183 Works

Data from: Unravelling the life history of Amazonian fishes through otolith microchemistry

Theodore W. Hermann, Donald J. Stewart, Karin E. Limburg & Leandro Castello
Amazonian fishes employ diverse migratory strategies, but the details of these behaviours remain poorly studied despite numerous environmental threats and heavy commercial exploitation of many species. Otolith microchemistry offers a practical, cost-effective means of studying fish life history in such a system. This study employed a multi-method, multi-elemental approach to elucidate the migrations of five Amazonian fishes: two ‘sedentary’ species (Arapaima sp. and Plagioscion squamosissimus), one ‘floodplain migrant’ (Prochilodus nigricans) and two long-distance migratory catfishes...

Data from: Winter food limits timing of pre-alternate molt in a short-distance migratory bird

Raymond M. Danner, Russell S. Greenberg, Julie E. Danner & Jeffrey R. Walters
1. Molt is critical for fitness for many organisms for several reasons: it allows growth and maintains the function of the integument for protection, thermoregulation and communication. 2. Feather molt in birds is costly and therefore typically does not overlap with migration or reproduction. In spring, the rapid succession of pre-alternate molt, migration (if a migrant), and breeding suggests that timing of molt could constrain the initiation of breeding. A tradeoff between time spent molting...

Data from: Relationships of the Indian phytosaur Parasuchus hislopi Lydekker, 1885

Christian F. Kammerer, Richard J. Butler, Saswati Bandyopadhyay & Michelle R. Stocker
The neotype skull of the Indian phytosaur Parasuchus hislopi Lydekker, 1885 (ISI R42) is re-evaluated and compared with the type material of other basal phytosaurs. Parasuchus hislopi is extremely similar to species previously placed in Paleorhinus (P. bransoni and P. angustifrons), sharing with them such characters as a series of nodes on the lateral surface of the jugal, paired ridges on the squamosal and a frontal depression. Parasuchus hislopi represents a valid species: it can...

Data from: Why are you swiping right? The impact of product orientation on swiping responses

Anneleen Van Kerckhove & Mario Pandelaere
Many apps require consumers to evaluate products by swiping them, to the right or left. This work explores whether product orientation affects the product evaluations communicated by swiping movements, compared with those made by pressing onscreen buttons. Building on stimulus-response compatibility (SRC) theory, which suggests that irrelevant product display features can activate certain behavioral responses when the product display and the behavioral response share a common dimension, this study predicts that the horizontal direction (left-to-right...

Data from: Conservation and divergence of gene expression plasticity following c. 140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca × Picea engelmannii)

Sam Yeaman, Kathryn A. Hodgins, Haktan Suren, Kristin A. Nurkowski, Jason A. Holliday, Loren H. Rieseberg & Sally N. Aitken
Species respond to environmental stress through a combination of genetic adaptation and phenotypic plasticity, both of which may be important for survival in the face of climatic change. By characterizing the molecular basis of plastic responses and comparing patterns among species, it is possible to identify how such traits evolve. Here, we use de novo transcriptome assembly and RNA-seq to explore how patterns of gene expression differ in response to temperature, moisture, and light regime...

Data from: Life histories and invasions: accelerated laying rate and incubation time in an invasive lizard, Anolis sagrei

Tamara L. Fetters & Joel W. McGlothlin
Faster life histories are correlated with greater invasion success across taxa. However, comparisons of life-history traits across native and invasive ranges are rare, and thus it is unknown whether invasions lead directly to evolutionary shifts in life histories. Here we compare life history traits of three invasive populations of brown anoles (Anolis sagrei) to a representative native population. In a common garden, we measured a number of reproductive traits including egg-laying rate and incubation period....

Data from: Identification of candidate effector genes of Pratylenchus penetrans

Paulo Vieira, Thomas Mayer, Sebastian Eves-Van Den Akker, Dana K. Howe, Inga Zasada, Thomas Baum, Jonathan D. Eisenback, Kathryn Kamo, Thomas R. Maier & Thomas J. Baum
Pratylenchus penetrans is one of the most important species among root lesion nematodes (RLNs) due to the detrimental and economic impact that it causes in a wide range of crops. Similar to other plant-parasitic nematodes (PPNs), P. penetrans harbors a significant number of secreted proteins that play key roles during parasitism. Here we combined spatially and temporally resolved next generation sequencing datasets of P. penetrans to select a list of candidate genes aimed at the...

