25 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...

Data from: Repeatability of adaptive radiation depends on spatial scale: regional versus global replicates of stickleback in lake versus stream habitats

Antoine Paccard, Dieta Hanson, Yoel E Stuart, Frank A Von Hippel, Martin Kalbe, Tom Klepaker, Skúli Skúlason, Bjarni K Kristjánsson, Daniel I Bolnick, Andrew P Hendry & Rowan D H Barrett
The repeatability of adaptive radiation is expected to be scale dependent, with determinism decreasing as greater spatial separation among “replicates” leads to their increased genetic and ecological independence. Threespine stickleback (Gasterosteus aculeatus) provide an opportunity to test whether this expectation holds for the early stages of adaptive radiation -their diversification in freshwater ecosystems has been replicated many times. To better understand the repeatability of that adaptive radiation, we examined the influence of geographic scale on...

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...

Data from: The multispecies coalescent over-splits species in the case of geographically widespread taxa

E. Anne Chambers & David M. Hillis
Many recent species delimitation studies rely exclusively on limited analyses of genetic data analyzed under the multispecies coalescent (MSC) model, and results from these studies often are regarded as conclusive support for taxonomic changes. However, most MSC-based species delimitation methods have well-known and often unmet assumptions. Uncritical application of these genetic-based approaches (without due consideration of sampling design, the effects of a priori group designations, isolation by distance, cytoplasmic–nuclear mismatch, and population structure) can lead...

Utilizing field collected insects for next generation sequencing: effects of sampling, storage, and DNA extraction methods

Kimberly Ballare, Nathaniel Pope, Antonio Castilla, Sarah Cusser, Richard Metz & Shalene Jha
DNA sequencing technologies continue to advance the biological sciences, expanding opportunities for genomic studies of non-model organisms for basic and applied questions. Despite these opportunities, many next-generation sequencing protocols have been developed assuming a substantial quantity of high molecular weight DNA (>100 ng), which can be difficult to obtain for many study systems. In particular, the ability to sequence field-collected specimens that exhibit varying levels of DNA degradation remains largely unexplored. In this study we...

Explaining illness with evil: Pathogen prevalence fosters moral vitalism

Brock Bastian, Christin-Melanie Vauclair, Steve Loughnan, Paul Bain, Ashwini Ashokkumar, Maja Becker, Michal Bilewicz, Emma Collier-Baker, Carla Crespo, Paul W. Eastwick, Ronald Fischer, Malte Friese, Ángel Gómez, Valeschka M. Guerra, Jose Luis Castellanos Guevara, Katja Hanke, Nic Hooper, Li-Li Huang, Shi Junqi, Minoru Karasawa, Peter Kuppens, Siri Leknes, Müjde Peker, Cesar Pelay, Afoditi Pina … & William B. Swann
Pathogens represent a significant threat to human health leading to the emergence of strategies designed to help manage their negative impact. We examined how spiritual beliefs developed to explain and predict the devastating effects of pathogens and spread of infectious disease. Analysis of existing data in Studies 1 and 2 suggests that moral vitalism (beliefs about spiritual forces of evil) is higher in geographical regions characterized by historical higher levels of pathogens. Furthermore, drawing on...

Spatial and temporal patterns in particle retention in vuggy porous media

Hasan Khan, Masa Prodanovic & David DiCarlo
Vuggy porous media with five different vug configurations are fabricated: no vug, single vug, two vugs in series, two vugs in parallel, and random distribution of vugs. Suspended glass beads (50 micron diameter and 1% vol/vol) are injected in the vuggy core and temporal CT scans are conducted.

