24 Works

Data from: The evolutionary origin of somatic cells under the dirty work hypothesis

Heather J. Goldsby, David B. Knoester, Charles Ofria & Benjamin Kerr
Reproductive division of labor is a hallmark of multicellular organisms. However, the evolutionary pressures that give rise to delineated germ and somatic cells remain unclear. Here we propose a hypothesis that the mutagenic consequences associated with performing metabolic work favor such differentiation. We present evidence in support of this hypothesis gathered using a computational form of experimental evolution. Our digital organisms begin each experiment as undifferentiated multicellular individuals, and can evolve computational functions that improve...

Data from: Neuraminidase inhibitors for preventing and treating influenza in healthy adults and children

Tom Jefferson, Mark A. Jones, Peter Doshi, Chris B. Del Mar, Rokuro Hama, Matthew J. Thompson, Elizabeth A. Spencer, Igho Onakpoya, Kamal R. Mahtani, David Nunan, Jeremy Howick, Carl J. Heneghan & Igho J Onakpoya
PLEASE NOTE, THESE DATA ARE ALSO REFERRED TO IN TWO OTHER ARTICLES. PLEASE SEE http://dx.doi.org/10.1136/bmj.g2547 AND http://dx.doi.org/10.1136/bmj.g2545 FOR MORE INFORMATION. Background: Neuraminidase inhibitors (NIs) are stockpiled and recommended by public health agencies for treating and preventing seasonal and pandemic influenza. They are used clinically worldwide. Objectives: To describe the potential benefits and harms of NIs for influenza in all age groups by reviewing all clinical study reports of published and unpublished randomised, placebo-controlled trials and...

Data from: A new species of horned lizard (genus Phrynosoma) from Guerrero, México, with an updated multilocus phylogeny

Adrián Nieto-Montes De Oca, Diego Arenas-Moreno, Elizabeth Beltrán-Sánchez & Adam D. Leaché
We describe a new species of Phrynosoma from central northeastern Guerrero, México; perform a phylogenetic analysis of mitochondrial and nuclear sequence data to estimate its phylogenetic relationships; and investigate the monophyly of Phrynosoma asio, P. braconnieri, and P. taurus. The new species can be distinguished from all of its congeners by the possession of a unique combination of morphological characteristics. The molecular genetic data include three fragments of the mitochondrial genome and six nuclear genes...

Data from: Improving the efficacy of web-based educational outreach in ecology

Gregory R. Goldsmith, Andrew D. Fulton, Colin D. Witherill & Javier F. Espeleta
Scientists are increasingly engaging the web to provide formal and informal science education opportunities. Despite the prolific growth of web-based resources, systematic evaluation and assessment of their efficacy remains limited. We used clickstream analytics, a widely available method for tracking website visitors and their behavior, to evaluate >60,000 visits over three years to an educational website focused on ecology. Visits originating from search engine queries were a small proportion of the traffic, suggesting the need...

Data from: \"De novo transcriptome assembly of the mountain fly Drosophila nigrosparsa using short RNA-seq reads\" in Genomic Resources Notes Accepted 1 August 2014-30 September 2014

Wolfgang Arthofer, Francesco Cicconardi, Nicola Palmieri, Viola Nolte, Christian Schlötterer, Birgit C. Schlick-Steiner, Florian M. Steiner, Marcelo Vallinoto, David A. Weese, B. L. Banbury, R. B. Harris, David S. Kang, Cheolho Sim, Thomas F. Duda, A. D. Leaché, Miguel Carneiro, Coralie Nourisson & Fernando Sequeira
Drosophila (Drosophila) nigrosparsa is a habitat specialist restricted to the European montane/alpine zone (Bächli 2008). Mountain biodiversity is considered highly vulnerable to ongoing climate warming (IPCC 2013), and organisms at high altitudes have only limited possibility to shift to cooler habitats at elevations above (Pertoldi & Bach 2007). For such species, rapid evolution may offer a solution for long-term survival. We are establishing D. nigrosparsa as a model system to test the extent and tempo...