AEMON-J/DSOS Archive: \"Hacking Limnology\" Workshop + Virtual Summit in Data Science & Open Science in Aquatic Research

Michael Meyer, Robert Ladwig, Isabella Oleksy, Jorrit Mesman, Jacob Zwart, Alli Cramer, Kaelin Cawley, johannes feldbauer, Patricia Tran, Gregor Moreira, Muhammed Shikhani, Deviyani Gurung, Robert Hensley, Elena Matta, Ryan McClure, Thomas Petzoldt, Nuria Lopez, Karline Soetaert, Mridul Thomas, Simon Topp, , Elizabeth McDaniel, Laura Schaerer, Stefano Mezzini, Charuleka Varadharajan … & Abdou Bah
This OSF project is meant to serve as a long-term storage repository for presentations and workshop materials for the Aquatic Ecosystem Modeling-Junior (AEMON-J) and Virtual Summit: Incorporating Data Science and Open Science (DSOS) communities. Contributors in this repository include past presenters and workshop organizers. Contributors are only responsible for those individual presentations that are labeled with their surname.

Scutellaria Extract Inhibits Proliferation and Migration of Brain-Metastatic Lung Cancer Cells via Regulation of Multiple Signaling Pathways

Robert E. Wright III, Lubana Shahin, Venumadhavi Gogineni, Zahin Hussain, Aroma Naeem, Sudha Sadasivan, Indrajit Sinha, Melody Neely, Sharon K. Michellhaugh, Sandeep Mittal, Nirmal Joshee & Prahlad Parajuli

Micro-CT scans of Mt. Simon sandstone at residual conditions used for contact angle measurements and analyzing the influence of clay regions

Laura Dalton, Dustin Crandall, James McClure, Min Fang & Ryan Armstrong
Micro-computed tomography tiff stacks of a Mt. Simon core at residual conditions. The core is from a depth of 6,926 ft, the sub-sample tested is 0.25 inch diameter by 1 inch length. This data was used to complete contact angle measurements and analyze the influence of clay-rich regions in the pore space on residual trapping efficiency.

Assessing Microplastic Pollution in Four Mile Run, an Urban Stream in Northern Virginia

Kurt Moser, Tessa Naughton-Rockwell, Louisa Wang, Ethan Litmans & Amanda Manoogian
Microplastics are pollutants of concern in waterways and oceans for their persistence and impact on aquatic life and food webs. This study demonstrates a low-cost land-based sampling method to assess the extent of microplastic pollution found in Four Mile Run, an urban stream in Northern Virginia. Microplastic particle counts in environmental and treated wastewater ranged from 0.01-0.24 particles L-1 (mean 0.08 particles L-1) and from 2 to 446 µg L-1 (mean 70 µg L-1), with...

Green Light SONATA: Improvisation at the Intersection of Art and Science

Montasir Abbas, Charles Nichols, Anne Elise Thomas & Qichao Wang
The Green Light SONATA project originated with a hunch in the engineering domain, but could only materialize through true collaboration of researchers working across disciplines. The project tested the hypothesis that translating simulated traffic information into music could lead to musical resolution of persistent traffic congestion. Our team—consisting of civil engineers, a composer/performer/computer music researcher, and an ethnomusicologist—proceeded to construct a model of an intersection in which each direction of traffic flow was assigned a...

Labeled Hyperspectral and RGB Images of Several Tree Species

Ryan Brown & Josh Moser
A dataset of hyperspectral and RGB images of different tree species on the Virginia Tech campus. These images were captured at different lighting and exposure levels and include labeling information that will allow for classification tasks to be performed. The dataset is designed to highlight differences in classification accuracy and techniques when using traditional RGB images as opposed to hyperspectral images. Each image is stored in a .zip file separate from the required header file....

