132,269 Works

Data from: Significance Analysis of Prognostic Signatures

Andrew H. Beck, Nicholas W. Knoblauch, Marco M. Hefti, Jennifer Kaplan, Stuart J. Schnitt, Aedin C. Culhane, Markus S. Schroeder, John Quackenbush, Benjamin Haibe-Kains & Thomas Risch
A major goal in translational cancer research is to identify biological signatures driving cancer progression and metastasis. A common technique applied in genomics research is to cluster patients using gene expression data from a candidate prognostic gene set, and if the resulting clusters show statistically significant outcome stratification, to associate the gene set with prognosis, suggesting its biological and clinical importance. Recent work has questioned the validity of this approach by showing in several breast...
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Data from: One QTL for intra- and interspecific variation in a sex pheromone

Astrid T. Groot, Heike Staudacher, Andrea Barthel, Olive Inglis, Richard G. Santangelo, Steffi Gebauer-Jung, Heiko Vogel, Jennifer Emerson, Coby Schal, David G. Heckel, Fred Gould & Gerhard Schoefl
Even though premating isolation is hypothesized to be a major driving force in speciation, its genetic basis is poorly known. In the noctuid moth Heliothis subflexa, one group of sex pheromone components, the acetates, emitted by the female, plays a crucial isolating role in preventing interspecific matings to males of the closely related Heliothis virescens, in which females do not produce acetates and males are repelled by them. We previously found intraspecific variation in acetates...
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Data from: Forward chemical genetic screens in Arabidopsis identify genes that influence sensitivity to the phytotoxic compound sulfamethoxazole

Darrell Desveaux, Karl J. Schreiber, Ryan S. Austin, Yunchen Gong, Jianfeng Zhang, Pauline Fung, Pauline W. Wang & David S. Guttman
BACKGROUND: The sulfanilamide family comprises a clinically important group of antimicrobial compounds which also display bioactivity in plants. While there is evidence that sulfanilamides inhibit folate biosynthesis in both bacteria and plants, the complete network of plant responses to these compounds remains to be characterized. As such, we initiated two forward genetic screens in Arabidopsis in order to identify mutants that exhibit altered sensitivity to sulfanilamide compounds. These screens were based on the growth phenotype...
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Data from: Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

Catherine E. Wagner, Irene Keller, Samuel Wittwer, Oliver M. Selz, Salome Mwaiko, Lucie Greuter, Arjun Sivasundar & Ole Seehausen
Although population genomic studies using next generation sequencing (NGS) data are becoming increasingly common, studies focusing on phylogenetic inference using these data are in their infancy. Here, we use NGS data generated from reduced representation genomic libraries of restriction-site-associated DNA (RAD) markers to infer phylogenetic relationships among 16 species of cichlid fishes from a single rocky island community within Lake Victoria's cichlid adaptive radiation. Previous attempts at sequence-based phylogenetic analyses in Victoria cichlids have shown...
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Data from: Genome-wide single nucleotide polymorphism analysis reveals recent genetic introgression from domestic pigs into Northwest European wild boar populations

Daniel J. Goedbloed, Hendrik-Jan Megens, Pim Van Hooft, Juanma M. Herrero-Medrano, Walburga Lutz, Panoraia Alexandri, Richard P. M. A. Crooijmans, Sip E. Van Wieren, Ronald C. Ydenberg, Herbert H. T. Prins & Martien Groenen
Present-day genetic introgression from domestic pigs into European wild boar has been suggested in various studies. However, no hybrids have been identified beyond doubt mainly because available methods were unable to quantify the extent of introgression and rule out natural processes. Genetic introgression from domestic pigs may have far-reaching ecological consequences by altering traits like the reproduction rate or immunology of wild boar. In this study, we demonstrate a novel approach to investigate genetic introgression...
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Data from: Reference-free transcriptome assembly in non-model animals from next generation sequencing data

