32 Works

Plant biodiversity data and environmental and spatial data from Jebel Ichkeul, a limestone mountain in northern Tunisia (1983)

D.A. Kirk, K. Hébert & F. B. Goldsmith
Records for herbaceous and woody plants at 78 nested quadrats on a limestone mountain (Jebel Ichkeul) in Le Parc National de L’Ichkeul are presented. Data for plants represent percent cover (Braun-Blanquet scale), to identify environmental gradients and investigate phytosociology of plant communities. Environmental variables are also presented: altitude, slope, aspect, rock out cropping, index of grazing intensity (78 sites) and olive tree densities by size class (69 sites). Soil pH was collected for 50 sites....

Data from: Coupling of palaeontological and neontological reef coral data improves forecasts of biodiversity responses under global climatic change

Lewis A. Jones, Philip D. Mannion, Alexander Farnsworth, Paul J. Valdes, Sarah-Jane Kelland & Peter A. Allison
Reef corals are currently undergoing climatically-driven poleward range expansions, with some evidence for equatorial range retractions. Predicting their response to future climate scenarios is critical to their conservation, but ecological models are based only on short-term observations. The fossil record provides the only empirical evidence for the long-term response of organisms under perturbed climate states. The palaeontological record from the Last Interglacial (LIG; 125,000 years ago), a time of global warming, suggests that reef corals...

Data from: Cross-species hybridization and the origin of North African date palms

Jonathan M. Flowers, Khaled M. Hazzouri, Muriel Gros-Balthazard, Ziyi Mo, Konstantina Koutroumpa, Andreas Perrakis, Sylvie Ferrand, Hussam S. M. Khierallah, Dorian Q. Fuller, Frederique Aberlenc, Christini Fournaraki & Michael D. Purugganan
Date palm (Phoenix dactylifera L.) is a major fruit crop of arid regions that were domesticated 7,000 y ago in the Near or Middle East. This species is cultivated widely in the Middle East and North Africa, and previous population genetic studies have shown genetic differentiation between these regions. We investigated the evolutionary history of P. dactylifera and its wild relatives by resequencing the genomes of date palm varieties and five of its closest relatives....

Data from: Current ecology, not ancestral dispersal patterns, influences menopause symptom severity

Yuping Yang, Megan Arnot & Ruth Mace
All human females who reach midlife experience menopause, however, it is currently unclear why women experience this period of infertility, and why it is accompanied by many unpleasant symptoms. Using primary data from four ethnic groups in China, we test an existing theory that age of menopause and its symptoms are the result of intragenomic conflict between maternally and paternally inherited genes, with the outcome of such conflict predicted to be contingent on the ancestral...

Data from: Near-infrared dual bioluminescence imaging in mouse models of cancer using infraluciferin

James Anderson & Martin Pule
Bioluminescence imaging (BLI) is ubiquitous in scientific research for the sensitive tracking of biological processes in small animal models. However, due to the attenuation of visible light by tissue, and the limited set of near-infrared bioluminescent enzymes, BLI is largely restricted to monitoring single processes in vivo. Here we show, that by combining stabilised colour mutants of firefly luciferase (FLuc) with the luciferin (LH2) analogue infraluciferin (iLH2), near-infrared dual BLI can be achievedin vivo. The...

Annual estimates of occupancy for bryophytes, lichens and invertebrates in the UK (1970-2015)

C.L. Outhwaite, G.D. Powney, T.A. August, R.E. Chandler, S. Rorke, O. Pescott, M. Harvey, H.E. Roy, R. Fox, K. Walker, D.B. Roy, K. Alexander, S. Ball, T. Bantock, T. Barber, B.C. Beckmann, T. Cook, J. Flanagan, A. Fowles, P. Hammond, P. Harvey, D. Hepper, D. Hubble, J. Kramer, P. Lee … & N.J.B. Isaac
This dataset provides annual estimates of species occupancy and species trend estimates in the form of growth rates for 5,293 UK invertebrate, bryophyte and lichen species for the period 1970 to 2015. Estimates are provided at the country level for England, Scotland, Wales and Northern Ireland as well as for the UK and Great Britain (GB) where possible. These data were generated using observations of species collated by UK recording schemes and societies as the...

