25 Works

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.

Data from: Larval pheromones act as colony-wide regulators of collective foraging behavior in honeybees

Rong Ma, Gabriel Villar, Christina M. Grozinger & Juliana Rangel
When animals move or forage in groups, collective behaviors arise from independent decisions that individuals make based on limited information about the environment. In decentralized systems in which individuals use local cues to decide how to allocate their time amongst multiple tasks, a “global” signal detectable over large distances by all members of the group could have a profound effect on task allocation and coordination. Honey bees provide a unique opportunity to study how information...

Data from: A reciprocal translocation radically reshapes sex-linked inheritance in the common frog

Melissa A. Toups, Nicolas Rodrigues, Nicolas Perrin & Mark Kirkpatrick
X and Y chromosomes can diverge when rearrangements block recombination between them. Here we present the first genomic view of a reciprocal translocation that causes two physically unconnected pairs of chromosomes to be coinherited as sex chromosomes. In a population of the common frog (Rana temporaria), both pairs of X and Y chromosomes show extensive sequence differentiation, but not degeneration of the Ys. A new method based on gene trees shows both chromosomes are sex-linked....

Data from: Metabolic physiology explains macroevolutionary trends in the melanic colour system across amniotes

Chad M. Eliason & Julia A. Clarke
Metabolism links organisms to their environment through its effects on thermoregulation, feeding behaviour, and energetics. Genes involved in metabolic processes have known pleiotropic effects on some melanic colour traits. Understanding links between physiology and melanic colour is critical for understanding the role of, and potential constraints on, colour production. Despite considerable variation in metabolic rates and presumed ancestral melanic colouration in vertebrates, few studies have looked at a potential relationship between these two systems in...

Data from: A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates

Lina Maria Valencia, Amely Martins, Edgardo Manuel Martín Ortiz Valencia, Anthony Di Fiore & Edgardo M. Ortiz
Until recently, most phylogenetic and population genetics studies of nonhuman primates have relied on mitochondrial DNA and/or a small number of nuclear DNA markers, which can limit our understanding of primate evolutionary and population history. Here, we describe a cost-effective reduced representation method (ddRAD-seq) for identifying and genotyping large numbers of SNP loci for taxa from across the New World monkeys, a diverse radiation of primates that shared a common ancestor ~20-26 mya. We also...

Data from: Sympatric serpentine endemic Monardella (Lamiaceae) species maintain habitat differences despite hybridization

Kathleen M. Kay, Suzie Woolhouse, Brett A. Smith, Nathaniel S. Pope & Nishanta Rajakaruna
Ecological differentiation and genetic isolation are thought to be critical in facilitating coexistence between related species, but the relative importance of these phenomena, and the interactions between them, are not well understood. Here we examine divergence in abiotic habitat affinity and the extent of hybridization and introgression between two rare species of Monardella (Lamiaceae) that are both restricted to the same serpentine soil exposure in California. Although broadly sympatric, they are found in microhabitats that...

Data from: Real or fake? natural and artificial social stimuli elicit divergent behavioral and neural responses in mangrove rivulus, Kryptolebias marmoratus

Cheng-Yu Li, Hans A. Hofmann, Melissa L. Harris & Ryan L. Earley
Understanding how the brain processes social information and generates adaptive behavioural responses is a major goal in neuroscience. We examined behaviour and neural activity patterns in socially relevant brain nuclei of hermaphroditic mangrove rivulus fish (Kryptolebias marmoratus) provided with different types of social stimuli: stationary model opponent, regular mirror, non-reversing mirror and live opponent. We found that: i) individuals faced with a regular mirror were less willing to interact with, delivered fewer attacks towards, and...

Data from: Variation in host plant usage and diet breadth predict sibling preference and performance in the neotropical tortoise beetle Chelymorpha alternans (Coleoptera: Chrysomelidae: Cassidinae)

Colin R. Morrison, Clement Aubert & Donald M. Windsor
Specialized interactions between insects and the plants that they consume are one of the most ubiquitous and consequential ecological associations on the plant. Decades of investigation suggest that a narrow diet favors an individual phytophagous insect’s performance relative to a dietary generalist. However, this body of research has tended to approach questions of diet breadth and host usage from the perspective of temperate plant – insect associations. Relationships between diet breadth, host usage and variation...

