39 Works

Data from: Hypothesis: a plastically-produced phenotype predicts host specialization and can precede subsequent mutations in bacteriophage

Colin S. Maxwell
The role of phenotypic plasticity in the evolution of new traits is controversial due to a lack of direct evidence. Phage host range becomes plastic in the presence of restriction-modification (R-M) systems in their hosts. I modeled the evolution of phage host range in the presence of R-M systems. The model makes two main predictions. The first prediction is that the offspring of the first phage to gain a new methylation pattern by infecting a...

Data from: A convolutional neural network for detecting sea turtles in drone imagery

Patrick C. Gray, Abram B. Fleishman, David J. Klein, Matthew W. McKown, Vanessa S. Bézy, Kenneth J. Lohmann & David W. Johnston
1. Marine megafauna are difficult to observe and count because many species travel widely and spend large amounts of time submerged. As such, management programs seeking to conserve these species are often hampered by limited information about population levels. 2. Unoccupied aircraft systems (UAS, aka drones) provide a potentially useful technique for assessing marine animal populations, but a central challenge lies in analyzing the vast amounts of data generated in the images or video acquired...

Data from: Challenges and solutions for analyzing dual RNA-seq data for non-model host/pathogen systems

Kayleigh R. O'Keeffe & Corbin D. Jones
1. Dual RNA-seq simultaneously profiles the transcriptomes of a host and pathogen during infection and may reveal the mechanisms underlying host-pathogen interactions. Dual RNA-seq is inherently a mixture of transcripts from at least two species (host and pathogen), so this mixture must be computationally sorted into host and pathogen components. Sorting relies on aligning reads to respective reference genomes, which may be unavailable for both species in non-model host-pathogen pairs. This lack of genomic resources...

Data from: Explosion-generated infrasound recorded on ground and airborne microbarometers at regional distances

Eliot F. Young, Daniel C. Bowman, Jonathan M. Lees, Viliam Klein, Steven J. Arrowsmith & Courtney Ballard
Recent work in deploying infrasound (low frequency sound) sensors on aerostats and free flying balloons has shown them to be viable alternatives to ground stations. However, no study to date has compared the performance of surface and free floating infrasound microbarometers with respect to acoustic events at regional (100s of kilometers) range. The prospect of enhanced detection of aerial explosions at similar ranges, such as those from bolides, has not been investigated either. We examined...

Evaluating the effects of land-use change and future climate change on vulnerability of coastal landscapes to saltwater intrusion

Abinash Bhattachan, Ryan Emanuel, Marcelo Ardon, Emily Bernhardt, Steven Anderson, Matthew Stillwagon, Emily Ury, Todd Bendor & Justin Wright
The exposure of freshwater-dependent coastal ecosystems to saltwater is a present-day impact of climate and land-use changes in many coastal regions, with the potential to harm freshwater and terrestrial biota, alter biogeochemical cycles and reduce agricultural yields. Land-use activities associated with artificial drainage infrastructure (canals, ditches, and drains) could exacerbate saltwater exposure. However, studies assessing the effects of artificial drainage on the vulnerability of coastal landscapes to saltwater exposure are lacking. We examined the extent...

Data from: Association of orthostatic hypotension with incident dementia, stroke, and cognitive decline

Andreea M. Rawlings, Stephen P. Juraschek, Gerardo Heiss, Tim Hughes, Michelle L. Meyer, Elizabeth Selvin, A. Richey Sharrett, B. Gwen Windham & Rebecca F. Gottesman
Objective: To examine associations between orthostatic hypotension (OH) with dementia and long-term cognitive decline, and update previously published results in the same cohort for stroke with an additional 16 years of follow-up. Methods: We analyzed data from 11709 participants without a history of coronary heart disease or stroke who attended the baseline exam (1987-1989) of the prospective Atherosclerosis Risk in Communities (ARIC) study. OH was defined as a drop in systolic blood pressure (BP) of...

Data from: Variation across mitochondrial gene trees provides evidence for systematic error: how much gene tree variation is biological?

Emilie J. Richards, Jeremy M. Brown, Anthony J. Barley, Rebecca A. Chong & Robert C. Thomson
The use of large genomic datasets in phylogenetics has highlighted extensive topological variation across genes. Much of this discordance is assumed to result from biological processes. However, variation among gene trees can also be a consequence of systematic error driven by poor model fit, and the relative importance of biological versus methodological factors in explaining gene tree variation is a major unresolved question. Using mitochondrial genomes to control for biological causes of gene tree variation,...

