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: Bioprinted liver provides early insight into the role of Kupffer cells in TGF-β1 and methotrexate-induced fibrogenesis

Leah M. Norona, Deborah G. Nguyen, David A. Gerber, Sharon C. Presnell, Merrie Mosedale & Paul B. Watkins
Hepatic fibrosis develops from a series of complex interactions among resident and recruited cells making it a challenge to replicate using standard in vitro approaches. While studies have demonstrated the importance of macrophages in fibrogenesis, the role of Kupffer cells (KCs) in modulating the initial response remains elusive. Previous work demonstrated utility of 3D bioprinted liver to recapitulate basic fibrogenic features following treatment with fibrosis-associated agents. In the present study, culture conditions were modified to...

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: A maladaptive combination of traits contributes to the maintenance of a Drosophila hybrid zone

Brandon S. Cooper, Alisa Sedghifar, W. Thurston Nash, Aaron A. Comeault & Daniel R. Matute
Drosophila teissieri and D. yakuba diverged approximately 3 mya and are thought to share a large, ancestral, African range [1, 2, 3]. These species now co-occur in parts of continental Africa and in west Africa on the island of Bioko [1, 4]. While D. yakuba is a human commensal, D. teissieri seems to be associated with Parinari fruits, restricting its range to forests [4, 5, 6]. Genome data indicate introgression, despite no evidence of contemporary...

Data from: Living shorelines enhanced the resilience of saltmarshes to Hurricane Matthew (2016)

Carter S. Smith, Brandon Puckett, Rachel K. Gittman & Charles H. Peterson
Nature-based solutions, such as living shorelines, have the potential to restore critical ecosystems, enhance coastal sustainability, and increase resilience to natural disasters; however, their efficacy during storm events compared to traditional hardened shorelines is largely untested. This is a major impediment to their implementation and promotion to policy-makers and homeowners. To address this knowledge gap, we evaluated rock sill living shorelines as compared to natural marshes and hardened shorelines (i.e. bulkheads) in North Carolina, USA...

Data from: Optimizing prevention of HIV mother to child transmission: duration of antiretroviral therapy and viral suppression at delivery among pregnant Malawian women

Maganizo B. Chagomerana, William C. Miller, Jennifer H. Tang, Irving F. Hoffman, Bryan C. Mthiko, Jacob Phulusa, Mathias John, Allan Jumbe & Mina C. Hosseinipour
Background: Effective antiretroviral therapy during pregnancy minimizes the risk of vertical HIV transmission. Some women present late in their pregnancy for first antenatal visit; whether these women achieve viral suppression by delivery and how suppression varies with time on ART is unclear. Methods: We conducted a prospective cohort study of HIV-infected pregnant women initiating antiretroviral therapy for the first time from June 2015 to November 2016. Multivariable Poisson models with robust variance estimators were used...

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: Oyster aquaculture impacts Zostera marina epibiont community composition in Akkeshi-ko estuary, Japan

Carter S. Smith, Minako Ito, Mizuho Namba & Masahiro Nakaoka
Coastal fisheries are in decline worldwide, and aquaculture has become an increasingly popular way to meet seafood demand. While finfish aquaculture can have substantial adverse effects on coastal ecosystems due mostly to necessary feed inputs, bivalves graze on natural phytoplankton and are often considered for their positive ecosystem services. We conducted two independent studies to investigate the effects of long-line Crassostrea gigas oyster aquaculture on Zostera marina seagrass beds and associated epibiont communities in Akkeshi-ko...

Data from: A host immune hormone modifies parasite species interactions and epidemics: insights from a field manipulation.

Fletcher W. Halliday, James Umbanhowar & Charles E. Mitchell
Parasite epidemics can depend on priority effects, and parasite priority effects can result from the host immune response to prior infection. Yet we lack experimental evidence that such immune-mediated priority effects influence epidemics. To address this research gap, we manipulated key host immune hormones, then measured the consequences for within-host parasite interactions, and ultimately parasite epidemics in the field. Specifically, we applied plant immune-signaling hormones to sentinel plants, embedded into a wild host population, and...

