353 Works

Bidisperse sphere packs generated under gravity

Abhishek Bihani & Hugh Daigle
Bidisperse sphere packs were generated under the effect of gravity to model mudrocks and study the petrophysical properties consisting of small (clay) and large (silt) grains. Multiple, periodic, dense, bidisperse sphere packs were created with large grain volume concentrations (VL) increasing from 0 to 100 %. This was done for large to small grain radius ratios of 2:1, 5:1, 7:1, and 10:1 with constant sphere pack length 10 units in x, y, z directions. The...

Guelph dolomite

Hasan Khan & Gary Pope
Medical CT scans of Guelph dolomite for fracture characterization. The core was imaged in Department of Petroleum and Geosystems Engineering, UT Austin.

Pore scale study of water adsorption and subsequent methane transport in clay in the presence of wettability heterogeneity

Rui Xu, Masa Prodanovic & Christopher Landry

Seismogenesis at Hikurangi Integrated Research Experiment (SHIRE) onshore seismic acquisition field report

Katie Jacobs, Stuart A Henrys, D Okaya, H Van Avendonk, Jenny Black, Dan H. N. Barker, Sapthala C Karalliyadda, E Kurashimo, Wanda R. Stratford, M Savage, R Sullivan, Zane R. Bruce & L Hughes
This report documents the acquisition and archiving of a major controlled source and passive seismic imaging project, the Seismogenesis Hikurangi Integrated Research Experiment (SHIRE). The SHIRE project aims to identify and quantify factors controlling the long-term evolution of the Hikurangi margin and the mode of slip along the subduction megathrust. The components of the data volume were acquired in two phases; between October 2017 – April 2018 (SHIRE I) and February–March 2019 (SHIRE II). The...

A Positive Spin on a Negative Narrative: How the Media Portrays Fraternities and What Fraternities Can Do About It

Zachary Taylor, Jennifer Zamora, Arianne McArdle & Mario Villa

Reversible diffusion-weighted imaging lesions in acute ischemic stroke: a systematic review

Nandakumar Nagaraja, John Forder, Steven Warach & Jośe Merino
Supplemental data: NNagaraja_12292019_DWI_Reversal_In_AIS_Review_Supplemental_File Supplemental Figure e-1: DWI reversal in acute ischemic stroke Supplemental Table e-1: Search Strategy Supplemental Table e-2: Variables extracted for the review Supplemental Table e-3: Imaging protocols for included studies Supplemental Table e-4: DWIR definitions used in the selected studies Supplemental Table e-5: Imaging characteristics of patients Supplemental Table e-6: QUADAS-2 tool for quality assessment of diagnostic accuracy studies by evaluating risk of bias and applicability concerns.

Ferrofluid displacement in a simple 2.5D micromodel

Ningyu Wang, Yifei Liu, Luming Cha, Masa Prodanovic & Matthew Balhoff
The dataset contains a series of images of a varying-depth converging-diverging single-channel micromodel during ferrofluid flooding without and then with an external magnetic field. One image shows the initial oil saturation after ferrofluid flooding without a magnetic field, and twelve images show the oil saturation after the magnetic field was turned on. Only eight pores in the flow channel are shown in these images, while there are more than 100 pores in the flow channel....

Data from: Stronger selective constraint on downstream genes in the oxidative phosphorylation pathway of cetaceans

Ran Tian, Shixia Xu, Simin Chai, Daiqing Yin, Harold Zakon & Guang Yang
The oxidative phosphorylation (OXPHOS) pathway is an efficient way to produce energy via adenosine triphosphate (ATP), which is critical for sustaining an energy supply for cetaceans in a hypoxic environment. Several studies have shown that natural selection may shape the evolution of the genes involved in OXPHOS. However, how network architecture drives OXPHOS protein sequence evolution remains poorly explored. Here, we investigated the evolutionary patterns of genes in the OXPHOS pathway across six cetacean genomes...

Data from: Effects of founding genetic variation on adaptation to a novel resource

Deepa Agashe, Jay J Falk & Daniel I Bolnick
Population genetic theory predicts that adaptation in novel environments is enhanced by genetic variation for fitness. However, theory also predicts that under strong selection, demographic stochasticity can drive populations to extinction before they can adapt. We exposed wheat-adapted populations of the flour beetle (Tribolium castaneum) to a novel suboptimal corn resource, to test the effects of founding genetic variation on population decline and subsequent extinction or adaptation. As previously reported, genetically diverse populations were less...

Data from: Geographic determinants of gene flow in two sister species of tropical Andean frogs

Carlos E. Guarnizo & David C. Cannatella
Complex interactions between topographic heterogeneity, climatic and environmental gradients, and thermal niche conservatism are commonly assumed to indicate the degree of biotic diversification in montane regions. Our aim was to investigate factors that disrupt gene flow between populations and to determine if there is evidence of downslope asymmetric migration in highland frogs with wide elevational ranges and thermal niches. We determined the role of putative impediments to gene flow (as measured by least-cost path (LCP)...