Vincent Cahais, Philippe Gayral, Georgia Tsagkogeorga, José Melo-Ferreira, Marion Ballenghien, Lucy Weinert, Ylenia Chiari, Khalid Belkhir, Vincent Ranwez & Nicolas Galtier
Next-generation sequencing (NGS) technologies offer the opportunity for population genomic study of non-model organisms sampled in the wild. The transcriptome is a convenient and popular target for such purposes. However, designing genetic markers from NGS transcriptome data requires assembling gene-coding sequences out of short reads. This is a complex task owing to gene duplications, genetic polymorphism, alternative splicing and transcription noise. Typical assembling programmes return thousands of predicted contigs, whose connection to the species true...
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Data from: Bayesian methods for estimating GEBVs of threshold traits

Qin Zhang, Chong-Long Wang, Xiangdong Ding, Ji-Ying Wang, Jiangfeng Liu, Wei-Xuan Fu, Zhe Zhang & Zong-Jun Yin
Estimation of genomic breeding values is the key step in genomic selection. Many methods have been proposed for continuous traits, but methods for threshold traits are still scarce. Here we introduced threshold model to the framework of genomic selection, and specifically we extended the three Bayesian methods BayesA, BayesB and BayesCπ based on threshold model for estimating genomic breeding values of threshold traits, and the extended methods are correspondingly termed BayesTA, BayesTB and BayesTCπ. Computing...
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Data from: De novo characterization of the Timema cristinae transcriptome facilitates marker discovery and inference of genetic divergence.

Aaron A. Comeault, Mathew Sommers, Tanja Schwander, C. Alex Buerkle, Timothy E. Farkas, Patrik Nosil & Thomas L. Parchman
Adaptation to different ecological environments can promote speciation. Although numerous examples of such ‘ecological speciation’ exist, the genomic basis of the process, and the role of gene flow in it, remains less understood. This is, at least in part, because systems that are well characterized in terms of their ecology often lack genomic resources. In this study we characterize the transcriptome of Timema cristinae stick insects, a system that has been researched intensively in terms...
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Data from: Multilocus estimation of selfing and its heritability

Nathan S. McClure, Michael C. Whitlock & M C Whitlock
We describe a new method of estimating the selfing rate (S) in a mixed mating population based on a population structure approach that accounts for possible intergenerational correlation in selfing rate, giving rise to an estimate of the upper limit for heritability of selfing rate (h^2). A correlation between generations in selfing rate is shown to affect one- and two-locus probabilities of identity by descent. Conventional estimates of selfing rate based on a population structure...
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Data from: Insights into the genetic history of French cattle from dense SNP data on 47 worldwide breeds

Mathieu Gautier, Denis Laloë & Katayoun Moazami-Goudarzi
BACKGROUND: Modern cattle originate from populations of the wild extinct aurochs through a few domestication events which occurred about 8,000 years ago. Newly domesticated populations subsequently spread worldwide following breeder migration routes. The resulting complex historical origins associated with both natural and artificial selection have led to the differentiation of numerous different cattle breeds displaying a broad phenotypic variety over a short period of time. METHODOLOGY/PRINCIPAL FINDINGS: This study gives a detailed assessment of cattle...
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Data from: Phylogenetic treatment and taxonomic revision of the trapdoor spider genus Aptostichus Simon (Araneae, Mygalomorphae, Euctenizidae)

Jason Bond
This systematic study documents the taxonomy, diversity, and distribution of 40 species of the predominately Californian trapdoor spider genus Aptostichus Simon, 1891. Thirty-three of these species are newly described: Aptostichus dantrippi, Aptostichus cabrillo, Aptostichus pennjillettei, Aptostichus asmodaeus, Aptostichus nateevansi, Aptostichus chiricahua, Aptostichus icenoglei, Aptostichus isabella, Aptostichus muiri, Aptostichus barackobamai, Aptostichus sinnombre, Aptostichus hedinorum, Aptostichus aguacaliente, Aptostichus chemehuevi, Aptostichus sarlacc, Aptostichus derhamgiulianii, Aptostichus anzaborrego, Aptostichus serrano, Aptostichus mikeradtkei, Aptostichus edwardabbeyi, Aptostichus killerdana, Aptostichus cahuilla, Aptostichus satleri,...
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Data from: The trouble with isolation by distance

Patrick G. Meirmans
The genetic population structure of many species is characterised by a pattern of isolation by distance (IBD): due to limited dispersal, individuals that are geographically close tend to be genetically more similar than individuals that are far apart. Despite the ubiquity of IBD in nature, many commonly used statistical tests are based on a null model that is completely non-spatial, the Island model. Here, I argue that patterns of spatial autocorrelation deriving from IBD present...
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Data from: A migratory northern ungulate in the pursuit of spring: jumping or surfing the green wave?