Data from: Beyond novelty effect: a mixed-methods exploration into the motivation for long-term activity tracker use

Grace Shin, Yuanyuan Feng, Mohammad Hossein Jarrahi & Nicci Gafinowitz
Objectives: Activity trackers hold the promise to support people in managing their health through quantified measurements about their daily physical activities. Monitoring personal health with quantified activity tracker-generated data provides patients with an opportunity to self-manage their health. Many activity tracker user studies have been conducted within short time frames, however, which makes it difficult to discover the impact of the activity tracker’s novelty effect or the reasons for the device’s long-term use. This study...

Data from: Systematic revision of Symbiodiniaceae highlights the antiquity and diversity of coral endosymbionts

Todd C. LaJeunesse, John Everett Parkinson, Paul W. Gabrielson, Hae Jin Jeong, James Davis Reimer, Christian R. Voolstra & Scott R. Santos
The advent of molecular data has transformed the science of organizing and studying life on Earth. Genetics-based evidence provides fundamental insights into the diversity, ecology, and origins of many biological systems, including the mutualisms between metazoan hosts and their micro-algal partners. A well-known example is the dinoflagellate endosymbionts (“zooxanthellae”) that power the growth of stony corals and coral reef ecosystems. Once assumed to encompass a single panmictic species, genetic evidence has revealed a divergent and...

Data from: Uncertainty in geographic estimates of performance and fitness

H. Arthur Woods, Joel G. Kingsolver, Samuel B. Fey & David A. Vasseur
1. Thermal performance curves (TPCs) have become key tools for predicting geographic distributions of performance by ectotherms. Such TPC-based predictions, however, may be sensitive to errors arising from diverse sources. 2. We analyzed potential errors that arise from common choices faced by biologists integrating TPCs with climate data by constructing case studies focusing on experimental sets of TPCs and simulating geographic patterns of mean performance. We first analyzed differences in geographic patterns of performance derived...

Data from: The genomic and ecological context of hybridization affects the probability that symmetrical incompatibilities drive hybrid speciation

Aaron A. Comeault
Despite examples of homoploid hybrid species, theoretical work describing when, where, and how we expect homoploid hybrid speciation to occur remains relatively rare. Here, I explore the probability of homoploid hybrid speciation due to “symmetrical incompatibilities” under different selective and genetic scenarios. Through simulation, I test how genetic architecture and selection acting on traits that do not themselves generate incompatibilities interact to affect the probability that hybrids evolve symmetrical incompatibilities with their parent species. Unsurprisingly,...

Data from: Geomagnetic field influences upward movement of young Chinook salmon emerging from nests

Nathan F. Putman, Michelle M. Scanlan, Amanda M. Pollock, Joseph P. O'Neil, Ryan B. Couture, Joseph S. Stoner, Thomas P. Quinn, Kenneth J. Lohmann, David L.G. Noakes & David L. G. Noakes
Organisms use a variety of environmental cues to orient their movements in three-dimensional space. Here, we show that the upward movement of young Chinook salmon (Oncorhynchus tshawytscha) emerging from gravel nests is influenced by the geomagnetic field. Fish in the ambient geomagnetic field travelled farther upwards through substrate than did fish tested in a field with the vertical component inverted. This suggests that the magnetic field is one of several factors that influences emergence from...

Data from: Speciation in sympatry with ongoing secondary gene flow and an olfactory trigger in a radiation of Cameroon cichlids

Jelmer W. Poelstra, Emilie J. Richards & Christopher H. Martin
The process of sympatric speciation in nature remains a fundamental unsolved problem. Cameroon crater lake cichlid radiations were long regarded as one of the most compelling examples; however, recent work showed that their origins were more complex than a single colonization event followed by isolation. Here, we performed a detailed investigation of the speciation history of a radiation of Coptodon cichlids from Lake Ejagham using whole-genome sequencing data. The existence of this radiation is remarkable...

Data from: Complex data produce better characters

B.K. Kirchoff, S.J. Richter, D.L. Remington & E. Wisniewski
Two studies were conducted to explore the use of complex data in character description and hybrid identification. In order to determine if complex data allow the production of better characters, eight groups of plant systematists were given two classes of drawings of plant parts, and asked to divide them into character states (clusters) in two separate experiments. The first class of drawings consisted only of cotyledons. The second class consisted of triplets of drawings: a...

