene via duplication and inversion

Simon Henry Martin
Supergenes maintain adaptive clusters of alleles in the face of genetic mixing. Although usually attributed to inversions, supergenes can be complex, and reconstructing the precise processes that led to recombination suppression and their timing is challenging. We investigated the origin of the BC supergene, which controls variation in warning colouration in the African Monarch butterfly, Danaus chrysippus. By generating chromosome-scale assemblies for all three alleles, we identified multiple structural differences. Most strikingly, we find that...

Triparental ageing in a laboratory population of an insect with maternal care

Hilary Cope, Edward Ivimey-Cook & Jacob Moorad
Parental age at reproduction influences offspring size and survival by affecting pre- and postnatal conditions in a wide variety of species, including humans. However, most investigations into this manifestation of ageing focus upon maternal age effects; the effects of paternal age and interactions between maternal and paternal age are often neglected. Furthermore, even when maternal age effects are studied, pre- and postnatal effects are often confounded. Using a cross-fostered experimental design, we investigated the joint...

Congeneric predators fill discrete niches created by the relative abundances of their prey species

Eliot Miller, Oisin Mac Aodha, Emma Greig, David Bonter & Wesley Hochachka
To what degree is niche partitioning driven by underlying patterns in resources such as food, rather than by competition itself? Do discrete niches exist? We address these questions in the context of Cooper’s and Sharp-shinned Hawks, two broadly sympatric, North American, bird-eating raptors in the genus Accipiter. We find that the resource base, as quantified by body masses of birds at bird feeders, is approximately lognormal (smallest birds are most abundant), with lesser modes (peaks)...

Work and Family Lives Dataset

Sarah Cunningham-Burley, Lynn Jamieson & Jeni Harden
This project explores the ways in which working parents and their primary school-aged children negotiate their work and family lives over time, drawing on the changing experiences and perceptions of a varied sample of fourteen families over three waves of interviews (2007-2010). Set in a southern area of Scotland, the research investigated the impact of issues raised by working parenthood on the dynamics of everyday family life and practices. It provides insights into how parents...

Predictability of thermal fluctuations influences functional traits of a cosmopolitan marine diatom

Raissa Gill, Sinead Collins, Phoebe Argyle, Michaela Larsson, Robert Fleck & Martina Doblin
Evolutionary theory predicts that organismal plasticity should evolve in environments that fluctuate regularly. However, in environments that fluctuate less predictably, plasticity may be constrained because environmental cues become less reliable for expressing the optimum phenotype. Here we examine how the predictability of +5 °C temperature fluctuations impacts the phenotype of the marine diatom Thalassiosira pseudonana. Thermal regimes were informed by temperatures experienced by microbes in an ocean simulation, and featured regular or irregular temporal sequences...

Global biogeography of warning colouration in the butterfly Danaus chrysippus

Wanzhen Liu, David A. S. Smith, Gayatri Raina, Rowan Stanforth, Ivy Ng’Iru, Piera Ireri, Dino J. Martins, Ian J. Gordon & Simon H. Martin
Warning colouration provides a textbook example of natural selection, but the frequent observation of polymorphism in aposematic species presents an evolutionary puzzle. We investigated biogeography and polymorphism of warning patterns in the widespread butterfly Danaus chrysippus using records from citizen science (n=5467), museums (n=8864), and fieldwork (n=2586). We find that polymorphism in three traits controlled by known mendelian loci is extensive. Broad allele frequency clines, hundreds of km wide, suggest a balance between long-range dispersal...

The symmetry spectrum in a hybridising, tropical group of rhododendrons

Valerie L. Soza, Ricardo Kriebel, Elizabeth Ramage, Benjamin Hall & Alex Twyford
Many diverse plant clades possess bilaterally symmetrical flowers and specialized pollination syndromes suggesting these traits may promote diversification. We examine the evolution of diverse floral morphologies and the association with diversification history in a species-rich tropical radiation of Rhododendron. We used restriction-site associated DNA sequencing on 114 taxa from Rhododendron sect. Schistanthe to reconstruct phylogenetic relationships, infer colonization of Southeast Asia and examine hybridization. We then captured and quantified floral variation using geometric morphometric analyses...

