22 Works

Data from: Sexual antagonism for resistance and tolerance to infection in Drosophila melanogaster

Crystal M. Vincent & Nathaniel P. Sharp
A critical task in evolutionary genetics is to explain the persistence of heritable variation in fitness-related traits such as immunity. Ecological factors can maintain genetic variation in immunity, but less is known about the role of other factors, such as antagonistic pleiotropy, on immunity. Sexually dimorphic immunity—with females often being more immune-competent—may maintain variation in immunity in dioecious populations. Most eco-immunological studies assess host resistance to parasites rather than the host's ability to maintain fitness...

Data from: Early back-to-Africa migration into the Horn of Africa

Jason A. Hodgson, Connie J. Mulligan, Ali Al-Meeri & Ryan L. Raaum
Genetic studies have identified substantial non-African admixture in the Horn of Africa (HOA). In the most recent genomic studies, this non-African ancestry has been attributed to admixture with Middle Eastern populations during the last few thousand years. However, mitochondrial and Y chromosome data are suggestive of earlier episodes of admixture. To investigate this further, we generated new genome-wide SNP data for a Yemeni population sample and merged these new data with published genome-wide genetic data...

Data from: Reconciling hierarchical taxonomy with molecular phylogenies

Ben G. Holt & Knud Andreas Jønsson
Taxonomy has a history dating back to Aristotle (350BC) and has facilitated a wide range of developments in the biological sciences. Linnaeus’ Systema Naturae assumed that organisms were static creations of God and formulated the hierarchical framework of classification that we currently use. Today we know that organisms continuously evolve and it is generally accepted that these hierarchies are arbitrary constructs (Coyne and Orr 2004). The arbitrary nature of these higher taxonomic ranks does not...

Data from: New quantitative approaches reveal the spatial preference of nuclear compartments in mammalian fibroblasts

David J. Weston, Richard A. Russell, Elizabeth Batty, Kirsten Jensen, David A. Stephens, Niall M. Adams & Paul S. Freemont
The nuclei of higher eukaryotic cells display compartmentalization and certain nuclear compartments have been shown to follow a degree of spatial organization. To date, the study of nuclear organization has often involved simple quantitative procedures that struggle with both the irregularity of the nuclear boundary and the problem of handling replicate images. Such studies typically focus on inter-object distance, rather than spatial location within the nucleus. The concern of this paper is the spatial preference...

Data from: Untangling interactions: do temperature and habitat fragmentation gradients simultaneously impact biotic relationships?

Poppy Lakeman-Fraser & Rob M. Ewers
Gaining insight into the impact of anthropogenic change on ecosystems requires investigation into interdependencies between multiple drivers of ecological change and multiple biotic responses. Global environmental change drivers can act simultaneously to impact the abundance and diversity of biota, but few studies have also measured the impact across trophic levels. We firstly investigated whether climate (using temperature differences across a latitudinal gradient as a surrogate) interacts with habitat fragmentation (measured according to fragment area and...

Data from: Distinguishing between reservoir exposure and human-to-human transmission for emerging pathogens using case onset data

Adam Kucharski, Harriet L. Mills, Amy Pinsent, Christophe Fraser, Maria Van Kerkhove, Christl A. Donnelly, Steven Riley & Harriet Mills
Pathogens such as MERS-CoV, influenza A/H5N1 and influenza A/H7N9 are currently generating sporadic clusters of spillover human cases from animal reservoirs. The lack of a clear human epidemic suggests that the basic reproductive number R0 is below or very close to one for all three infections. However, robust cluster-based estimates for low R0 values are still desirable so as to help prioritise scarce resources between different emerging infections and to detect significant changes between clusters...

Data from: Extensive introgression in a malaria vector species complex revealed by phylogenomics

Michael C. Fontaine, James B. Pease, Aaron Steele, Robert M. Waterhouse, Daniel E. Neafsey, Igor V. Sharakhov, Xiofang Jiang, Andrew B. Hall, Flaminia Catteruccia, Evdoxia Kakani, Sarah N. Mitchell, Yi-Chieh Wu, Hilary A. Smith, R. Rebecca Love, Mara K. Lawniczak, Michel A. Slotman, Scott J. Emrich, Matthew W. Hahn & Nora J. Besansky
Introgressive hybridization is now recognized as a widespread phenomenon, but its role in evolution remains contested. Here we use newly available reference genome assemblies to investigate phylogenetic relationships and introgression in a medically important group of Afrotropical mosquito sibling species. We have identified the correct species branching order to resolve a contentious phylogeny, and show that lineages leading to the principal vectors of human malaria were among the first to split. Pervasive autosomal introgression between...