Data from: Phenotypic plasticity drives a depth gradient in male conspicuousness in threespine stickleback, Gasterosteus aculeatus

Chad D. Brock, Molly E. Cummings & Daniel I. Bolnick
Signal evolution is thought to depend on both a signal's detectability or conspicuousness (signal design) as well as any extractable information it may convey to a potential receiver (signal content). While theoretical and empirical work in sexual selection has largely focused on signal content, there has been a steady accrual of evidence that signal design is also important for trait evolution. Despite this, relatively little attention has been paid to spatial variation in the conspicuousness...

Data from: Ontogenetic stage-specific quantitative trait loci contribute to divergence in developmental trajectories of sexually dimorphic fins between medaka populations

Maiko Kawajiri, Kohta Yoshida, Shingo Fujimoto, Daniel Frikli Mokodongan, Mark Ravinet, Mark Kirkpatrick, Kazunori Yamahira & Jun Kitano
Sexual dimorphism can evolve when males and females differ in phenotypic optima. Genetic constraints can, however, limit the evolution of sexual dimorphism. One possible constraint is derived from alleles expressed in both sexes. Because males and females share most of their genome, shared alleles with different fitness effects between sexes are faced with intralocus sexual conflict. Another potential constraint is derived from genetic correlations between developmental stages. Sexually dimorphic traits are often favoured at adult...

Data from: Best practices for justifying fossil calibrations

James F. Parham, Philip C. J. Donoghue, Christopher J. Bell, Tyler D. Calway, Jason J. Head, Patricia A. Holroyd, Jun G. Inoue, Randall B. Irmis, Walter G. Joyce, Daniel T. Ksepka, José S. L. Patané, Nathan D. Smith, James E. Tarver, Marcel Van Tuinen, Ziheng Yang, Kenneth D. Angielczyk, Jenny M. Greenwood, Christy A. Hipsley, Jacobs Louis, Peter J. Makovicky, Johannes Müller, Krister T. Smith, Jessica M. Theodor, Rachel C. M. Warnock, Michael J. Benton … & Louis Jacobs
Our ability to correlate biological evolution with climate change, geological evolution, and other historical patterns is essential to understanding the processes that shape biodiversity. Combining data from the fossil record with molecular phylogenetics represents an exciting synthetic approach to this challenge. The first molecular divergence dating analysis (Zuckerkandl and Pauling 1962) was based on a measure of the amino acid differences in the hemoglobin molecule; with replacement rates established (calibrated) using inaccurate paleontological age estimates...

IS-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria

Jessika Consuegra, Joël Gaffé, Richard E. Lenski, Thomas Hindre, Jeffrey E. Barrick, Olivier Tenaillon & Dominique Schneider
The long-term dynamics of IS elements and their effects on bacteria are poorly understood, including whether they are primarily genomic parasites or important drivers of adaptation by natural selection. Here, we investigate the dynamics of IS elements and their contribution to genomic evolution and fitness during a long-term experiment with Escherichia coli. This data set includes the Rmd file to analyze the genomic and metagenomic data (Tenaillon et al. 2016 and Good et al. 2017)...

F2R polymorphisms and clopidogrel efficacy and safety in patients with minor stroke or TIA: supplemental figures and tables

Yuesong Pan, Runqi Wangqin, Hao Li, Yilong Wang, Xia Meng, S. Claiborne Johnston, Tabassome Simon, Jinxi Lin, Xingquan Zhao, Liping Liu, David Wang & Yongjun Wang
Objective: To investigate the association between protease-activated receptors-1 (PAR-1) gene F2R polymorphisms and efficacy of clopidogrel for minor stroke or transient ischemic attack (TIA). Methods: Three single-nucleotide polymorphisms (CYP2C19*2 [681G>A, rs4244285], CYP2C19*3 [636G>A, rs4986893] and F2R [IVSn-14 A/T, rs168753] were genotyped among 2,924 patients randomized to clopidogrel plus aspirin (n=1461) or aspirin alone (n=1463). The primary efficacy outcome was new stroke (ischemic or hemorrhagic) and the safety outcome was any bleeding. Results: Overall, 859(29.4%) were...

Data for: Landscape scale variation in the hydrologic niche of California coast redwood

Emily J. Francis, Gregory P. Asner, Katharine J. Mach & Christopher B. Field
Topoclimatic diversity within forest landscapes can underlie variation in water availability, which may correspond to patterns in habitat suitability of tree species with differing hydrologic niches. However, the trade-off between the collection of data at a fine grain size over large spatial extents has limited comprehensive analyses of landscape scale variation in habitat suitability. We present a fine scale analysis of the roles of topographic gradients in moisture availability, soil water storage, and fog frequency...

Combined-evidence analyses of ultraconserved elements and morphological data: an empirical example in iguanian lizards

Simon Scarpetta
Genomic datasets generated by next-generation sequencing are increasingly prevalent in phylogenetics, but morphological data are required to phylogenetically place fossils, corroborate molecular hypotheses, and date phylogenies. Combined-evidence analyses provide an integrative assessment of tree topology. However, no attempt has been made to simultaneously analyze next-generation genomic datasets and morphological data, and the future of morphology in the context of genomic data is uncertain. I conducted combined-evidence analyses that include genomic and morphological datasets, specifically, with...

