1,402 Works

Data from: Testing for unequal rates of morphological diversification in the absence of a detailed phylogeny: case study from characiform fishes

Brian Sidlauskas
This study develops the random phylogenies rate test (RAPRATE), a likelihood method that simulates morphological evolution along randomly generated phylogenies, and uses it to determine whether a considerable difference in morphological diversity between two sister clades of South American fishes should be taken as evidence of differing rates of morphological change or lineage turnover. Despite identical ages of origin, similar species richness, and sympatric geographic distributions, the morphological and ecological diversity of the superfamily Anostomoidea...

Data from: Additional molecular support for the new chordate phylogeny

Frédéric Delsuc, Georgia Tsagkogeorga, Nicolas Lartillot & Hervé Philippe
Recent phylogenomic analyses have suggested tunicates instead of cephalochordates as the closest living relatives of vertebrates. In direct contradiction with the long accepted view of Euchordates, this new phylogenetic hypothesis for chordate evolution has been the object of some skepticism. We assembled an expanded phylogenomic dataset focused on deuterostomes. Maximum-likelihood using standard models and Bayesian phylogenetic analyses using the CAT site-heterogeneous mixture model of amino-acid replacement both provided unequivocal support for the sister-group relationship between...

UMFOS data set

Wei Jin, Rebecca M. Riley, Russell D. Wolfinger, Kevin P. White, Gisele Passador-Gurgel & Greg Gibson
Gene Expression Profiling Results; this is an excel file with all of the extracted raw fluorescence intensities for Jin et al at the top, log2 at the bottom

Data from: Similar evolutionary potentials in an obligate ant parasite and its two host species

Pleuni S Pennings, Alexandra Achenbach & Susanne Foitzik
PLEASE NOTE: an additional file will be added to this data package: R script to calculate D and Gst for mtDNA (from a fasta file) and the associated p-values. It is also available here: . ABSTRACT: The spatial structure of host-parasite coevolution is shaped by population structure and genetic diversity of the interacting species. We analyzed these population genetic parameters in three related ant species: the parasitic slavemaking ant Protomognathus americanus and its two host...

Data from: The making of a rapid plant invader: genetic diversity and differentiation in the native and invaded range of Senecio inaequidens

Susanne Lachmuth, Walter Durka & Frank M Schurr
To become invasive, exotic species have to succeed in the consecutive phases of introduction, naturalization and invasion. Each of these phases leaves traces in genetic structure, which may affect the species' success in subsequent phases. We examine this interplay of genetic structure and invasion dynamics in the South African Ragwort (Senecio inaequidens), one of Europe's fastest plant invaders. We used AFLP and microsatellite markers to analyze 19 native African and 32 invasive European populations. In...

Data from: Stability of Cladistic Relationships between Cetacea and Higher-Level Artiodactyl Taxa

John Gatesy, Michel C. Milinkovitch, Victor Waddell & Michael J. Stanhope
Over the past ten years, the phylogenetic relationships among higher level artiodactyl taxa have been examined with multiple data sets. Many of these data sets suggest that Artiodactyla (even-toed ungulates) is paraphyletic and that Cetacea (whales) represents a highly derived "artiodactyl" subgroup. In this report, phylogenetic relationships between Cetacea and artiodactyls are tested with a combination of 15 published data sets plus new DNA sequence data from two nuclear loci, interphotoreceptor retinoid binding protein (IRBP)...

Data from: An unusual new neosauropod dinosaur from the lower Cretaceous Hastings Beds Group of East Sussex, England

Michael P. Taylor & Darren Naish
Xenoposeidon proneneukos gen. et sp. nov. is a neosauropod represented by BMNH R2095, a well-preserved partial mid-to-posterior dorsal vertebra from the Berriasian–Valanginian Hastings Beds Group of Ecclesbourne Glen, East Sussex, England. It was briefly described by Lydekker in 1893, but it has subsequently been overlooked. This specimen's concave cotyle, large lateral pneumatic fossae, complex system of bony laminae and camerate internal structure show that it represents a neosauropod dinosaur. However, it differs from all other...

Data from: Towards a worldwide wood economics spectrum

Amy E. Zanne, G. Lopez-Gonzalez, David A. Coomes, Jugo Ilic, Steven Jansen, Simon L. Lewis, Regis B. Miller, Nathan G. Swenson, Michael C. Wiemann & Jerome Chave
Wood performs several essential functions in plants, including mechanically supporting aboveground tissue, storing water and other resources, and transporting sap. Woody tissues are likely to face physiological, structural and defensive trade-offs. How a plant optimizes among these competing functions can have major ecological implications, which have been under-appreciated by ecologists compared to the focus they have given to leaf function. To draw together our current understanding of wood function, we identify and collate data on...

Data from: A morphometric study of species boundaries of the wild potato Solanum series Conicibaccata: a replicated field trial in Andean Peru

Diego Fajardo, Raul Castillo, Alberto Salas & David M. Spooner
Solanum series Conicibaccata contains about 40 wild potato (section Petota) species distributed from southern Mexico to central Bolivia. It contains diploids (2n = 2x = 24), tetraploids (2n = 4x = 48) and hexaploids (2n = 6x = 72) and some polyploids are likely allopolyploids. Our morphological phenetic study in an Andean site in central Peru (12°S, 3200 m altitude) is a replicated study from one done in the north central United States (45°N, 180...