Data from: Sex drives intra-cellular conflict in yeast

Ellie Harrison, R. Craig MacLean, Vassiliki Koufopanou & Austin Burt
Theory predicts that sex can drive the evolution of conflict within the cell. During asexual reproduction genetic material within the cell is inherited as a single unit, selecting for cooperation both within the genome as well as between the extra-genomic elements within the cell (e.g. plasmids and endosymbionts). Under sexual reproduction this unity is broken down as parental genomes are distributed between meiotic progeny. Genetic elements able to transmit to more than 50% of meiotic...

Data from: Rates of dinosaur body mass evolution indicate 170 million years of sustained ecological innovation on the avian stem lineage

Roger B. J. Benson, Nicolás E. Campione, Matthew T. Carrano, Philip D. Mannion, Corwin Sullivan, Paul Upchurch & David C. Evans
Large-scale adaptive radiations might explain the runaway success of a minority of extant vertebrate clades. This hypothesis predicts, among other things, rapid rates of morphological evolution during the early history of major groups, as lineages invade disparate ecological niches. However, few studies of adaptive radiation have included deep time data, so the links between extant diversity and major extinct radiations are unclear. The intensively studied Mesozoic dinosaur record provides a model system for such investigation,...

Data from: Poor infant and young child feeding practices and sources of caregivers’ feeding knowledge in rural Hebei Province, China: findings from a cross-sectional survey

Qiong Wu, Robert W. Scherpbier, Michelle Helena Van Velthoven, Li Chen, Wei Wang, Ye Li, Yanfeng Zhang & Josip Car
Objectives: To obtain a general overview of infant and young child feeding practices in one rural county in China and identify current delivery channels and challenges. Design: A cross-sectional study. Setting: A rural county, Zhao County, in Hebei Province, China. Participants: 10 clusters were first selected within each township (16 townships in total) with proportional to population size sampling. In each cluster, a name list was used to select 13 children aged 0–23 months. We...

Data from: Spatial and temporal escape from fungal parasitism in natural communities of anciently asexual bdelloid rotifers

Christopher G. Wilson & Paul W. Sherman
Sexual reproduction is costly, but it is nearly ubiquitous among plants and animals, whereas obligately asexual taxa are rare and almost always short-lived. The Red Queen hypothesis proposes that sex overcomes its costs by enabling organisms to keep pace with coevolving parasites and pathogens. If so, the few cases of stable long-term asexuality ought to be found in groups whose coevolutionary interactions with parasites are unusually weak. In theory, antagonistic coevolution will be attenuated if...

Data from: Sex-biased immunity is driven by relative differences in reproductive investment

Crystal M. Vincent & Darryl T. Gwynne
Sex differences in immunity are often observed, with males generally having a weaker immune system than females. However, recent data in a sex-role-reversed species in which females compete to mate with males suggest that sexually competitive females have a weaker immune response. These findings support the hypothesis that sexual dimorphism in immunity has evolved in response to sex-specific fitness returns of investment in traits such as parental investment and longevity, but the scarcity of data...

Data from: Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey (Pygathrix nemaeus)

Amrita Srivathsan, John C. M. Sha, Alfried P. Vogler & Rudolf Meier
Fecal samples are of great value as a non-invasive means to gather information on the genetics, distribution, demography, diet, and parasite infestation of endangered species. Direct shotgun sequencing of fecal DNA could give information on these simultaneously, but this approach is largely untested. Here we use two fecal samples to characterize the diet of two Red-Shanked Doucs Langurs (Pygathrix nemaeus) that were fed a known combination of foliage, fruits, vegetables and cereals. Illumina HiSeq sequencing...

Data from: How can we get close to zero?: the potential contribution of biomedical prevention and the investment framework towards an effective response to HIV

John G. Stover, Timothy B. Hallett, Zunyou Wu, Mitchell Warren, Chaitra Gopalappa, Carel Pretorius, Peter D. Ghys, Julio Montaner, Bernhard Schwartländer & John Stover
Background: In 2011 an Investment Framework was proposed that described how the scale-up of key HIV interventions could dramatically reduce new HIV infections and deaths in low and middle income countries by 2015. This framework included ambitious coverage goals for prevention and treatment services resulting in a reduction of new HIV infections by more than half. However, it also estimated a leveling in the number of new infections at about 1 million annually after 2015....

Data from: Efficient inference of recombination hot regions in bacterial genomes

Koji Yahara, Xavier Didelot, M Azim. Ansari, Samuel K. Sheppard & Daniel Falush
In eukaryotes, detailed surveys of recombination rates have shown variation at multiple genomic scales and the presence of “hotspots” of highly elevated recombination. In bacteria, studies of recombination rate variation are less developed, in part because there are few analysis methods that take into account the clonal context within which bacterial evolution occurs. Here we focus in particular on identifying “hot regions” of the genome where DNA is transferred frequently between isolates. We present a...