Longitudinal white-matter abnormalities in sports-related concussion: a diffusion MRI study of the NCAA-DoD CARE Consortium

Yu-Chien Wu, Jaroslaw Harezlak, Nahla Elsaid, Zikai Lin, Qiuting Wen, Sourajit Mustafi, Larry Riggen, Kevin Koch, Andrew Nencka, Timothy Meier, Andrew Mayer, Yang Wang, Christopher Giza, John DiFiori, Kevin Guskiewicz, Jason Mihalik, Stephen LaConte, Stefan Duma, Steven Broglio, Andrew Saykin, Michael McCrea & Thomas McAllister
Objective To study longitudinal recovery trajectories of white-matter after sports-related concussion (SRC), we performed diffusion tensor imaging (DTI) on collegiate athletes who sustained SRC. Methods Collegiate athletes (n=219, 82 concussed athletes, 68 contact-sport controls, and 69 non-contact-sport controls) were included from the Concussion Assessment, Research and Education (CARE) Consortium. The participants completed clinical assessments and DTI at four time points: 24-48-hours post-injury, asymptomatic state, seven days following return-to-play, and six-months post-injury. Tract-based spatial statistics were...

Managing, Collecting, and Sharing Data with OSF - VU Amsterdam

Tycho Hofstra, S. Sandt, Meron Vermaas, B.J.J. Hattink, Lena Karvovskaya, T.J.A.G. Münker, Brett Olivier, C Dijk, Jessica Hrudey, APC Van der Jagt, Lannie Ligthart, W Hugens, A Taimounti, Sam Heijnen, Koen Leuveld, Kacana Khadjavi, Mark Bruyneel, Elisa Rodenburg, H.J. Jorritsma, Haiyan Wang, Petra van Aken, Jolien Scholten, DA Unger, N.A. Dieleman, R.A. Onyango … & M. Hashemi Shabestari
Test Description

Supplementary material: How should functional relationships be evaluated using phylogenetic comparative methods? A case study using metabolic rate and body temperature

Josef Uyeda, Nic Bone, Sean McHugh, Jonathan Rolland & Matthew Pennell
Phylogenetic comparative methods are often used to test functional relationships between traits. However, million-year macroevolutionary observational datasets cannot definitively prove causal links between traits --- correlation does not equal causation and experimental manipulation over such timescales is impossible. While this caveat is widely understood, it is far less appreciated that different phylogenetic approaches make different causal assumptions about the functional relationships of traits. In order to make meaningful inferences, it is critical that our statistical...

Host traits and environment interact to drive persistence of bat populations impacted by white-nose syndrome

Alexander Grimaudo, Joseph Hoyt, Steffany Yamada, Carl Herzog, Alyssa Bennett & Kate Langwig
Emerging infectious diseases have resulted in severe population declines across diverse taxa. In some instances, despite attributes associated with high extinction risk, disease emergence and host declines are followed by host stabilization for unknown reasons. While host, pathogen, and the environment are recognized as important factors that interact to determine host-pathogen coexistence, they are often considered independently. Here, we use a translocation experiment to disentangle the role of host traits and environmental conditions in driving...

Data For: The developing bird pelvis passes through ancestral Archosaurian and Dinosaurian conditions

Christopher Griffin, João Botelho, Michael Hanson, Matteo Fabbri, Daniel Smith-Paredes, Ryan Carney, Mark Norell, Shiro Egawa, Stephen Gatesy, Timothy Rowe, Ruth Elsey, Sterling Nesbitt & Bhart-Anjan Bhullar
Living birds (Aves) have bodies dramatically modified from the ancestral reptilian condition. The avian pelvis in particular experienced dramatic changes during the transition from early archosaurs to living birds. This stepwise transformation is well documented by an excellent fossil record; however, the ontogenetic alterations that underly it are less well-understood. We used embryological imaging techniques to examine the morphogenesis of avian pelvic tissues in three dimensions, allowing direct comparison with the fossil record. Many ancestral...

Data from: Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum

Michael A. Hardigan, Emily Crisovan, John P. Hamilton, Jeongwoon Kim, Parker Laimbeer, Courtney P. Leisner, Norma C. Manrique-Carpintero, Linsey Newton, Gina M. Pham, Brieanne Vaillancourt, Xueming Yang, Zixian Zeng, David S. Douches, Jiming Jiang, Richard E. Veilleux & C. Robin Buell
Clonally reproducing plants have the potential to bear a significantly greater mutational load than sexually reproducing species. To investigate this possibility, we examined the breadth of genome-wide structural variation in a panel of monoploid/doubled monoploid clones generated from native populations of diploid potato (Solanum tuberosum), a highly heterozygous asexually propagated plant. As rare instances of purely homozygous clones, they provided an ideal set for determining the degree of structural variation tolerated by this species, and...