Data from: Opsin clines in butterflies suggest novel roles for insect photopigments

Francesca D Frentiu, Furong Yuan, Wesley K Savage, Gary D Bernard, Sean P Mullen & Adriana D Briscoe
Nucleotide Sequence Files Raw DataZip archive of the fasta files containing sequences for each individual used in clinal analyses for 3 opsin genes and wingless and EF1-alpha genes.

Data from: Local adaptation limits lifetime reproductive success of dispersers in a wild salmon metapopulation

Daniel A. Peterson, Ray Hilborn & Lorenz Hauser
Demographic and evolutionary dynamics in wild metapopulations are critically affected by the balance between dispersal and local adaptation. Where populations are demographically interconnected by migration, gene flow is often assumed to prevent local adaptation. However, reduced fitness of immigrants may limit gene flow between populations adapted to distinct habitat types, although direct quantification of the lifetime reproductive success of immigrants in the wild is lacking. Here, we show that dispersers between stream-spawning populations of sockeye...

Data from: Weak phylogenetic signal in physiological traits of methane-oxidizing bacteria

Sascha Krause, Peter M. Van Bodegom, Will K. Cornwell & Paul L. E. Bodelier
The presence of phylogenetic signal is assumed to be ubiquitous. However, for microorganisms, this may not be true given that they display high physiological flexibility and have fast regeneration. This may result in fundamentally different patterns of resemblance, that is, in variable strength of phylogenetic signal. However, in microbiological inferences, trait similarities and therewith microbial interactions with its environment are mostly assumed to follow evolutionary relatedness. Here, we tested whether indeed a straightforward relationship between...

Data from: Evolutionary relatedness does not predict competition and co-occurrence in natural or experimental communities of green algae

Markos A. Alexandrou, John D. Hall, Charles F. Delwiche, Bradley J. Cardinale, Keith Fritschie, Bastian Bentlage, Anita Narwani, Patrick A. Venail, M. Sabrina Pankey & Todd H. Oakley
The competition-relatedness hypothesis (CRH) predicts that the strength of competition is the strongest among closely related species and decreases as species become less related. This hypothesis is based on the assumption that common ancestry causes close relatives to share biological traits that lead to greater ecological similarity. Although intuitively appealing, the extent to which phylogeny can predict competition and co-occurrence among species has only recently been rigorously tested, with mixed results. When studies have failed...

Data from: Dispersal ability and habitat requirements determine landscape-level genetic patterns in desert aquatic insects

Ivan C. Phillipsen, Emily H. Kirk, Michael T. Bogan, Meryl C. Mims, Julian D. Olden & David A. Lytle
Species occupying the same geographic range can exhibit remarkably different population structures across the landscape, ranging from highly diversified to panmictic. Given limitations on collecting population-level data for large numbers of species, ecologists seek to identify proximate organismal traits—such as dispersal ability, habitat preference and life history—that are strong predictors of realized population structure. We examined how dispersal ability and habitat structure affect the regional balance of gene flow and genetic drift within three aquatic...

Data from: Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information

Sergey Ovchinnikov, Hetunandan Kamisetty & David Baker
Do the amino acid sequence identities of residues that make contact across protein interfaces covary during evolution? If so, such covariance could be used to predict contacts across interfaces and assemble models of biological complexes. We find that residue pairs identified using a pseudo-likelihood based method to covary across protein-protein interfaces in the 50S ribosomal unit and 28 additional bacterial protein complexes with known structure are almost always in contact in the complex provided that...

Data from: Latitudinal and photic effects on diel foraging and predation risk in freshwater pelagic ecosystems

Adam Hansen, David Beauchamp, David A. Beauchamp & Adam G. Hansen
1. Clark & Levy (1988) described an antipredation window for smaller planktivorous fish during crepuscular periods when light permits feeding on zooplankton, but limits visual detection by piscivores. Yet, how the window is influenced by the interaction between light regime, turbidity and cloud cover over a broad latitudinal gradient remains unexplored. 2. We evaluated how latitudinal and seasonal shifts in diel light regimes alter the foraging-risk environment for visually-feeding planktivores and piscivores across a natural...