Data from: Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data

Cuong Q. Tang, Aelys M. Humphreys, Diego Fontaneto & Timothy G. Barraclough
1. Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The Generalized Mixed Yule Coalescent (GMYC) and the Poisson Tree Process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes. 2. Here we assess how robust the GMYC and PTP are to different phylogenetic...

Data from: Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks

Ge Tan, Manuel Gil, Ari P. Löytynoja, Nick Goldman & Christophe Dessimoz
Multiple sequence aligners typically work by progressively aligning the most closely related sequences or group of sequences according to guide trees. In PNAS, Boyce et al. report that alignments reconstructed using simple chained trees (i.e., comb-like topologies) with random leaf assignment performed better in protein structure-based benchmarks than those reconstructed using phylogenies estimated from the data as guide trees. The authors state that this result could turn decades of research in the field on its...

Data from: A Silurian short-great-appendage arthropod

Derek J. Siveter, Derek E. G. Briggs, David J. Siveter, Mark D. Sutton, David J. Legg, Sarah Joomun & D. Legg
A new arthropod, Enalikter aphson gen. et sp. nov., is described from the Silurian (Wenlock Series) Herefordshire Lagerstätte of the UK. It belongs to the Megacheira (=short-great-appendage group), which is recognized here, for the first time, in strata younger than mid-Cambrian age. Discovery of this new Silurian taxon allows us to identify a Devonian megacheiran representative, Bundenbachiellus giganteus from the Hunsrück Slate of Germany. The phylogenetic position of megacheirans is controversial: they have been interpreted...

Data from: Comparative genomics of the mimicry switch in Papilio dardanus

Martijn J. T. N. Timmermans, Simon W. Baxter, Rebecca Clark, David G. Heckel, Heiko Vogel, Steve Collins, Alexie Papanicolaou, Iva Fukova, Mathieu Joron, Martin J. Thompson, Chris D. Jiggins, Richard H. Ffrench-Constant & Alfried P. Vogler
The African Mocker Swallowtail, Papilio dardanus, is a textbook example in evolutionary genetics. Classical breeding experiments have shown that wing pattern variation in this polymorphic Batesian mimic is determined by the polyallelic H locus that controls a set of distinct mimetic phenotypes. Using bacterial artificial chromosome (BAC) sequencing, recombination analyses and comparative genomics, we show that H co-segregates with an interval of less than 500 kb that is collinear with two other Lepidoptera genomes and...

Data from: Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles

Tomochika Fujisawa, Alfried P. Vogler & Timothy G. Barraclough
Comparative analysis is a potentially powerful approach to study the effects of ecological traits on genetic variation and rate of evolution across species. However, the lack of suitable datasets means that comparative studies of correlates of genetic traits across an entire clade have been rare. Here, we use a large DNA-barcode dataset (5062 sequences) of water beetles to test the effects of species ecology and geographical distribution on genetic variation within species and rates of...

Data from: Patterns of relapse in extrapulmonary small cell carcinoma: retrospective analysis of outcomes from two cancer centres

Spyridon Gennatas, Jillian Noble, Susannah Stanway, Ranga Gunapala, Mahfuja Chowdhury, Andrew Wotherspoon, Taqdir Benepal & Sanjay Popat
Objectives: We conducted a retrospective review of patients with extrapulmonary small cell carcinomas (EPSCCs) to explore the distribution, treatments, patterns of relapse and outcomes by primary site. Setting: We have reviewed the outcomes of one of the largest data sets of consecutive patients with EPSCC identified from two major cancer centres. Participants: Consecutive patients with a histopathological diagnosis of EPSCC from the two institutions were retrospectively identified. Primary and secondary outcome measures: Outcomes were evaluated...

Data from: The evolution of scarab beetles tracks the consecutive rise of angiosperms and mammals

Dirk Ahrens, Julia Schwarzer & Alfried P. Vogler
Extant terrestrial biodiversity arguably is driven by the evolutionary success of angiosperm plants, but the evolutionary mechanisms and timescales of angiosperm-dependent radiations remain poorly understood. The Scarabaeoidea is a diverse lineage of predominantly plant- and dung-feeding beetles. Here, we present a phylogenetic analysis of Scarabaeoidea based on four DNA markers for a taxonomically comprehensive set of specimens and link it to recently described fossil evidence. The phylogeny strongly supports multiple origins of coprophagy, phytophagy and...

Registration Year

  • 2014

Resource Types

  • Dataset


  • Imperial College London
  • University of Oxford
  • University of Toronto
  • Institute of Vertebrate Paleontology and Paleoanthropology
  • London School of Hygiene & Tropical Medicine
  • University of Notre Dame
  • Royal Ontario Museum
  • Capital Institute of Pediatrics
  • Joint United Nations Programme on HIV/AIDS
  • University of Cambridge