Contrasting responses to climate change at Himalayan treelines revealed by population demographics of two dominant species

Kumar Mainali, Bharat Shrestha, Ravi Sharma, Arjun Adhikari, Eliezer Gurarie, Michael Singer & Camille Parmesan
Alpine treelines are expected to shift upward due to recent climate change. However, interpretation of changes in montane systems has been problematic because effects of climate change are frequently confounded with those of land use changes. The eastern Himalaya, particularly Langtang National Park, Central Nepal, has been relatively undisturbed for centuries and thus presents an opportunity for studying climate change impacts on alpine treeline uncontaminated by potential confounding factors. We studied two dominant species, Abies...

Ice-age persistence and genetic isolation of the disjunct distribution of larch in Alaska

Joseph Napier, Matias Fernandez, Guillaume De Lafontaine & Feng Sheng Hu
Larix laricina (eastern larch, tamarack) is a transcontinental North American conifer with a prominent disjunction in the Yukon isolating the Alaskan distribution from the rest of its range. We investigate whether in situ persistence during the Last Glacial Maximum (LGM) or long-distance postglacial migration from south of the ice sheets resulted in the modern-day Alaskan distribution. We analyzed variation in three chloroplast DNA regions of 840 trees from a total of 69 populations (24 new...

Season of prescribed fire determines grassland restoration outcomes after fire exclusion and overgrazing

Erin N. Novak, Michelle Bertelsen, Dick Davis, Devin M. Grobert, Kelly G. Lyons, Jason P. Martina, W. Matt McCaw, Matthew O'Toole & Joseph W. Veldman
Fire exclusion and mismanaged grazing are globally important drivers of environmental change in mesic C4 grasslands and savannas. Although interest is growing in prescribed fire for grassland restoration, we have little long-term experimental evidence of the influence of burn season on the recovery of herbaceous plant communities, encroachment by trees and shrubs, and invasion by exotic grasses. We conducted a prescribed fire experiment (seven burns between 2001 and 2019) in historically fire-excluded and overgrazed grasslands...

No sex differences in learning in wild bumblebees

Felicity Muth
Females and males often face different sources of selection, resulting in dimorphism in morphological, physiological, and even cognitive traits. Sex differences are often studied in respect to spatial cognition, yet the different ecological roles of males and females might shape cognition in multiple ways. For example, in dietary generalist bumblebees (Bombus), the ability to learn associations is critical to female workers, who face informationally-rich foraging scenarios as they collect nectar and pollen from thousands of...

Data from: A genomic approach for distinguishing between recent and ancient admixture as applied to cattle

Emily Jane McTavish & David M. Hillis
Genomic data facilitate opportunities to track complex population histories of divergence and gene flow. We developed a metric, scaled block size (SBS), that uses the unrecombined block size of introgressed regions of chromosomes to differentiate between recent and ancient admixture, and applied it to reconstructing admixture in cattle. Cattle are descendants of two independently domesticated lineages, taurine and indicine, that diverged 200,000 or more years ago. Several breeds have hybrid ancestry between these divergent lineages....

Data from: Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments

Holly M. Bik, Way Sung, Paul De Ley, James G. Baldwin, Jyotsna Sharma, Axayácatl Rocha-Olivares & W. Kelley Thomas
Microbial eukaryotes (nematodes, protists, fungi, etc., loosely referred to as meiofauna) are ubiquitous in marine sediments and likely play pivotal roles in maintaining ecosystem function. Although the deep-sea benthos represents one of the world’s largest habitats, we lack a firm understanding of the biodiversity and community interactions amongst meiobenthic organisms in this ecosystem. Within this vast environment key questions concerning the historical genetic structure of species remain a mystery, yet have profound implications for our...

Data from: How bird clades diversify in response to climatic and geographic factors

Genoveva Rodriguez-Castaneda, Anouschka R. Hof & Roland Jansson
While the environmental correlates of global patterns in standing species richness are well understood, it is poorly known which environmental factors promote diversification (speciation minus extinction) in clades. We tested several hypotheses for how geographic and climatic variables should affect diversification using a large dataset of bird sister genera endemic to the New World. We found support for the area, evolutionary speed, environmental predictability and climatic stability hypotheses, but productivity and topographic complexity were rejected...

Data from: Partitioning the effects of isolation by distance, environment, and physical barriers on genomic divergence between parapatric threespine stickleback

Jesse N. Weber, Gideon S. Bradburd, Yoel E. Stuart, William E. Stutz & Daniel I. Bolnick
Genetic divergence between populations is shaped by a combination of drift, migration, and selection, yielding patterns of isolation-by-distance (IBD) and isolation-by-environment (IBE). Unfortunately, IBD and IBE may be confounded when comparing divergence across habitat boundaries. For instance, parapatric lake and stream threespine stickleback (Gasterosteus aculeatus) may have diverged due to selection against migrants (IBE), or mere spatial separation (IBD). To quantitatively partition the strength of IBE and IBD, we used recently-developed population genetic software (BEDASSLE)...

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  • The University of Texas at Austin
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  • Smithsonian Tropical Research Institute