Richard Bischof, Leif Egil Loe, Erling L. Meisingset, Barbara Zimmermann, Bram Van Moorter & Atle Mysterud
The Forage Maturation Hypothesis (FMH) states that herbivores migrate along a phenological gradient of plant development in order to maximize energy intake. Despite strong support for the FMH, the actual relationship between plant phenology and ungulate movement has remained enigmatic. We linked plant phenology (MODIS-NDVI) and space use of 167 migratory and 78 resident red deer (Cervus elaphus) using a space-time-time matrix of "springness", defined as the instantaneous rate of green-up (IRG). Consistent with the...
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Data from: Prey preference of snow leopard (Panthera uncia) in South Gobi, Mongolia

Wasim Shehzad, Thomas Michael McCarthy, François Pompanon, Lkhagvajav Purevjav, Eric Coissac, Tiayyba Riaz & Pierre Taberlet
Accurate information about the diet of large carnivores that are elusive and inhabit inaccessible terrain, is required to properly design conservation strategies. Predation on livestock and retaliatory killing of predators have become serious issues throughout the range of the snow leopard. Several feeding ecology studies of snow leopards have been conducted using classical approaches. These techniques have inherent limitations in their ability to properly identify both snow leopard feces and prey taxa. To examine the...
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Data from: A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing

John E. McCormack, Michael G. Harvey, Brant C. Faircloth, Nicholas G. Crawford, Travis C. Glenn & Robb T. Brumfield
Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed...
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Data from: Identification of glucose kinase dependent and independent pathways for carbon control of primary metabolism, development and antibiotic production in Streptomyces coelicolor by quantitative proteomics

Jacob Gubbens, Marleen Janus, Bogdan I. Florea, Hermen S. Overkleeft, Gilles P. Van Wezel & Herman S. Overkleeft
Members of the soil-dwelling prokaryotic genus Streptomyces are indispensable for the recycling of complex polysaccharides, and produce a wide range of natural products. Nutrient availability is a major determinant for the switch to development and antibiotic production in streptomycetes. Carbon catabolite repression (CCR), a main signaling pathway underlying this phenomenon, was so far considered fully dependent on the glycolytic enzyme glucose kinase (Glk). Here we provide evidence of a novel Glk-independent pathway in Streptomyces coelicolor,...
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Data from: Carrion fly-derived DNA as a tool for comprehensive and cost-effective assessment of mammalian biodiversity

Sebastien Calvignac-Spencer, Kevin Merkel, Nadine Kutzner, Hjalmar Kühl, Christophe Boesch, Peter M. Kappeler, Sonja Metzger, Grit Schubert & Fabian H. Leendertz
Large-scale monitoring schemes are essential in assessing global mammalian biodiversity, and in this framework leeches have recently been promoted as an indirect source of DNA from terrestrial mammal species. Carrion feeding flies are ubiquitous and can be expected to feed on many vertebrate carcasses. Hence, we tested whether fly-derived DNA analysis may also serve as a novel tool for mammalian diversity surveys. We screened DNA extracted from 201 carrion flies collected in tropical habitats of...
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Data from: Linkage disequilibrium and effective population size when generations overlap

John D. Robinson & Gregory R. Moyer
Estimates of effective population size are critical for species of conservation concern. Genetic datasets can be used to provide robust estimates of this important parameter. However, the methods used to obtain these estimates assume that generations are discrete. We used simulated data to assess the influences of overlapping generations on estimates of effective size provided by the linkage disequilibrium method. Our simulations focus on two factors: the degree of reproductive skew exhibited by the focal...
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Data from: How random is social behaviour? Disentangling social complexity through the study of a wild house mouse population

Nicolas Perony, Claudio J. Tessone, Barbara König & Frank Schweitzer
Out of all the complex phenomena displayed in the behaviour of animal groups, many are thought to be emergent properties of rather simple decisions at the individual level. Some of these phenomena may also be explained by random processes only. Here we investigate to what extent the interaction dynamics of a population of wild house mice (Mus domesticus) in their natural environment can be explained by a simple stochastic model. We first introduce the notion...
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Data from: Differential effects of landscape-level environmental features on genetic structure in three co-distributed tree species in Central America