Data from: Early Triassic benthic invertebrates from the Great Bank of Guizhou, South China: systematic palaeontology and palaeobiology

William J. Foster, Daniel J. Lehrmann, Jaime A. Hirtz, Mackenzie White, Meiyi Yu, Li Ji & Rowan C. Martindale
To further our understanding on the evolution, selectivity, and ecological composition of marine communities following the latest Permian mass extinction, new collections from underrepresented regions in the immediate extinction aftermath are required. Here, we provide new systematic data and the first palaeobiological account of the benthic invertebrate community from the Great Bank of Guizhou, South China. We systematically describe 3 brachiopod species, 26 bivalve species, 11 gastropod species, 1 microconchid, and 1 crinoid species. The...

Data from: Nocturnal giants: evolution of the sensory ecology in elephant birds and other palaeognaths inferred from digital brain reconstructions

Christopher R. Torres & Julia A. Clarke
The recently-extinct Malagasy elephant birds (Palaeognathae, Aepyornithiformes) included the largest birds that ever lived. Elephant bird neuroanatomy is understudied but can shed light on the lifestyle of these enigmatic birds. Paleoneurological studies can provide clues to the ecologies and behaviors of extinct birds because avian brain shape is correlated with neurological function. We digitally reconstruct endocasts of two elephant bird species, Aepyornis maximus and A. hildebrandti, and compare them with representatives of all major extant...

Data from: A growth-defense trade-off is general across native and exotic grasses

Robert W. Heckman, Fletcher W. Halliday & Charles E. Mitchell
High-resource environments typically favor quick-growing, poorly-defended plants, while resource-poor environments typically favor slow-growing, well-defended plants. The prevailing hypothesis explaining this pattern states that, as resource availability increases, well-defended, slow-growing species are replaced by poorly defended, fast-growing species. A second hypothesis states that greater resource availability increases allocation to growth at the expense of defense, within species. Regardless of mechanism, if exotic species are released from enemies relative to natives, shifts in allocation to growth and...

Data from: Development of an adrenocortical cancer humanized mouse model to characterize anti-PD1 effects on tumor microenvironment

Julie Lang, Anna Capasso, Kimberly R. Jordan, Jena D. French, Adwitiya Kar, Stacey M. Bagby, Jacob Barbee, Betelehem W. Yacob, Lia S. Head, Kenneth D. Tompkins, Brian M. Freed, Hilary Somerset, Toshimasa J. Clark, Todd M. Pitts, Well A. Messersmith, S. Gail Eckhardt, Margaret E. Wierman, Stephen Leong & Katja Kiseljak-Vassiliades
Context: While the development of immune checkpoint inhibitors has transformed treatment strategies of several human malignancies, research models to study immunotherapy in ACC are lacking. Objective: To explore the effect of anti-PD1 immunotherapy on the alteration of the immune milieu in ACC in a newly generated preclinical model and correlate with the response of the matched patient. Design, Setting and Intervention: To characterize the CU-ACC2-M2B patient-derived xenograft in a humanized mouse model, evaluate the effect...

A Test of the Repeatability of Measurements of Relative Fitness in the Long-Term Evolution Experiment with Escherichia coli

Jeffrey E. Barrick, Daniel E. Deatherage & Richard E. Lenski
Experimental studies of evolution using microbes have a long tradition, and these studies have increased greatly in number and scope in recent decades. Most such experiments have been short in duration, typically running for weeks or months. A venerable exception, the long-term evolution experiment (LTEE) with Escherichia coli has continued for 30 years and 70,000 bacterial generations. The LTEE has become one of the cornerstones of the field of experimental evolution, in general, and the...