Rapid and specific degradation of endogenous proteins in mouse models using auxin-inducible degrons

Andrew Wood
Auxin-inducible degrons are a chemical genetic tool for targeted protein degradation and are widely used to study protein function in cultured mammalian cells. Here we develop CRISPR-engineered mouse lines that enable rapid and highly specific degradation of tagged endogenous proteins in vivo. Most but not all cell types are competent for degradation. By combining ligand titrations with genetic crosses to generate animals with different allelic combinations, we show that degradation kinetics depend upon the dose...

Data from: Climatic niche lability but growth form conservatism in the African woody flora

Anaïs-Pasiphaé Gorel, Olivier J. Hardy, Gilles Dauby, Kyle G. Dexter, Ricardo A. Segovia, Kathy Steppe & Adeline Fayolle
Climatic niche evolution during the diversification of tropical plants has received little attention in Africa. To address this, we characterized the climatic niche of >4000 tropical African woody species, distinguishing two broad bioclimatic groups (forest vs. savanna) and six subgroups. We quantified niche conservatism versus lability at the genus level and for higher clades, using a molecular phylogeny of >800 genera. Although niche stasis at speciation is prevalent, numerous clades individually cover vast climatic spaces...

Circum-Arctic distribution of chemical anti-herbivore compounds arctic shrubs

Elin Lindén, Mariska Te Beest, Ilka Abreu, Thomas Moritz, Maja Sundqvist, Isabel C Barrio, Julia Boike, John Bryant, Kari Anne Bråthen, Agata Buchwal, Guillermo Bueno, Alain Cuerrier, Dagmar Egelkraut, Bruce Forbes, Martin Hallinger, Monique Heijmans, Luise Hermanutz, David S Hik, Annika Hofgaard, Milena Holmgren, Diane C Huebner, Toke Hoye, Ingibjörg Jónsdóttir, Elina Kaarlejärvi, Emilie Kissler … & Johan Olofsson
Spatial variation in plant chemical defence towards herbivores can help us understand variation in herbivore top-down control of shrubs in the Arctic and possibly also shrub responses to global warming. Less defended, non-resinous shrubs could be more influenced by herbivores than more defended, resinous shrubs. However, sparse field measurements limit our current understanding of how much of the circum-Arctic variation in defence compounds is explained by taxa or defence functional groups (resinous/non-resinous). We measured circum-Arctic...

Morphometric analysis of lungfish endocasts elucidates early dipnoan palaeoneurological evolution

Alice Clement, Tom Challands, Richard Cloutier, Laurent Houle, Per Ahlberg, Shaun Collin & John Long
Lungfish (Dipnoi) are lobe-finned fish (Sarcopterygii) that have persisted for over 400 million years from the Devonian Period to present day. They are the extant sister group to tetrapods and thus have the ability to provide unique insight into the condition of the earliest tetrapods as well as their own evolutionary history. The evolution of their dermal skull and dentition is relatively well understood, but this is not the case for the central nervous system....

Diversification of Crassula: Phylogenetic analysis and life-form traits

Marc Fradera-Soler, Meng Lu & Olwen M. Grace
These datasets are associated with the published paper - "Evidence linking life form to a major shift in diversification rate in Crassula" (DOI:10.1002/ajb2.1797) Crassula L. (Crassulaceae) is a characteristic element of the southern African flora, occurring in a wide range of habitats, and it exhibits a remarkable diversity of life forms. However, whether any particular life-form trait has shaped species diversification in Crassula has remained unexplored. Our study aimed to investigate diversification patterns within Crassula...

Registration Year

  • 2022

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  • University of Edinburgh
  • Ghent University
  • UK Centre for Ecology & Hydrology
  • University of Queensland
  • University of Glasgow
  • University of Aberdeen
  • University of Lausanne
  • University of Nottingham
  • Newcastle University
  • Swedish University of Agricultural Sciences