Data from: The RNA-binding protein Celf1 post-transcriptionally regulates p27Kip1 and Dnase2b to control fiber cell nuclear degradation in lens development

Archana D. Siddam, Carole Gautier-Courteille, Linette Perez-Campos, Deepti Anand, Atul Kakrana, Christine A. Dang, Vincent Legagneux, Agnès Méreau, Justine Viet, Jeffrey M. Gross, Luc Paillard & Salil A. Lachke
Opacification of the ocular lens, termed cataract, is a common cause of blindness. To become transparent, lens fiber cells undergo degradation of their organelles, including their nuclei, presenting a fundamental question: does signaling/transcription sufficiently explain differentiation of cells progressing toward compromised transcriptional potential? We report that a conserved RNA-binding protein Celf1 post-transcriptionally controls key genes to regulate lens fiber cell differentiation. Celf1-targeted knockout mice and celf1-knockdown zebrafish and Xenopus morphants have severe eye defects/cataract. Celf1...

Guelph Dolomite characterization

Hasan Khan, Andres Gonzales, Masa Prodanovic, Zoya Heidari & D. Nicolas Espinoza
This project is part of a Guelph dolomite (GD) petrophysical characterization study. Multi-scale CT scans are conducted on a GD core (30 mm x 75 mm) at a resolution of 23 um. Medical CT (low resolution - 250 microns), permeability and NMR study are also done on the sample. Digital sub-sample is created and vug have been segmented. Vug characterization is attempted by using the surface to volume ratio to determine the vug shape and...

Data from: Evolution of the plastid genomes in diatoms

Mengjie Yu, Matt P. Ashworth, Nahid H. Hajrah, Mohammad A. Khiyami, Mumdooh J. Sabir, Alawiah M. Alhebshi, Abdulrahman L. Al-Malki, Jamal S. M. Sabir, Edward C. Theriot, Robert K. Jansen & Jamal S.M. Sabir
Diatoms are a monophyletic group of eukaryotic, single-celled heterokont algae. Despite years of phylogenetic research, relationships among major groups of diatoms remain uncertain. Here we assess diatom phylogenetic relationships using the plastid genome (plastome). The 22 previously published diatom plastomes showed variable genome size, gene content and extensive rearrangement. We report another 18 diatom plastome sequences ranging in size from 119,120 to 201,816 bp. Plagiogramma staurophorum had the largest plastome sequenced so far due to...

Data from: Duration of propagule pressure affects non-native plant species abundances

Gabriel L. De Jong & Norma L. Fowler
Premise of the study: Invasions by non-native species are known to be related to present propagule pressure (e.g., the number of non-native seeds arriving in a site each year). However, previous studies have mostly ignored the potential effects of the length of time that a site has experienced propagule pressure. This study is novel in studying past as well as present propagule pressure and in demonstrating the importance of past propagule pressure. Methods: We tested...

Data from: Egg boon fatty acids reveal effects of a climatic event on a marine food web

Lee A. Fuiman
Flow of essential fatty acids (EFAs) through food webs is critical for the health of individual animals, populations, and communities. Planktonic eggs may play a central role in marine systems because they are highly concentrated in EFAs, superabundant, and consumed by a variety of species. Previous research suggests that egg fatty acid composition should not be useful for trophodynamic studies because it should be tightly regulated to meet the nutritional needs of embryos. Eight years...

Data from: Comparison of spatial and temporal genetic differentiation in a harmful dinoflagellate species emphasises impact of local processes

Ingrid Sassenhagen, Yida Gao, Yesid Lozano-Duque, Michael L. Parsons, Tyler B. Smith & Deana L. Erdner
Population genetic studies provide insights into intraspecific diversity and dispersal patterns of microorganisms such as protists, which help understanding invasions, harmful algal bloom development and occurrence of seafood poisoning. Genetic differentiation across geography has been reported in many microbial species indicating significant dispersal barriers among different habitats. Temporal differentiation has been less studied and its frequency, drivers and magnitude are poorly understood due to a lack of integral studies. The toxic dinoflagellate species /Gambierdiscus caribaeus/...