Synthetic fractures with varying roughness and mineralogy

Javier E. Santos & Honggeun Jo
Synthetic fractures were created to quantify the effect of heterogeneity in surface roughness and mineralogy (which affects wettability) for multiphase flow. This project includes: 1) Rough fractures 2) Slits exhibiting different mineral shape (circles and bands) 3) A heterogeneously wet fracture The matlab codes to create the geometries can be found at: https://github.com/je-santos/syntheticFractures

Data from: Isolation by instability: historical climate change shapes population structure and genomic divergence of treefrogs in the Neotropical Cerrado savanna

Mariana M. Vasconcellos, Guarino R. Colli, Jesse N. Weber, Edgardo M. Ortiz, T. Rodrigues Miguel & David C. Cannatella
Although the impact of Pleistocene glacial cycles on the diversification of the tropical biota was once dismissed, increasing evidence suggests that Pleistocene climatic fluctuations greatly affected the distribution and population divergence of tropical organisms. Landscape genomic analyses coupled with paleoclimatic distribution models provide a powerful way to understand the consequences of past climate changes on the present-day tropical biota. Using genome-wide SNP data and mitochondrial DNA, combined with projections of the species distribution across the...

Data from: phenotools: an R package for visualizing and analyzing phenomic datasets

Chad M. Eliason, Scott V. Edwards & Julia A. Clarke
1.Phenotypic data is crucial for understanding genotype–phenotype relationships, assessing the tree of life, and revealing trends in trait diversity over time. Large‐scale description of whole organisms for quantitative analyses (phenomics) presents several challenges, and technological advances in the collection of genomic data outpace those for phenomic data. Reasons for this disparity include the time‐consuming and expensive nature of collecting discrete phenotypic data and mining previously‐published data on a given species (both often requiring anatomical expertise...

Data from: Species richness mediates within-species nutrient resorption: implications for the biodiversity-productivity relationship

Xiao-Tao Lü, Yan-Yu Hu, Amelia A. Wolf & Xingguo Han
1.Between-species variation in nutrient resorption is one of the mechanisms explaining the positive relationship between biodiversity and primary productivity. Yet, the role of within-species variations in nutrient resorption in mediating the relationship between biodiversity and productivity remains unclear. 2.We examined how within-species nutrient resorption, and ultimately productivity, respond to changes in species richness by using four traits related to nitrogen and phosphorus use in four dominant species from different plant functional groups in a biodiversity...

Data from: Convergent regulatory evolution and loss of flight in palaeognathous birds

Timothy B. Sackton, Phil Grayson, Alison Cloutier, Zhirui Hu, Jun S. Liu, Nicole E. Wheeler, Paul P. Gardner, Julia A. Clarke, Allan J. Baker, Michele Clamp & Scott V. Edwards
A core question in evolutionary biology is whether convergent phenotypic evolution is driven by convergent molecular changes in proteins or regulatory regions. We combined phylogenomic, developmental, and epigenomic analysis of 11 new genomes of paleognathous birds, including an extinct moa, to show that convergent evolution of regulatory regions, more so than protein-coding genes, is prevalent among developmental pathways associated with independent losses of flight. A Bayesian analysis of 284,001 conserved noncoding elements, 60,665 of which...

Offshore miocene sandstone (Folk McBride Collection)

Masa Prodanovic, Kitty Milliken & Ayaz Mehmani
Offshore miocene sandstone (Folk McBride Collection) Example thin section from an offshore Texas miocene sandstone. Quart-rich medium sand. Well number SMI 236 A4. To view the scanned thin-sections use VPViewer developed by Innova Plex, Inc. Please contact blee@innovaplex.com to obtain a license. The resolution for all samples and all magnifications is 1 micrometer per pixel. The file naming follows the template OffshoreMiocene_20.jpx_0.05x_1817_3486_ppl.jpg with: OffshoreMiocene_20 = Base name of the file 0.05x = magnification 1817, 3486...

Mimicking Geological Fabrics for Multiphase Flow Experiments

Prasanna Ganesan Krishnamurthy, David DiCarlo & Timothy Meckel
2D bead-packs (0.6 m x 0.6 m x 0.02 m) were generated with realistic geological features (cross-stratification and ripple lamination). To demonstrate an application of the technique, gravity unstable multiphase flow experiments were conducted in the generated bead-packs. This project contains time-lapse videos of these flow experiments.

