40 Works

Transforming Metadata into Linked Data to Improve Digital Collection Discoverability: A CONTENTdm Pilot Project

Greta Bahnemann, Michael J. Carroll, Paul Clough, Mario Einaudi, Chatham Ewing, Jeff Mixter, Jason Roy, Holly Tomren, Bruce Washburn & Elliot Williams

Data from: Fine-Scale Mapping of Recombination Rate in Drosophila Refines its Correlation to Diversity and Divergence

R. J. Kulathinal, S. M. Bennett, C. L. Fitzpatrick & Mohamed A. F. Noor
Regional rates of recombination often correlate with levels of nucleotide diversity, and either selective or neutral hypotheses can explain this relationship. Regional recombination rates also correlate with nucleotide differences between human and chimpanzee, consistent with models where recombination is mutagenic; however, a lack of correlation is observed in the Drosophila melanogaster group, consistent with models invoking natural selection. Here, we revisit the relationship among recombination, diversity, and interspecies difference by generating empirical estimates of these...

Data from: Inbreeding depression and drift load in small populations at demographic disequilibrium

Rachel B. Spigler, Konstantinos Theodorou & Shu-Mei Chang
Inbreeding depression is a major driver of mating system evolution and has critical implications for population viability. Theoretical and empirical attention has been paid to predicting how inbreeding depression varies with population size. Lower inbreeding depression is predicted in small populations at equilibrium, primarily due to higher inbreeding rates facilitating purging and/or fixation of deleterious alleles (drift load), but predictions at demographic and genetic disequilibrium are less clear. In this study, we experimentally evaluate how...

Data from: Neurotrophins induce fission of mitochondria along embryonic sensory axons

Gianluca Gallo
Neurotrophins are growth factors that have a multitude of roles in the nervous system. We report that neurotrophins induce the fission of mitochondria along embryonic chick sensory axons driven by combined PI3K and Mek-Erk signaling. Following an initial burst of fission a new steady state of neurotrophin-dependent mitochondria length is established. Mek-Erk controls the activity of the fission mediator Drp1 GTPase, while PI3K may contribute to the actin dependent aspect of fission. Drp1-mediated fission is...

Data from: Experimental study of species invasion – early population dynamics and role of disturbance in invasion success

David Reznick, Sebastiano De Bona, Andres Lopez-Sepulcre, Mauricio Torres, Ronald Bassar, Paul Bentzen & Joseph Travis
Much of our understanding of natural invasions is retrospective, based on data acquired after invaders become established. As a consequence, we know little about the characteristics of the early population growth and habitat use of the invaders during establishment. Here we report on experimental introductions of guppies into natural streams in which we conducted monthly censuses of each population. Two of the four introductions were in streams with thinned canopies, which mimics a common form...

Robert R. Blake, With Recognition of Jane S. Mouton

Deborah Cai, Edward Fink & Cameron Walker

Public Shaming and Attacks on Social Media: The Case of White Evangelical Christians

Deborah Cai & Colleen Tollen

Data from: Temporal and gefitinib-sensitive regulation of cardiac cytokine expression via chronic β-adrenergic receptor stimulation

Laurel A. Grisanti, Ashley A. Repas, Jennifer A. Talarico, Jessica I. Gold, Rhonda L. Carter, Walter J. Koch & Douglas G. Tilley
Chronic stimulation of β-adrenergic receptors (βAR) can promote survival signaling via transactivation of epidermal growth factor receptor (EGFR), but ultimately alters cardiac structure and contractility over time, in part via enhanced cytokine signaling. We hypothesized that chronic catecholamine signaling will have a temporal impact on cardiac transcript expression in vivo, in particular cytokines, and that EGFR transactivation plays a role in this process. C57BL/6 mice underwent infusion with vehicle or isoproterenol (Iso) ± gefitinib (Gef)...

Predation shapes invertebrate diversity in tropical but not temperate seagrass communities

Amy Freestone, Elizabeth Carroll, Katherine Papacostas, Gregory Ruiz, Mark Torchin & Brent Sewall
1. The hypothesis that biotic interactions are stronger at lower relative to higher latitudes has a rich history, drawing from ecological and evolutionary theory. While this hypothesis suggests that stronger interactions at lower latitudes may contribute to the maintenance of contemporary patterns of diversity, there remain few standardized biogeographic comparisons of community effects of species interactions. 2. Using marine seagrasses as a focal ecosystem of conservation importance and sessile marine invertebrates as model prey, we...

Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches

Beatriz Mello, Qiqing Tao, Jose Barba-Montoya & Sudhir Kumar
Simultaneous molecular dating of population and species divergences is essential in many biological investigations, including phylogeography, phylodynamics, and species delimitation studies. In these investigations, multiple sequence alignments consist of both intra- and inter-species samples (mixed samples). As a result, the phylogenetic trees contain inter-species, inter-population, and within-population divergences. Bayesian relaxed clock methods are often employed in these analyses, but they assume the same tree prior for both inter- and intra-species branching processes and require specification...

Data from: On the occurrence of false positives in tests of migration under an isolation with migration model

Jody Hey, Yujin Chung & Arun Sethuraman
The population genetic study of divergence is often carried out using a Bayesian genealogy sampler, like those implemented in ima2 and related programs, and these analyses frequently include a likelihood ratio test of the null hypothesis of no migration between populations. Cruickshank and Hahn (2014, Molecular Ecology, 23, 3133–3157) recently reported a high rate of false-positive test results with ima2 for data simulated with small numbers of loci under models with no migration and recent...

Data from: β-adrenergic receptor-dependent alterations in murine cardiac transcript expression are differentially regulated by gefitinib in vivo

Jennifer A. Talarico, Rhonda L. Carter, Laurel A. Grisanti, Justine E. Yu, Ashley A. Repas & Douglas G. Tilley
β-adrenergic receptor (βAR)-mediated transactivation of epidermal growth factor receptor (EGFR) has been shown to promote cardioprotection in a mouse model of heart failure and we recently showed that this mechanism leads to enhanced cell survival in part via regulation of apoptotic transcript expression in isolated primary rat neonatal cardiomyocytes. Thus, we hypothesized that this process could regulate cardiac transcript expression in vivo. To comprehensively assess cardiac transcript alterations in response to acute βAR-dependent EGFR transactivation,...

¡Que viva la música! Repaso de conversación en español

Norma Corrales-Martin

Data from: Changes in spatial variance during a grassland to shrubland state transition

Zak Ratajczak, Paolo D'Odorico, Jesse B. Nippert, Scott L. Collins, Nathaniel A. Brunsell & Sujith Ravi
State transitions are changes in ecosystem structure and self-reinforcing feedbacks that are initiated when an exogenous driver variable crosses a threshold. Reversing state transitions is difficult and costly. While some state transitions are relatively rapid, many take years to decades. Outside of theoretical models, very little is known about slower state transitions and how they unfold in time and space. We quantified changes in spatial variance as a mesic grassland ecosystem shifts to a shrub-dominated...

Data from: Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: new approaches to long-standing problems

Andrea M. Quattrini, Brant C. Faircloth, Luisa F. Dueñas, Thomas C.L. Bridge, Mercer R. Brügler, Ivan F. Calixto-Botía, Danielle M. DeLeo, Sylvain Foret, Santiago Herrera, Simon M.Y. Lee, David J. Miller, Carlos Prada, Gandhi Rádis-Baptista, Catalina Ramírez-Portilla, Juan A. Sánchez, Estefania Rodriguez, Catherine S. McFadden, Tom C. L. Bridge & Simon M. Y. Lee
Anthozoans (e.g., corals, anemones) are an ecologically important and diverse group of marine metazoans that occur from shallow to deep waters worldwide. However, our understanding of the evolutionary relationships among the ~7500 species within this class is hindered by the lack of phylogenetically informative markers that can be reliably sequenced across a diversity of taxa. We designed and tested 16,308 RNA baits to capture 720 Ultraconserved Element loci and 1,071 exon loci. Library preparation and...

Data from: Niche divergence by deep-sea octocorals in the genus Callogorgia across the continental slope of the Gulf of Mexico

Andrea M. Quattrini, Samuel E. Georgian, Luke Byrnes, Alex Stevens, Rosalia Falco & Erik E. Cordes
Environmental variables that are correlated with depth have been suggested to be among the major forces underlying speciation in the deep sea. This study incorporated phylogenetics and ecological niche models (ENM) to examine whether congeneric species of Callogorgia (Octocorallia: Primnoidae) occupy different ecological niches across the continental slope of the Gulf of Mexico (GoM), and whether this niche divergence could be important in the evolution of these closely related species. Callogorgia americana americana, C. americana...

Data from: A highly social, land-dwelling fish defends territories in a constantly fluctuating environment

Terry J. Ord & Shi-Tong Tonia Hsieh
The Pacific leaping blenny (Alticus arnoldorum) is a marine fish that has made a highly successful transition to land. We report an extensive field study on the behavior of this remarkable fish and how it has coped with life on land. The fish occurs in great abundance above the waterline along the rocky coastlines of Micronesia. We found them to be terrestrial in all aspects of their adult daily life, but heavily constrained by large...