Data from: The contribution of maternal effects to selection response: an empirical test of competing models

Joel William McGlothlin & Laura F. Galloway
Maternal effects can dramatically influence the evolutionary process, in some cases facilitating and in others hindering adaptive evolution. Maternal effects have been incorporated into quantitative genetic models using two theoretical frameworks: the variance-components approach, which partitions variance into direct and maternal components, and the trait-based approach, which assumes that maternal effects are mediated by specific maternal traits. Here, we demonstrate parallels between these models and test their ability to predict evolutionary change. First, we show...

Data from: Changing measurements or changing movements? Sampling scale and movement model identifiability across generations of biologging technology

Leah R. Johnson, Philipp H. Boersch-Supan, Richard A. Phillips & Sadie J. Ryan
1. Animal movement patterns contribute to our understanding of variation in breeding success and survival of individuals, and the implications for population dynamics. 2. Over time, sensor technology for measuring movement patterns has improved. Although older technologies may be rendered obsolete, the existing data are still valuable, especially if new and old data can be compared to test whether a behavior has changed over time. 3. We used simulated data to assess the ability to...

Ancient and modern colonization of North America by hemlock woolly adelgid, Adelges tsugae (Hemiptera: Adelgidae), an invasive insect from East Asia

Nathan P. Havill, Shigehiko Shiyake, Ashley Lamb Galloway, Robert G. Foottit, Guoyue Yu, Annnie Paradis, Joseph Elkinton, Michael E. Montgomery, Masakazu Sano, Adalgisa Caccone & Annie Paradis
Hemlock woolly adelgid, Adelges tsugae, is an invasive pest of hemlock trees (Tsuga) in eastern North America. We used 14 microsatellites and mitochondrial COI sequences to assess its worldwide genetic structure and reconstruct its colonization history. The resulting information about its life cycle, biogeography and host specialization could help predict invasion by insect herbivores. We identified eight endemic lineages of hemlock adelgids in central China, western China, Ulleung Island (South Korea), western North America, and...

Data from: Using host-associated differentiation to track source population and dispersal distance among insect vectors of plant pathogens

Gina M. Angelella, Andy P. Michel, Ian Kaplan, G.M. Angelella & A.P. Michel
Small, mobile insects are notoriously challenging to track across landscapes and manage in agricultural fields. However, genetic differentiation among insect populations and host-plants acquired through host-associated differentiation could be exploited to infer movement within crop systems and damage potential. Although many insects exhibit host-associated differentiation, management strategies for insect vectors of plant pathogens assume a homogenous population. Nevertheless, phenotypic changes derived from host-associated differentiation could manifest in altered behavior or physiology affecting the likelihood of...

Data from: Using camera trapping and hierarchical occupancy modelling to evaluate the spatial ecology of an African mammal community

Lindsey N. Rich, David A. W. Miller, Hugh S. Robinson, J. Weldon McNutt & Marcella J. Kelly
Emerging conservation paradigms have shifted from single to multi-species approaches focused on sustaining biodiversity. Multi-species hierarchical occupancy modelling provides a method for assessing biodiversity while accounting for multiple sources of uncertainty. We analysed camera trapping data with multi-species models using a Bayesian approach to estimate the distributions of a terrestrial mammal community in northern Botswana and evaluate community, group, and species-specific responses to human disturbance and environmental variables. Groupings were based on two life-history traits:...

Data from: Urban living alters moult dynamics in a passerine

Sydney F. Hope, Frank A. Stabile & Luke K. Butler
Urbanization and habitat fragmentation can alter the timing of life history events, potentially leading to phenological mismatches, carryover effects, and fitness costs. Whereas urbanization and fragmentation are known to alter important aspects of breeding in many bird species, little is known about the effects of urbanization and habitat fragmentation on moult. To investigate the effects of urbanization and fragmentation on the annual moult, we compared the moult dynamics (onset, duration, and intensity) of urban, fragmented...

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