Data from: Evaluating the contribution of dispersal to community structure in Neotropical passerine birds

Nicholas M.A. Crouch, João M.G. Capurucho, Shannon J. Hackett & John M. Bates
For two centuries evolutionary biologists have sought to explain elevated biodiversity in the Neotropics. Although different process are known to be important, it is still not uncommon for researchers to emphasize a single mechanism. Recently, arguments have highlighted the importance of dispersal shaping community structure and evolution across the region. We examine this hypothesis by visualizing spatial variation in community structure for the majority of South American passerines (Aves) across the northern half of South...

Data from: Experimentally-induced variation in neuroendocrine processes affects male reproductive behavior, sperm characteristics, and social interactions

Bridget M. Nugent, Kelly A. Stiver, Hans A. Hofmann & Suzanne H. Alonzo
While extensive research has focused on how social interactions evolve, the fitness consequences of the neuroendocrine mechanisms underlying these interactions have rarely been documented, especially in the wild. Here, we measure how the neuroendocrine mechanisms underlying male behavior affecting mating success and sperm competition in the ocellated wrasse (Symphodus ocellatus). In this species, males exhibit three alternative reproductive types. ‘Nesting males’ provide parental care, defend territories, and form cooperative associations with unrelated ‘satellites’, who cheat...

Hydrate-Bearing Sand

Xiongyu Chen, D. Nicolas Espinoza, Masa Prodanovic & Rahul Verma
This project includes high resolution micro-CT images of one xenon hydrate growth experiment in sand. Data are from a paper by Xiongyu Chen, Rahul Verma, D. Nicolas Espinoza and Masa Prodanovic, published in Water Resources Research in 2018, titled "Pore-Scale Determination of Gas Relative Permeability in Hydrate-Bearing Sediments Using X-Ray Computed Micro-Tomography and Lattice Boltzmann Method" Conditions for xenon hydrate growth in sand: T=23C, P_initial =3.72 MPa. Aqueous phase is 10wt% NaBr brine. The image...

Data from: Systematic analysis of complex genetic interactions

Elena Kuzmin, Benjamin VanderSluis, Wen Wang, Guihong Tan, Raamesh Deshpande, Yiqun Chen, Matej Usaj, Attila Balint, Mojca Mattiazzi Usaj, Jolanda Van Leeuwen, Elizabeth N. Koch, Carles Pons, Andrius Jonas Dagilis, Michael Pryszlak, Jason Zi Yang Wang, Julia Hanchard, Margot Riggi, Kaicong Xu, Hamed Heydari, Bryan-Joseph San Luis, Ermira Shuteriqi, Hongwei Zhu, Nydia Van Dyk, Sara Sharifpoor, Michael Costanzo … & Chad L. Myers
To systematically explore complex genetic interactions, we constructed ~200,000 yeast triple mutants and scored negative trigenic interactions. We selected double-mutant query genes across a broad spectrum of biological processes, spanning a range of quantitative features of the global digenic interaction network and tested for a genetic interaction with a third mutation. Trigenic interactions often occurred among functionally related genes, and essential genes were hubs on the trigenic network. Despite their functional enrichment, trigenic interactions tended...

Data from: Species delimitation in endangered groundwater salamanders: implications for aquifer management and biodiversity conservation

Thomas J Devitt, April M Wright, David C Cannatella & David M Hillis
Groundwater-dependent species are among the least-known components of global biodiversity, as well as some of the most vulnerable because of rapid groundwater depletion at regional and global scales. The karstic Edwards–Trinity aquifer system of west-central Texas is one of the most species-rich groundwater systems in the world, represented by dozens of endemic groundwater-obligate species with narrow, naturally fragmented distributions. Here, we examine how geomorphological and hydrogeological processes have driven population divergence and speciation in a...

Data from: CO2 enrichment and soil type additively regulate grassland productivity

H. Wayne Polley, Michael J. Aspinwall, Harold P. Collins, Anne E. Gibson, Richard A. Gill, Robert B. Jackson, Virginia L. Jin, Albina R. Khasanova, Lara G. Reichmann & Philip A. Fay
Atmospheric CO2 enrichment usually increases aboveground productivity (ANPP) of grassland vegetation, but the magnitude of the ANPP-CO2 response differs among ecosystems. Soil properties affect ANPP via multiple mechanisms and vary over topographic to geographic gradients, but have received little attention as potential modifiers of the ANPP-CO2 response. We assessed effects of three soil types, sandy loam, silty clay, and clay, on the ANPP response of perennial C3/C4 grassland communities to a subambient to elevated CO2...