Data from: How to best smash a snail: the effect of tooth shape on crushing load

S. B. Crofts & A. P. Summers
Organisms that are durophagous, hard prey consumers, have a diversity of tooth forms. To determine why we see this variation, we tested whether some tooth forms break shells better than others. We measured the force needed with three series of aluminium tooth models, which varied in concavity and the morphology of a stress concentrating cusp, to break a shell. We created functionally identical copies of two intertidal snail shells: the thicker shelled Nucella ostrina and...

Data from: A hybrid phylogenetic–phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification

Adam D. Leaché, Philipp Wagner, Charles W. Linkem, Wolfgang Böhme, Theodore J. Papenfuss, Rebecca A. Chong, Brian R. Lavin, Aaron M. Bauer, Stuart V. Nielsen, Eli Greenbaum, Mark-Oliver Rödel, Andreas Schmitz, Matthew LeBreton, Ivan Ineich, Laurent Chirio, Caleb Ofori-Boateng, Edem A. Eniang, Sherif Baha El Din, Alan R. Lemmon & Frank T. Burbrink
Africa is renowned for its biodiversity and endemicity, yet little is known about the factors shaping them across the continent. African Agama lizards (45 species) have a pan-continental distribution, making them an ideal model for investigating biogeography. Many species have evolved conspicuous sexually dimorphic traits, including extravagant breeding coloration in adult males, large adult male body sizes, and variability in social systems among colorful versus drab species. We present a comprehensive time-calibrated species tree for...

Data from: A revised design for microarray experiments to account for experimental noise and uncertainty of probe response

Alex E. Pozhitkov, Peter A. Noble, Jaroslaw Bryk, Diethard Tautz & Jarosław Bryk
Background: Although microarrays are analysis tools in biomedical research, they are known to yield noisy output that usually requires experimental confirmation. To tackle this problem, many studies have developed rules for optimizing probe design and devised complex statistical tools to analyze the output. However, less emphasis has been placed on systematically identifying the noise component as part of the experimental procedure. One source of noise is the variance in probe binding, which can be assessed...

Data from: Species delimitation using genome-wide SNP data

Adam D. Leaché, Vladimir N. Minin, Remco R. Bouckaert & Matthew K. Fujita
The multispecies coalescent has provided important progress for evolutionary inferences, including increasing the statistical rigor and objectivity of comparisons among competing species delimitation models. However, Bayesian species delimitation methods typically require brute force integration over gene trees via Markov chain Monte Carlo (MCMC), which introduces a large computation burden and precludes their application to genomic-scale data. Here we combine a recently introduced dynamic programming algorithm for estimating species trees that bypasses MCMC integration over gene...

Data from: The effects of Medieval dams on genetic divergence and demographic history in brown trout populations

Michael M. Hansen, Morten T. Limborg, Anne-Laure Ferchaud & Jose-Martin Pujolar
Background: Habitat fragmentation has accelerated within the last century, but may have been ongoing over longer time scales. We analyzed the timing and genetic consequences of fragmentation in two isolated lake-dwelling brown trout populations. They are from the same river system (the Gudenå River, Denmark) and have been isolated from downstream anadromous trout by dams established ca. 600-800 years ago. For reference, we included ten other anadromous populations and two hatchery strains. Based on analysis...

Data from: The role of mitochondrial introgression in illuminating the evolutionary history of Nearctic treefrogs

, Brian Tilston Smith, Adrian Nieto-Montes De Oca, Uri Omar Garcia-Vazquez, Brett R. Riddle & Robert W. Bryson
Inferring the evolutionary history of lineages often becomes difficult when gene histories are in conflict with each other. Introgression, for example, can cause DNA sequences from one species to be more similar to sequences of a different species and lead to incongruence amongst gene trees. However, incorporating congruent and incongruent locus-specific phylogenetic estimates with the geographical distribution of lineages may provide valuable insight into evolutionary processes important to speciation. In this study, we investigated mitochondrial...