Prey exploits the auditory illusions of eavesdropping predators

Henry Legett, Claire Hemingway & Ximena Bernal
Mating signals have evolved to attract target receivers, even to the point of exploiting receivers through perceptual manipulation. Signals, however, can also expose signalers to non-target receivers, including predators and parasites, and thus have also evolved to decrease enemy attraction. Here we show that male treefrogs (Smilisca sila) reduce their attractiveness to eavesdropping enemies (bats and midges) by overlapping their calls at near-perfect synchrony with the calls of neighboring conspecifics. By producing calls that closely...

Mass estimation of extinct taxa and phylogenetic hypothesis both influence analyses of character evolution in a large clade of birds (Telluraves)

Nicholas Crouch & Roberta Mason-Gamer
Incorporating extinct taxa in phylogenetic comparative methods is rapidly becoming invaluable in studies of character evolution. An increasing number of studies have evaluated the effects of extinct taxa, and different numbers of extinct taxa, on model selection and parameter estimation. Body mass is a well-studied phenotype, but individual mass estimates may vary dramatically depending on the particular measurement used. Here, we perform an analysis of body mass evolution in a large clade of principally arboreal...

Data from: DNA methylation predicts immune gene expression in introduced house sparrows (Passer domesticus)

Holly J. Kilvitis, Aaron W. Schrey, Alexandria K. Ragsdale, Alejandro Berrio, Steve M. Phelps & Lynn B. Martin
Populations undergoing range expansions are often faced with novel selective pressures, and to cope with such challenges, populations must either adapt quickly or exhibit phenotypic plasticity. This latter option allows for rapid phenotypic adjustments and persistence in novel environments, and thus could be advantageous at range‐edges. Our previous research on house sparrows in Kenya—a site of ongoing range expansion— and a growing literature suggests that invasion success is facilitated by epigenetic regulation of gene expression....

Data from: A liquid-like organelle at the root of motile ciliopathy

Ryan L. Huizar, Chanjae Lee, Alexander A. Boulgakov, Amjad Horani, Fan Tu, Edward M. Marcotte, Steven L. Brody & John B. Wallingford
Motile ciliopathies are characterized by specific defects in cilia beating that result in chronic airway disease, subfertility, ectopic pregnancy, and hydrocephalus. While many patients harbor mutations in the dynein motors that drive cilia beating, the disease also results from mutations in so-called Dynein Axonemal Assembly Factors (DNAAFs) that act in the cytoplasm. The mechanisms of DNAAF action remain poorly defined. Here, we show that DNAAFs concentrate together with axonemal dyneins and chaperones into organelles that...

Data from: Multi-scalar drivers of biodiversity: local management mediates wild bee community response to regional urbanization

Kimberly Ballare, Jack Neff, Rebecca Ruppel & Shalene Jha
It is critical to understand the specific drivers of biodiversity across multiple spatial scales, especially within rapidly urbanizing areas, given the distinct management recommendations that may result at each scale. However, drivers of biodiversity patterns and interactions between drivers are often only measured and modeled at a single scale. In this study, we assessed bee community composition at three time periods in 20 grassland and 20 agriculture sites located across two major metroplexes. We examined...

Data from: A trait-based approach to predict population genetic structure in bees

Margarita M. Lopez-Uribe, Shalene Jha & Antonella Soro
Understanding population genetic structure is key to developing predictions about species susceptibility to environmental change, such as habitat fragmentation and climate change. It has been theorized that life-history traits may constrain some species in their dispersal and lead to greater signatures of population genetic structure. In this study, we use a quantitative comparative approach to assess if patterns of population genetic structure in bees are driven by three key species-level life-history traits: body size, sociality,...

Registration Year

  • 2019

Resource Types

  • Dataset


  • The University of Texas at Austin
  • University of Lisbon
  • Harvard University
  • Pennsylvania State University
  • University of Bath
  • Victoria University of Wellington
  • Hólar University College
  • Sun Yat-sen University
  • Plymouth University
  • Nobel Academy