Monica F. Poelchau, Jim L. Hamrick & J. L. Hamrick
Landscape genetic studies use spatially explicit population genetic information to determine the physical and environmental causes of population genetic structure on regional scales. Comparative studies that identify common barriers to gene flow across multiple species within a community are important to both understand the evolutionary trajectories of populations and to prioritize habitat conservation. Here, we use a comparative landscape genetic approach to ask whether gradients in temperature or precipitation seasonality structure genetic variation across three...
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Data from: The design of a beautiful weapon: compensation for opposing sexual selection on a trait with two functions

Stefan Dennenmoser & John H. Christy
Male fiddler crabs, genus Uca, have one greatly enlarged claw with which they court females and threaten and fight other males. Longer claws are more effective signals but are thought to be less effective weapons because the relative closing force at the tip of the claw decreases with claw length. We studied claw morphology and fighting in Uca terpsichores and Uca beebei and found a mechanism that may resolve opposing selection for signaling and fighting...
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Data from: Vertebral architecture in the earliest stem tetrapods

Stephanie E. Pierce, Per E. Ahlberg, John R. Hutchinson, Julia L. Molnar, Sophie Sanchez, Paul Tafforeau & Jennifer A. Clack
The construction of the vertebral column has been used as a key anatomical character in defining and diagnosing early tetrapod groups. Rhachitomous vertebrae - in which there is a dorsally placed neural arch and spine, an anteroventrally placed intercentrum and paired, posterodorsally placed pleurocentra - have long been considered the ancestral morphology for tetrapods. Nonetheless, very little is known about vertebral anatomy in the earliest stem tetrapods, as most specimens remain trapped in surrounding matrix,...
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Data from: More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

Nicholas G. Crawford, Brant C. Faircloth, John E. McCormack, Robb T. Brumfield, Kevin Winker, Travis C. Glenn, B. C. Faircloth, R. T. Brumfield, J. E. McCormack, T. C. Glenn & N. G. Crawford
We present the first genomic-scale analysis addressing the phylogenetic position of turtles, using over 1,000 loci from representatives of all major reptile lineages including tuatara. Previously, studies of morphological traits positioned turtles either at the base of the reptile tree or with lizards, snakes, and tuatara (lepidosaurs), whereas molecular analyses typically allied turtles with crocodiles and birds (archosaurs). A recent analysis of shared microRNA families found that turtles are more closely related to lepidosaurs. To...
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Data from: Slowly switching between environments facilitates reverse evolution in small populations

Longzhi Tan & Jeff Gore
Natural populations must constantly adapt to ever-changing environmental conditions. A particularly interesting question is whether such adaptations can be reversed by returning the population to an ancestral environment. Such evolutionary reversals have been observed in both natural and laboratory populations. However, the factors that determine the reversibility of evolution are still under debate. The timescales of environmental change vary over a wide range, but little is known about how the rate of environmental change influences...
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Data from: Runaway sexual selection leads to good genes

Christopher H. Chandler, Charles Ofria & Ian Dworkin
Mate choice and sexual displays are widespread in nature, but their evolutionary benefits remain controversial. Theory predicts these traits can be favored by runaway sexual selection, in which preference and display reinforce one another due to genetic correlation; or by good genes benefits, in which mate choice is advantageous because extreme displays indicate a well-adapted genotype. However, these hypotheses are not mutually exclusive, and the adaptive benefits underlying mate choice can themselves evolve. In particular,...
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Registration Year

  • 2012
    132,269

Resource Types

  • Dataset
    132,269

Affiliations

  • Centre for Ecology and Hydrology
    10
  • University of Georgia
    3
  • Louisiana State University of Alexandria
    2
  • University of California, Los Angeles
    2
  • British Geological Survey
    2
  • Boston University
    2
  • Princeton University
    1
  • University of Virginia
    1
  • Dalhousie University
    1
  • Panthera Corporation
    1
  • Robert Koch Institute
    1
  • French National Institute for Agricultural Research
    1
  • King's College London
    1
  • San Diego State University
    1
  • Leiden University
    1