Data from: Signals of heterogeneous selection at an MHC locus in geographically proximate ecotypes of sockeye salmon

Wesley A. Larson, James E. Seeb, Tyler H. Dann, Daniel E. Schindler & Lisa W. Seeb
The genes of the major histocompatibility complex (MHC) are an important component of the vertebrate immune system and can provide insights into the role of pathogen-mediated selection in wild populations. Here we examined variation at the MHC class II peptide binding region in 27 populations of sockeye salmon (Oncorhynchus nerka), distributed among three distinct spawning ecotypes, from a complex of interconnected rivers and lakes in southwestern Alaska. We also obtained genotypes from 90 putatively neutral...

Data from: Phylogenomic resolution of the Hemichordate and Echinoderm clade

Johanna T. Cannon, Kevin M. Kocot, Damien S. Waits, David A. Weese, Billie J. Swalla, Scott R. Santos & Kenneth M. Halanych
Ambulacraria, comprising Hemichordata and Echinodermata, is closely related to Chordata, making it integral to understanding chordate origins and polarizing chordate molecular and morphological characters. Unfortunately, relationships within Hemichordata and Echinodermata have remained unresolved, compromising our ability to extrapolate findings from the most closely related molecular and developmental models outside of Chordata (e.g., the acorn worms Saccoglossus kowalevskii and Ptychodera flava and the sea urchin Strongylocentrotus purpuratus). To resolve long-standing phylogenetic issues within Ambulacraria, we sequenced...

Data from: Practical performance of tree comparison metrics

Mary K. Kuhner, Jon A. Yamato & Jon Yamato
The phylogenetic literature contains numerous measures for assessing differences between two phylogenetic trees. Individual measures have been criticized on various grounds, but little is known about their comparative performance in typical applications. We evaluate the performance of nine tree distance measures on two tasks: (1) distinguishing trees separated by lesser versus greater numbers of recombinations, and (2) distinguishing trees inferred with lower versus higher quality data. We find that when the trees being compared are...

Data from: \"Comparative genomic resources for spiny lizards (genus Sceloporus)\" in Genomic Resources Notes accepted 1 August 2014-30 September 2014

Rebecca B. Harris & Adam D. Leaché
To advance comparative genomic studies of the spiny fence lizards (genus Sceloprous), we provide the genomic annotations for 35 Sceloporus species.

Data from: Octopaminergic modulation of the visual flight speed regulator of Drosophila

Floris Van Breugel, Marie P. Suver & Michael H. Dickinson
Recent evidence suggests that flies' sensitivity to large-field optic flow is increased by the release of octopamine during flight. This increase in gain presumably enhances visually mediated behaviors such as the active regulation of forward speed, a process that involves the comparison of a vision-based estimate of velocity with an internal set point. To determine where in the neural circuit this comparison is made, we selectively silenced the octopamine neurons in the fruit fly Drosophila,...

Data from: Parallel signatures of selection in temporally-isolated lineages of pink salmon

Lisa W. Seeb, Ryan K. Waples, Morten T. Limborg, Kenneth I. Warheit, Carita E. Pascal & Jim E. Seeb
Studying the effect of similar environments on diverse genetic backgrounds has long been a goal of evolutionary biologists with studies typically relying on experimental approaches. Pink salmon, a highly-abundant and widely-ranging salmonid, provide a naturally-occurring opportunity to study the effects of similar environments on divergent genetic backgrounds due to a strict two-year semelparous life-history. The species is composed of two reproductively-isolated lineages with overlapping ranges that share the same spawning and rearing environments in alternate...

Registration Year

  • 2014
    24

Resource Types

  • Dataset
    24

Affiliations

  • University of Washington
    24
  • University of Michigan-Ann Arbor
    2
  • University of Queensland
    2
  • National Autonomous University of Mexico
    2
  • University of Oxford
    2
  • Georgia College & State University
    2
  • Baylor University
    1
  • Bond University
    1
  • University of California System
    1
  • Oregon State University
    1