Data from: It's about time: the temporal dynamics of phenotypic selection in the wild

Adam M. Siepielski, Joseph D. DiBattista & Stephanie M. Carlson
Selection is a central process in nature. Although our understanding of the strength and form of selection has increased, a general understanding of the temporal dynamics of selection in nature is lacking. Here, we assembled a database of temporal replicates of selection from studies of wild populations to synthesize what we do (and do not) know about the temporal dynamics of selection. Our database contains 5519 estimates of selection from 89 studies, including estimates of...

Data from: Gene expression profiles associated with the transition to parasitism in Ancylostoma caninum larvae

Jennifer M. Moser, Tori Freitas, Prema Arasu & Greg Gibson
Ancylostoma caninum is a common canine parasite responsible for anemia and death in infected dogs. Gene expression profiling was used to investigate molecular differences between two different forms of the third larval stage (L3s): infective free-living larvae and in vitro serum-stimulated larvae that mimic the initial stages of parasitism of a host. We developed an A. caninum cDNA microarray consisting of 4191 EST clones, and used it to identify a set of 113 genes that...

Data from: Comparison of regional gene expression differences in the brains of the domestic dog and human

Erin Kennerly, Susanne Thomson, Natasha Olby, Matthew Breen & Greg Gibson
Comparison of the expression profiles of 2,721 genes in the cerebellum, cortex and pituitary gland of three American Staffordshire terriers, one beagle and one fox hound revealed regional expression differences in the brain but failed to reveal marked differences among breeds, or even individual dogs. Approximately 85 per cent (42 of 49 orthologue comparisons) of the regional differences in the dog are similar to those that differentiate the analogous human brain regions. A smaller percentage...

Data from: Association between nucleotide variation in Efgr and wing shape in Drosophila melanogaster

Arnar Palsson & Greg Gibson
As part of an effort to dissect quantitative trait locus effects to the nucleotide level, association was assessed between 238 single-nucleotide and 20 indel polymorphisms spread over 11 kb of the Drosophila melanogaster Egfr locus and nine relative warp measures of wing shape. One SNP in a conserved potential regulatory site for a GAGA factor in the promoter of alternate first exon 2 approaches conservative experimentwise significance (P < 0.00003) in the sample of 207...

Data from: Nucleotide variation in the Egfr locus of Drosophila melanogaster

Arnar Palsson, Ann Rouse, Rebecca Riley-Berger, Ian Dworkin & Greg Gibson
The Epidermal growth factor receptor is an essential gene with diverse pleiotropic roles in development throughout the animal kingdom. Analysis of sequence diversity in 10.9 kb covering the complete coding region and 6.4 kb of potential regulatory regions in a sample of 250 alleles from three populations of Drosophila melanogaster suggests that the intensity of different population genetic forces varies along the locus. A total of 238 independent common SNPs and 20 indel polymorphisms were...

Data from: Mixed-model reanalysis of primate data suggests tissue and species biases

Wen-Ping Hsieh, Tzu-Ming Chu, Russell D. Wolfinger & Greg Gibson
An emerging issue in evolutionary genetics is whether it is possible to use gene expression profiling to identify genes that are associated with morphological, physiological, or behavioral divergence between species and whether these genes have undergone positive selection. Some of these questions were addressed in a recent study (Enard et al. 2002) of the difference in gene expression among human, chimp, and orangutan, which suggested an accelerated rate of divergence in gene expression in the...

Data from: Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries

Morris Goodman, Kirstin N. Sterner, M. Munirul Islam, Monica Uddin, Chet C. Sherwood, Patrick R. Hof, Zhuo-Cheng Hou, Leonard Lipovich, Hui Jia, Lawrence I. Grossman, Derek E. Wildman, D. E. Wildman, L. I. Grossman, C. C. Sherwood, M. Islam, L. Lipovich, H. Jia, P. R. Hof, Z. C. Hou & K. N. Sterner
Specific sets of brain-expressed genes, such as aerobic energy metabolism genes, evolved adaptively in the ancestry of humans and may have evolved adaptively in the ancestry of other large-brained mammals. The recent addition of genomes from two afrotherians (elephant and tenrec) to the expanding set of publically available sequenced mammalian genomes provided an opportunity to test this hypothesis. Elephants resemble humans by having large brains and long life spans; tenrecs, in contrast, have small brains...

Data from: Extensive sex-specific nonadditivity of gene expression in Drosophila melanogaster

Greg Gibson, Rebecca Riley-Berger, Larry Harshman, Artyom Kopp, Scott Vacha, Sergey Nuzhdin & Marta Wayne
Assessment of the degree to which gene expression is additive and heritable has important implications for understanding the maintenance of variation, adaptation, phenotypic divergence, and the mapping of genotype onto phenotype. We used whole-genome transcript profiling using Agilent long-oligonucleotide microarrays representing 12,017 genes to demonstrate that gene transcription is pervasively nonadditive in Drosophila melanogaster. Comparison of adults of two isogenic lines and their reciprocal F1 hybrids revealed 5820 genes as significantly different between at least...