Data from: Targeted next-generation sequencing panels in the diagnosis of Charcot Marie Tooth disease

Andrea Cortese, Janel Wilcox, James M. Polke, Roy Poh, Mariola Skorupinska, Alexader Rossor, Matilde Laura, Pedro J. Tomaselli, Henry Houlden, Michael E. Shy & Mary M. Reilly
Objective: To investigate the effectiveness of targeted NGS panels in achieving a molecular diagnosis in CMT and related disorders in a clinical setting Methods: We prospectively enrolled 220 patients from two tertiary referral centres, one in London, UK (n=120) and one in Iowa, US (n=100) in whom a targeted CMT NGS panel had been requested as a diagnostic test. PMP22 duplication/deletion was previously excluded in demyelinating cases. We reviewed the genetic and clinical data upon...

Data from: Within- and between-group dynamics in an obligate cooperative breeder

Rosie Woodroffe, Helen O'Neill & Daniella Rabaiotti
1. Cooperative behaviour can have profound effects on demography. In many cooperative species, components of fitness (e.g. survival, reproductive success) are diminished in smaller social groups. These effects (termed group-level component Allee effects) may lead smaller groups to grow relatively slowly or fail to persist (termed group-level demographic Allee effects). 2. If these group-level effects were to propagate to the population level, small populations would grow slowly or decline to extinction (termed population-level demographic Allee...

Data from: Alien species richness is currently unbounded in all but the most urbanized bird communities

Toby P. Tsang, Ellie E. Dyer & Tim C. Bonebrake
Urban areas suffer high pressure of introductions of alien species compared to other habitats due to intensive human activities. As trading globally continues to rise, more species will likely be introduced into urban areas. To determine whether this increase in introduction pressure will lead to increased alien species richness in urban areas, or whether other processes would act to impose an upper limit on species richness, we examined how the shape of the relationship between...

Data from: Reprogramming the antigen specificity of B cells using genome-editing technologies

James E. Voss, Alicia Gonzalez-Martin, Raiees Andrabi, Roberta P. Fuller, Ben Murrell, Laura E. McCoy, Katelyn Porter, Deli Huang, Wenjuan Li, Devin Sok, Khoa Le, Bryan Briney, Morgan Chateau, Geoffrey Rogers, Lars Hangartner, Ann J. Feeney, David Nemazee, Paula Cannon & Dennis R. Burton
We have developed a method to introduce novel paratopes into the human antibody repertoire by modifying the immunoglobulin (Ig) genes of mature B cells directly using genome editing technologies. We used CRISPR-Cas9 in a homology directed repair strategy, to replace the heavy chain (HC) variable region in B cell lines with that from an HIV broadly neutralizing antibody, PG9. Our strategy is designed to function in cells that have undergone VDJ recombination using any combination...

Asynchronous Saturation of the Carbon Sink in African and Amazonian tropical forests

Wannes Hubau, Simon Lewis, Oliver Phillips, Kofi Kofi Affum-Baffoe, Hans Hans Beeckman, Aida Cuni-Sanchez, Corneille Ewango, Sophie Fauset, Douglas Sheil, Bonaventure Sonké, Martin Sullivan, Terry Sunderland, Sean Thomas, Katharine Abernethy, Stephen Adu-Bredu, Christian Amani, Timothy Baker, Lindsay Banin, Fidèle Baya, Serge Begne, Amy Bennett, Fabrice Benedet, Robert Bitariho & Yannick Bocko
Data and R-code from Hubau W et al. 2020. 'Asynchronous Saturation of the Carbon Sink in African and Amazonian tropical forests'. Nature 579, 80-87. 2020. DOI: 10.1038/s41586-020-2035-0. ABSTRACT: Structurally intact tropical forests sequestered ~50% of global terrestrial carbon uptake over the 1990s and early 2000s, offsetting ~15% of anthropogenic CO2 emissions1-3. Climate-driven vegetation models typically predict that this tropical forest ‘carbon sink’ will continue for decades4,5. However, recent inventories of intact Amazonian forests show declining...

Data from: Defining host–pathogen interactions employing an artificial intelligence workflow

Daniel Fisch, Artur Yakimovich, Barbara Clough, Joseph Wright, Monique Bunyan, Michael Howell, Jason Mercer & Eva Frickel
For image-based infection biology, accurate unbiased quantification of host–pathogen interactions is essential, yet often performed manually or using limited enumeration employing simple image analysis algorithms based on image segmentation. Host protein recruitment to pathogens is often refractory to accurate automated assessment due to its heterogeneous nature. An intuitive intelligent image analysis program to assess host protein recruitment within general cellular pathogen defense is lacking. We present HRMAn (Host Response to Microbe Analysis), an open-source image...