Data from: Short-term precipitation exclusion alters microbial responses to soil moisture in a wet tropical forest

Bonnie G. Waring & Christine V. Hawkes
Many wet tropical forests, which contain a quarter of global terrestrial biomass carbon stocks, will experience changes in precipitation regime over the next century. Soil microbial responses to altered rainfall are likely to be an important feedback on ecosystem carbon cycling, but the ecological mechanisms underpinning these responses are poorly understood. We examined how reduced rainfall affect- ed soil microbial abundance, activity, and community compo- sition using a 6-month precipitation exclusion experiment at La Selva...

Data from: Bee movement across heterogeneous tropical forests: multi-paternal genetic analyses reveal the importance of neighborhood composition for pollen-mediated gene flow

Megan C. O'Connell, Antonio R. Castilla, Leticia X. Lee & Shalene Jha
Animal pollination is critical for maintaining the reproduction and genetic diversity of many plant species, especially those in tropical ecosystems. Despite the threat to pollination posed by tropical deforestation, it remains an understudied process. In particular, little is known about these dynamics in multi-paternal, successional plant species whose fruits can contain substantial genetic diversity. Given the importance of successional plants in reforestation, quantifying the factors that impact their reproduction is essential for understanding plant gene...

Data from: Shifts in selective pressures on snake phototransduction genes associated with photoreceptor transmutation and dim-light ancestry

Ryan K. Schott, Alexander Van Nynatten, Daren C. Card, Todd A. Castoe, Belinda S.W. Chang & Belinda S W Chang
The visual systems of snakes are heavily modified relative to other squamates, a condition often thought to reflect their fossorial origins. Further modifications are seen in caenophidian snakes, where evolutionary transitions between rod and cone photoreceptors, termed photoreceptor transmutations, have occurred in many lineages. Little previous work, however, has focused on the molecular evolutionary underpinnings of these morphological changes. To address this, we sequenced seven snake eye transcriptomes and utilized new whole genome and targeted...

Data from: Phylogenetic analysis and a review of the history of the accidental phytoplankter, Phaeodactylum tricornutum Bohlin (Bacillariophyta)

Jamal S. M. Sabir, Edward C. Theriot, Robert K. Jansen, Matt P. Ashworth, Areej K. Al-Ghamdi, Nahid H. Hajrah, Abdelfatteh El Omri, Schonna R. Manning, Abdulrahman L. Al-Malki, Mumdooh J. Sabir & Dwight K. Romanovicz
The diatom Phaeodactylum tricornutum has been used as a model for cell biologists and ecologists for over a century. We have incorporated several new raphid pennates into a three gene phylogenetic dataset (SSU, rbcL, psbC), and recover Gomphonemopsis sp. as sister to P. tricornutum with 100% BS support. This is the first time a close relative has been identified for P. tricornutum with robust statistical support. We test and reject a succession of hypotheses for...

Data from: Quantifying uncertainty due to fission-fusion dynamics as a component of social complexity

Gabriel Ramos-Fernandez, Andrew J. King, Jacinta C. Beehner, Thore J. Bergman, Margaret C. Crofoot, Anthony Di Fiore, Julia Lehmann, Colleen M. Schaffner, Noah Snyder-Mackler, Klaus Zuberbühler, Filippo Aureli & Denis Boyer
Groups of animals (including humans) may show flexible grouping patterns, in which temporary aggregations or subgroups come together and split, changing composition over short temporal scales, i.e. fission and fusion). A high degree of fission-fusion dynamics may constrain the regulation of social relationships, introducing uncertainty in interactions between group members. Here we use Shannon's entropy to quantify the predictability of subgroup composition for three species known to differ in the way their subgroups come together...

Registration Year

  • 2018

Resource Types

  • Dataset


  • The University of Texas at Austin
  • King Abdulaziz University
  • University of Toronto
  • California Polytechnic State University
  • University of Alabama at Birmingham
  • University of Washington
  • Stanford University
  • University of Michigan-Ann Arbor
  • University of California System
  • North-West University