Data from: Insect rate-temperature relationships: environmental variation and the metabolic theory of ecology

Ulrike Irlich, John S. Terblanche, Tim M. Blackburn & Steven L. Chown
Much of the recent discussion concerning the form and underlying mechanistic basis of metabolic rate–temperature and development rate–temperature relationships has been precipitated by the development of the metabolic theory of ecology (MTE). Empirical tests of the theory’s fundamental equation are an essential component of establishing its validity. Here, we test the temperature component of the fundamental equation of the MTE as it applies to metabolic rate and development rate, using insects as model organisms. Specifically,...

Data from: A porous convection model for small-scale grass patterns

Sally Thompson & Karen E. Daniels
Spatial ecological patterns are usually ascribed to Turing‐type reaction‐diffusion or scale‐dependent feedback processes, but morphologically indistinguishable patterns can be produced by instabilities in fluid flow. We present a new hypothesis that suggests that fluid convection and chill damage to plants could form vegetation patterns with wavelengths ≈1–2 times the plant height. Previous hypotheses for small‐scale vegetation pattern formation relied on a Turing process driven by competition for water, which is thought to occur in large...

Data from: When are phylogenetic analyses misled by convergence? A case study in Texas cave salamanders

John J. Wiens, Paul T. Chippindale & David M. Hillis
Convergence, i.e., similarity between organisms that is not the direct result of shared phylogenetic history (and that may instead result from independent adaptations to similar environments), is a fundamental issue that lies at the interface of systematics and evolutionary biology. Although convergence is often cited as an important problem in morphological phylogenetics, there have been few well-documented examples of strongly supported and misleading phylogenetic estimates that result from adaptive convergence in morphology. In this article,...

Data from: Resolution of a Supertree/Supermatrix Paradox

John Gatesy, Conrad Matthee, Rob DeSalle & Cheryl Hayashi
Gatesy et al Data SetSuperArtio-1.dat

Data from: Assessing the complex architecture of polygenic traits in diverged yeast populations

Francisco A Cubillos, Eleonora Billi, Enikö Zörgö, Leopold Parts, Patrick Fargier, Stig Omholt, Anders Blomberg, Jonas Warringer, Edward J Louis & Gianni Liti
Phenotypic variation arising from populations adapting to different niches has a complex underlying genetic architecture. A major challenge in modern biology is to identify the causative variants driving phenotypic variation. Recently the baker’s yeast, Saccharomyces cerevisiae has emerged as a powerful model for dissecting complex traits. However, past studies using a laboratory strain were unable to reveal the complete architecture of polygenic traits. Here, we present a linkage study using 576 recombinant strains obtained from...

Data from: De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using next-generation sequencing techniques.

Francesco Angeloni, C A M Wagemaker, Mike S M Jetten, Huub J M Op Den Camp, Eva M Janssen-Megens, Kees-Jan Françoijs, Henk G Stunnenberg & N Joop Ouborg
Next-generation sequencing (NGS) technologies are increasingly applied in many organisms, including non-model organisms that are important for ecological and conservation purposes. Illumina and 454 sequencing are among the most used NGS technologies and have been shown to produce optimal results at reasonable costs when used together. Here, we describe the combined application of these two NGS technologies to characterize the transcriptome of a plant species of ecological and conservation relevance for which no genomic resource...

Data from: Dealing with allometry in linear and geometric morphometrics: a taxonomic case study in the Leporinus cylindriformis group (Characiformes: Anostomidae) with description of a new species from Suriname

Jan H. Mol, Richard P. Vari & Brian L. Sidlauskas
To achieve maximum efficacy, taxonomic studies that seek to distinguish amongst species must first account for allometric shape variation within species. Two recently developed software packages (SMATR and MorphoJ) offer regression-based allometric approaches that are notable for their statistical power and ease of use and that may prove highly useful to taxonomists working with linear or geometric morphometric data. We investigate species delimitation of the slender-bodied fishes in the Leporinus cylindriformis group using these programs...

Data from: Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia

Robert Alexander Pyron, Robert Alexander Pyron & R. Alexander Pyron
Were molecular data available for extinct taxa, questions regarding the origins of many groups could be settled in short order. As this is not the case, various strategies have been proposed to combine paleontological and neontological datasets. The use of fossil dates as node age calibrations for divergence time estimation from molecular phylogenies is commonplace. In addition, simulations suggest that the addition of morphological data from extinct taxa may improve phylogenetic estimation when combined with...

Registration Year

  • 2010

Resource Types

  • Dataset


  • North Carolina State University
  • University of Kansas
  • National Evolutionary Synthesis Center
  • University of Florida
  • Yale University
  • Palacký University, Olomouc
  • Stanford University
  • Duke University
  • George Washington University
  • University of Iceland
  • University of Alaska Fairbanks
  • University of Chicago
  • University of California, Davis
  • Anglia Ruskin University
  • Dalian Maritime University