Datasets for Comparison of methods for estimating omnidirectional landscape connectivity

Melissa Clark, Payton Phillips, Suraj Baral, Erin Koen & Jeff Bowman
This repository holds the raster data and the configuration files (.ini) files used to create the simulated resistance grids and omnidirectional connectivity methods in "Comparison of methods for estimating omnidirectional landscape connectivity". There are reisstance grids for each of the two sections (simulated resistance grids and omnidirectional connectivity methods) and .ini files for each run with each method (point, wall-to-wall, and omniscape. The .ini files can be run in Julia computing language. Ecological connectivity is...

Habitat suitability modeling to predict the spatial distribution of cold-water coral communities affected by the Deepwater Horizon oil spill

Samuel Georgian, Kody Kramer, Miles Saunders, William Shedd, Harry Roberts, Christopher Lewis, Chuck Fisher & Erik Cordes
Aim: The Deepwater Horizon disaster resulted in the largest accidental marine oil spill in history and caused extensive injury to deep-sea habitats, including cold-water coral communities dominated by Paramuricea species. One of the primary difficulties in assessing the full extent of the injury to cold-water coral ecosystems is the extreme paucity of observational data and the subsequent lack of knowledge of their distribution within the affected region. The aim of this study was to use...

Data from: Conformational dynamics in TRPV1 channels reported by an encoded coumarin amino acid

Ximena Steinberg, Marina A. Kasimova, Deny Cabezas-Bratesco, Jason D. Galpin, Ernesto Ladron-De-Guevara, Federica Villa, Vincenzo Carnevale, Leon Islas, Christopher A. Ahern & Sebastian E Brauchi
TRPV1 channels support the detection of noxious and nociceptive input. Currently available functional and structural data suggest that TRPV1 channels have two gates within their permeation pathway: one formed by a ′bundle-crossing′ at the intracellular entrance and a second constriction at the selectivity filter. To describe conformational changes associated with channel gating, the fluorescent non-canonical amino acid coumarin-tyrosine was genetically encoded at Y671, a residue proximal to the selectivity filter. Total internal reflection fluorescence microscopy...

Data from: Testing the depth-differentiation hypothesis in a deepwater octocoral

Andrea M. Quattrini, Iliana B. Baums, Timothy M. Shank, Cheryl L. Morrison & Erik E. Cordes
The depth-differentiation hypothesis proposes that the bathyal region is a source of genetic diversity and an area where there is a high rate of species formation. Genetic differentiation should thus occur over relatively small vertical distances, particularly along the upper continental slope (200–1000 m) where oceanography varies greatly over small differences in depth. To test whether genetic differentiation within deepwater octocorals is greater over vertical rather than geographical distances, Callogorgia delta was targeted. This species...

Data from: A multispecies coalescent model for quantitative traits

Fabio K. Mendes, Jesualdo A. Fuentes-González, Joshua G. Schraiber & Matthew W. Hahn
We present a multispecies coalescent model for quantitative traits that allows for evolutionary inferences at micro- and macroevolutionary scales. A major advantage of this model is its ability to incorporate genealogical discordance underlying a quantitative trait. We show that discordance causes a decrease in the expected trait covariance between more closely related species relative to more distantly related species. If unaccounted for, this outcome can lead to an overestimation of a trait's evolutionary rate, to...

Data from: Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy

Philip Lei Tzou, Soo-Yon Rhee, Sergei L. Kosakovsky Pond, Justen Manasa & Robert W. Shafer
Most HIV-1-infected individuals with virological failure (VF) on a pharmacologically-boosted protease inhibitor (PI)-containing regimen do not develop PI-resistance protease mutations. One proposed explanation is that mutations in HIV-1 gag or gp41 cytoplasmic domain might also reduce PI susceptibility. In a recent study of paired gag and gp41 sequences from individuals with VF on a PI-containing regimen, we did not identify PI-selected mutations and concluded that if such mutations existed, larger numbers of paired sequences from...

Data from: Global mammal betadiversity show parallel assemblage structure in similar but isolated environments

Caterina Penone, Ben G. Weinstein, Catherine H. Graham, Thomas M. Brooks, Carlo Rondinini, S. Blair Hedges, Ana D. Davidson & Gabriel C. Costa
The taxonomic, phylogenetic and trait dimensions of betadiversity each provide unique insight into the importance of historical isolation and environmental conditions in shaping global diversity. These three dimensions should, in general, be positively correlated. However, if similar environmental conditions filter species with similar trait values, then assemblages located in similar environmental conditions, but separated by large dispersal barriers, may show high taxonomic, high phylogenetic, but low trait betadiversity. Conversely, we expect lower phylogenetic diversity but...

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