Data from: Terrestrial mammalian wildlife responses to Unmanned Aerial Systems approaches

Emily Bennitt, Hattie L.A. Bartlam-Brooks, Tatjana Y. Hubel & Alan M. Wilson
Unmanned Aerial Systems (UAS) are increasingly being used recreationally, commercially and for wildlife research, but very few studies have quantified terrestrial mammalian reactions to UAS approaches. We used two Vertical Take-off and Landing (VTOL) UAS to approach seven herbivore species in the Moremi Game Reserve, Botswana, after securing the relevant permissions. We recorded responses to 103 vertical and 120 horizontal approaches, the latter from three altitudes above ground level (AGL). We ran mixed logistic regressions...

Data from: The impact of bilateral ongoing activity on evoked responses in mouse cortex

Daisuke Shimaoka, Nicholas A Steinmetz, Kenneth D Harris & Matteo Carandini
In the absence of external stimuli or overt behavior, the activity of the left and right cortical hemispheres shows fluctuations that are largely bilateral. Here we show that these fluctuations are largely responsible for the variability observed in cortical responses to sensory stimuli. Using widefield imaging of voltage and calcium signals, we measured activity in the cortex of mice performing a visual detection task. Bilateral fluctuations invested all areas, particularly those closest to the midline....

Data from: Limits to environmental masking of genetic quality in sexual signals

James Malcolm Howie, Harry Alexander Cordeaux Dawson, Andrew Pomiankowski & Kevin Fowler
There is considerable debate over the value of male sexual ornaments as signals of genetic quality. Studies alternately report that environmental variation enhances or diminishes the genetic signal, or leads to crossover where genotypes perform well in one environment but poorly in another. A unified understanding is lacking. We conduct a novel experimental test examining the dual effects of distinct categories of genetic (inbred versus crossed parental lines) and environmental quality (low, through high to...

Data from: The Chord-Normalized Expected Species Shared (CNESS)-distance represents a superior measure of species turnover patterns

Yi Zou & Jan Axmacher
1. Measures of β-diversity characterizing the difference in species composition between samples are commonly used in ecological studies. Nonetheless, commonly used dissimilarity measures require high sample completeness, or at least similar sample sizes between samples. In contrast, the Chord-Normalized Expected Species Shared (CNESS) dissimilarity measure calculates the probability of collecting the same set of species in random samples of a standardized size, and hence is not sensitive to completeness or size of compared samples. To...

Data from: Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis

Oliver Ratmann, M. Kate Grabowski, Matthew Hall, Tanya Golubchik, Chris Wymant, Lucie Abeler-Dörner, David Bonsall, Anne Hoppe, Andrew Leigh Brown, Tulio De Oliveira, Astrid Gall, Paul Kellam, Deenan Pillay, Joseph Kagaayi, Godfrey Kigozi, Thomas C. Quinn, Maria J. Wawer, Oliver Laeyendecker, David Serwadda, Ronald H. Gray, Christophe Fraser, &
To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these ‘source’ populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from...

Combined Protocol for Acute Malnutrition Study (ComPAS) dataset

Jeanette Bailey, Charles Opondo, Natasha Lelijveld, Bethany Marron, Pamela Onyoo, Eunice Musyoki, Susan Adongo, Andre Briend, Mark Manary & Marko Kerac

Data from: Bayesian estimation of species divergence times using correlated quantitative characters

Sandra Álvarez-Carretero, Anjali Goswami, Ziheng Yang & Mario Dos Reis
Discrete morphological data have been widely used to study species evolution, but the use of quantitative (or continuous) morphological characters is less common. Here, we implement a Bayesian method to estimate species divergence times using quantitative characters. Quantitative character evolution is modelled using Brownian diffusion with character correlation and character variation within populations. Through simulations, we demonstrate that ignoring the population variation (or population “noise”) and the correlation among characters leads to biased estimates of...