Data from: Cardiac vagal dysfunction moderates patterns of craving across the day in moderate to heavy consumers of alcohol

Rhiannon E. Mayhugh, Paul J. Laurienti, Jason Fanning, Lise Gauvin, Keri J. Heilman, Stephen W. Porges & W. Jack Rejeski
Background: Alcohol craving, a known correlate of vulnerability to Alcohol Use Disorder (AUD), has been found to be inversely related to cardiac vagal tone (CVT). Here we examine how resting CVT, CVT reactivity to a postural challenge, and their interaction influence craving during imposed alcohol abstinence and their usual drinking among moderate to heavy drinkers. Methods: Participants were recruited from the local community (final n=29) and assessed for CVT functioning via respiratory sinus arrhythmia (RSA)...

Data from: The analysis and interpretation of critical temperatures

Joel G. Kingsolver & James Umbanhowar
Critical temperatures are widely used to quantify the upper and lower thermal limits of organisms. But measured critical temperatures often vary with methodological details, leading to spirited discussions about the potential consequences of stress and acclimation during the experiments. We review a model based on the simple assumption that failure rate increases with increasing temperature, independent of previous temperature exposure, water loss or metabolism during the experiment. The model predicts that mean critical thermal maximal...

Data from: The evolution of sexual imprinting through reinforcement

D. Justin Yeh, Janette W. Boughman, Glenn-Peter Saetre & Maria R. Servedio
Reinforcement is the process whereby assortative mating evolves due to selection against costly hybridization. Sexual imprinting could evolve as a mechanism of reinforcement, decreasing hybridization, or it could potentially increase hybridization in genetically purebred offspring of heterospecific social pairs. We use deterministic population genetic simulations to explore conditions under which sexual imprinting can evolve through reinforcement. We demonstrate that a sexual imprinting component of female preference can evolve as a one-allele assortative mating mechanism by...

Data from: Improved access to early diagnosis and complete treatment of malaria in Odisha, India

Sreya Pradhan, Madan M. Pradhan, Ambarish Dutta, Naman K. Shah, Pyare L. Joshi, Khageshwar Pradhan, S.K. Sharma, Penny Grewal Daumerie, Jaya Banerji, Stephan Duparc, Kamini Mendis, Shiva Murugasampillay, Neena Valecha, Anupkumar R. Anvikar & S. K. Sharma
Background In 2013, the Comprehensive Case Management Programme (CCMP) was initiated to assess the impact of universal access to diagnosis and treatment and improved surveillance on malaria transmission in different settings in Odisha state, India. Methods Pairs of intervention and control sub-districts (blocks), matched on malaria incidence were selected in four districts with different transmission intensities. CCMP activities included training and supervision, ensuring no stock-outs of malaria tests and drugs, analysing verified surveillance data, stratifying...

Data from: Non-adaptive female pursuit of extra-pair copulations can evolve through hitchhiking

Nan Lyu, Maria R. Servedio & Yue-Hua Sun
Mounting evidence has indicated that engaging in extra-pair copulations (EPCs) might be maladaptive or detrimental to females. It is unclear why such non-adaptive female behavior evolves. In this study, we test two hypotheses about the evolution of female EPC behavior using population genetic models. First, we find that both male preference for allocating extra-effort to seek EPCs and female pursuit behavior without costs can be maintained and remain polymorphic in a population via frequency dependent...

Data from: Upper atmosphere heating from ocean-generated acoustic wave energy

Daniel C. Bowman & Jonathan M. Lees
Colliding sea surface waves generate the ocean microbarom, an acoustic signal that may transmit significant energy to the upper atmosphere. Previous estimates of acoustic energy flux from the ocean microbarom and mountain/wind interactions are on the order of 0.01 to 1 mW/m2, heating the thermosphere by tens of degrees Kelvin per day. We captured up going ocean microbarom waves with a balloon borne infrasound microphone; the maximum acoustic energy flux was approximately 0.05 mW/m2. This...

Data from: Near absence of differential gene expression in the retina of rainbow trout after exposure to a magnetic pulse: implications for magnetoreception

Robert R. Fitak, Lorian E. Schweikert, Benjamin R. Wheeler, David A. Ernst, Kenneth J. Lohmann & Sonke Johnsen
The ability to perceive Earth’s magnetic field, or magnetoreception, exists in numerous animals. Although the mechanism underlying magnetoreception has not been clearly established in any species, in salmonid fish it is hypothesized to occur by means of crystals of magnetite associated with nervous tissue such as the brain, olfactory organ, or retina. In this study, rainbow trout (Oncorhynchus mykiss) were exposed to a brief magnetic pulse known to disrupt magnetic orientation behavior in several animals....

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