Data from: Using museum specimens to track morphological shifts through climate change

Heidi J. MacLean, Matthew E. Nielsen, Joel G. Kingsolver & Lauren B. Buckley
Museum specimens offer a largely untapped resource for detecting morphological shifts in response to climate change. However, morphological shifts can be obscured by shifts in phenology or distribution or sampling biases. Additionally, interpreting phenotypic shifts requires distinguishing whether they result from plastic or genetic changes. Previous studies using collections have documented consistent historical size changes, but the limited studies of other morphological traits have often failed to support, or even test, hypotheses. We explore the...

Data from: The behavioral origins of novelty: did increased aggression lead to scale-eating in pupfishes?

Michelle E. St. John, Joseph A. McGirr & Christopher H. Martin
Behavioral changes in a new environment are often assumed to precede the origins of evolutionary novelties. Here, we examined whether an increase in aggression is associated with a novel scale-eating trophic niche within a recent radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas. We measured aggression using multiple behavioral assays and used transcriptomic analyses to identify differentially expressed genes in aggression and other behavioral pathways across three sympatric species in the San Salvador...

Data from: Application of benchmark concentration (BMC) analysis on zebrafish data – a new perspective for quantifying toxicity in alternative animal models

Jui-Hua Hsieh, Kristen Ryan, Alexander Sedykh, Ja-An Lin, Andrew J. Shapiro, Frederick Parham & Mamta Behl
Over the past decade, the zebrafish is increasingly being used as a model to screen for chemical-mediated toxicities including developmental toxicity (DT) and neurotoxicity (NT). One of the major challenges is lack of harmonization in data analysis approaches, thereby posing difficulty in comparing findings across laboratories. To address this, we sought to establish a unified data analysis strategy for both DT and NT data, by adopting the benchmark concentration (BMC) analysis. There are two critical...

Data from: Investigating behavioral drivers of seasonal Shiga-Toxigenic Escherichia Coli (STEC) patterns in grazing cattle using an agent-based model

Daniel E. Dawson, Jocelyn H. Keung, Monica G. Napoles, Michael R. Vella, Shi Chen, Mike Sanderson, Cristina Lanzas & Michael W. Sanderson
The causes of seasonal variability in pathogen transmission are not well understood, and have not been comprehensively investigated. In an example for enteric pathogens, incidence of Escherichia coli O157 (STEC) colonization in cattle is consistently higher during warmer months compared to cooler months in various cattle production systems. However, actual mechanisms for this seasonality remain elusive. In addition, the influence of host (cattle) behavior on this pattern has not been thoroughly considered. To that end,...

Data from: Direct detection of male quality can facilitate the evolution of female choosiness and indicators of good genes: evolution across a continuum of indicator mechanisms

Sumit Dhole, Caitlin A. Stern & Maria R. Servedio
The evolution of mating displays as indicators of male quality has been the subject of extensive theoretical and empirical research for over four decades. Research has also addressed the evolution of female mate choice favoring such indicators. Yet, much debate still exists about whether displays can evolve through the indirect benefits of female mate choice. Here, we use a population genetic model to investigate how the extent to which females can directly detect male quality...

Data from: Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data

Pengcheng Zhou, Shanna L. Resendez, Jose Rodriguez-Romaguera, Jessica C. Jimenez, Shay Q. Neufeld, Andrea Giovannucci, Johannes Friedrich, Eftychios A Pnevmatikakis, Garret D. Stuber, Rene Hen, Mazen A. Kheirbek, Bernardo L. Sabatini, Robert E. Kass & Liam Paninski
In vivo calcium imaging through microendoscopic lenses enables imaging of previously inaccessible neuronal populations deep within the brains of freely moving animals. However, it is computationally challenging to extract single-neuronal activity from microendoscopic data, because of the very large background fluctuations and high spatial overlaps intrinsic to this recording modality. Here, we describe a new constrained matrix factorization approach to accurately separate the background and then demix and denoise the neuronal signals of interest. We...

Data from: Gene exchange between two divergent species of the fungal human pathogen, Coccidioides

Colin Scott Maxwell, Kathleen Mattox, David A. Turissini, Marcus M. Teixeira, Bridget M. Barker & Daniel Ricardo Matute
The fungal genus Coccidioides is composed of two species, Coccidioides immitis and C. posadasii. These two species are the causal agents of coccidioidomycosis, a pulmonary disease also known as valley fever. The two species are thought to have shared genetic material due to gene exchange in spite of their long divergence. To quantify the magnitude of shared ancestry between them, we analyzed the genomes of a population sample from each species. Next, we inferred what...

Registration Year

  • 2018

Resource Types

  • Dataset


  • University of North Carolina
  • Duke University
  • Oregon State University
  • North Carolina State University
  • University of Montana
  • University of Washington
  • Sandia National Laboratories
  • Carnegie Mellon University
  • Howard Hughes Medical Institute
  • Reed College