Data from: Rapid morphological evolution in placental mammals post-dates the origin of the crown group

Thomas Halliday, Mario Dos Reis, Asif Tamuri, Henry Ferguson-Gow, Ziheng Yang & Anjali Goswami
Resolving the timing and pattern of early placental mammal evolution has been confounded by conflict among divergence date estimates from interpretation of the fossil record and from molecular-clock dating studies. Despite both fossil occurrences and molecular sequences favouring a Cretaceous origin for Placentalia, no unambiguous Cretaceous placental mammal has been discovered. Investigating the differing patterns of evolution in morphological and molecular data reveals a possible explanation for this conflict. Here, we quantified the relationship between...

Data from: Epidemiology of placenta previa accreta: a systematic review and meta-analysis

Eric Jauniaux, Lene Grønbeck, Catey Bunce, Jens Langhoff-Roos & Sally Collins
Objective To estimate the prevalence and incidence of placenta previa complicated by placenta accreta spectrum (PAS) and to examine the different criteria being used for the diagnosis. Design Systematic review and meta-analysis. Methods PubMed, Google Scholar, clinicalTrials.gov and MEDLINE were searched between August 1982 and September 2018 for studies reporting on placenta previa and placenta previa with PAS diagnosed in a defined obstetric population. Two independent reviewers performed the data extraction using a predefined protocol...

Data from: Onset of clinical and MRI efficacy of ocrelizumab in relapsing multiple sclerosis

Frederik Barkhof, Ludwig Kappos, Jerry S. Wolinsky, David K. B. Li, Amit Bar-Or, Hans-Peter Hartung, Shibeshih Belachew, Jian Han, Laura Julian, Annette Sauter, Julie Napieralski, Harold Koendgen & Stephen L. Hauser
Objective: To assess the onset of ocrelizumab efficacy on brain magnetic resonance imaging (MRI) measures of disease activity in the Phase II study in relapsing-remitting multiple sclerosis (RRMS), and relapse rate in the pooled Phase III studies in relapsing multiple sclerosis (RMS). Methods: Brain MRI activity was determined in the Phase II trial at monthly intervals in patients with RRMS receiving placebo, ocrelizumab (600 mg), or intramuscular interferon (IFN) β-1a (30 μg). Annualized relapse rate...

Data from: Phenotypic sexual dimorphism is associated with genomic signatures of resolved sexual conflict

Alison E Wright, Thea F Rogers, Matteo Fumagalli, Christopher R Cooney & Judith E Mank
Intra-locus sexual conflict, where an allele benefits one sex at the expense of the other, has an important role in shaping genetic diversity of populations through balancing selection. However, the potential for mating systems to exert balancing selection through sexual conflict on the genome remains unclear. Furthermore, the nature and potential for resolution of sexual conflict across the genome has been hotly debated. To address this, we analysed de novo transcriptomes from six avian species,...

Impact of mitonuclear interactions on life-history responses to diet

Florencia Camus, Michael O'Leary, Max Reuter & Nick Lane
Mitochondria are central to both energy metabolism and biosynthesis. Mitochondrial function could therefore influence resource allocation. Critically, mitochondrial function depends on interactions between proteins encoded by the mitochondrial and nuclear genomes. Severe incompatibilities between these genomes can have pervasive effects on both fitness and longevity. How milder deficits in mitochondrial function affect life-history trade-offs is less well understood. Here we analyse how mitonuclear interactions affect the trade-off between fecundity and longevity in Drosophila melanogaster. We...

Data from: Human-dominated land uses favour species affiliated with more extreme climates, especially in the tropics

Jessica Williams, Amanda Bates & Tim Newbold
The data are derived from the PREDICTS Project database (https://data.nhm.ac.uk/dataset/902f084d-ce3f-429f-a6a5-23162c73fdf7) used within the paper titled "Human-dominated land uses favour species affiliated with more extreme climates, especially in the tropics" (DOI: 10.1111/ecog.04806). If using this data, please make sure that the PREDICTS Project is also cited. For Williams_et_al_Ecography_data_CWM -> These data include, for the species assemblages in the analyses, the raw community weighted means (CWMs) for the extreme (maximum or minimum) and range-wide variation (standard deviations)...

Registration Year

  • 2019

Resource Types

  • Dataset


  • University College London
  • Imperial College London
  • University of Zurich
  • Royal Museum for Central Africa
  • University of Baghdad
  • Plymouth University
  • London School of Hygiene & Tropical Medicine
  • Ghent University
  • New York University Abu Dhabi
  • Université de Sherbrooke