30 Works

Data from: Adaptive periodicity in the infectivity of malaria gametocytes to mosquitoes

Petra Schneider, Samuel S.C. Rund, Natasha L. Smith, Kimberley F. Prior, Aidan J. O'Donnell, Sarah E. Reece & Samuel S. C. Rund
Daily rhythms in behaviour, physiology, and molecular processes are expected to enable organisms to appropriately schedule activities according to consequences of the daily rotation of the Earth. For parasites, this includes capitalizing on periodicity in transmission opportunities and for hosts/vectors, this may select for rhythms in immune defence. We examine rhythms in the density and infectivity of transmission forms (gametocytes) of rodent malaria parasites in the host’s blood, parasite development inside mosquito vectors, and potential...

Data from: The importance of growing up: juvenile environment influences dispersal of individuals and their neighbours

Stacy B. Endriss, Megan L. Vahsen, Ellyn V. Bitume, J. Grey Monroe, Kathryn G. Turner, Andrew P. Norton & Ruth A. Hufbauer
Dispersal is a key ecological process that is strongly influenced by both phenotype and environment. Here, we show that juvenile environment influences dispersal not only by shaping individual phenotypes, but also by changing the phenotypes of neighbouring conspecifics, which influence how individuals disperse. We used a model system (Tribolium castaneum, red flour beetles) to test how the past environment of dispersing individuals and their neighbours influences how they disperse in their current environment. We found...

Data from: Spatiotemporal incidence of Zika and associated environmental drivers for the 2015-2016 epidemic in Colombia

Amir S. Siraj, I. Rodriguez-Barraquer, Christopher M. Barker, Natalia Tejedor-Garavito, Dennis Harding, Christopher Lorton, Dejan Lukacevic, Gene Oates, Guido Espana, Moritz U. G. Kraemer, Carrie Manore, Michael A. Johansson, Andrew J. Tatem, Robert C. Reiner & T. Alex Perkins
Despite a long history of mosquito-borne virus epidemics in the Americas, the impact of the Zika virus (ZIKV) epidemic of 2015-2016 was unexpected. The need for scientifically informed decision-making is driving research to understand the emergence and spread of ZIKV. To support that research, we assembled a data set of key covariates for modeling ZIKV transmission dynamics in Colombia, where ZIKV transmission was widespread and the government made incidence data publically available. On a weekly...

Data from: A century of genetic variation inferred from a persistent soil-stored seed bank

Jennifer L. Summers, Brittany Bernik, Colin J. Saunders, Jason S. McLachlan & Michael J. Blum
Stratigraphic accretion of dormant propagules in soil can result in natural archives useful for studying ecological and evolutionary responses to environmental change. Few attempts have been made, however, to use soil-stored seed banks as natural archives, in part because of concerns over non-random attrition and mixed stratification. Here we examine the persistent seed bank of Schoenoplectus americanus, a foundational brackish marsh sedge, to determine whether it can serve as a resource for reconstructing historical records...

Planning Phase Iteration of Tech Design Doc (Thru Fall 2018)

Sandra Gesing, Richard Johnson, Natalie Meyers, John Wang & Noel Recla
Tech Design for PresQT planning project (funded by IMLS, award LG-72-16-0122-16 )

Replicating our Instructional Capacity: Developing Shared Workshops across Institutions

Danica Lewis, Barrie Hayes & Alexander Carroll
User communities are asking librarians for support finding non-textual information and data. Given that their instructional capacity is already stretched thin, many librarians are apprehensive about developing classes to support these emerging topics. To overcome these challenges, librarians at the NCSU Libraries and the UNC Health Sciences Library developed a shared suite of instructional materials for bioinformatics workshops that are now offered at both campuses. This presentation will discuss the benefits and challenges of developing...

Evaluation of R Packages with IRT 2PL Model

Shuya Zhang, Maxwell Hong & Alison Cheng
This simulation study compares the three most popular R packages: ltm, mirt and TAM, in terms of the accuracy and precision of item parameter estimation and computational efficiency for the IRT 2PL model. Ability parameters are simulated from a normal, uniform and a skewed distribution. Response matrices are simulated and the three packages are used to estimate item parameters. Bias and MSE of item parameter estimates and computing time are compared. Ultimately, the three packages...

Dissociating Morpheme Form and Meaning: Evidence for Morphological Decomposition of Compound Words during Reading

Teon Brooks & Peter Gordon
Compound words have two free morphemes whose individual meanings can have a transparent (e.g., roadside) or opaque (e.g., butterfly) relationship to the overall meaning. It is unclear when meaning is accessed during lexical processing of compounds (and other morphologically complex words), with conflicting results from priming in lexical-decision studies and from reading-time studies that examine how the characteristics of a compound affect its processing. The present studies examined eye-movement measures on target words in a...

Data from: Interbirth intervals in wild baboons: environmental predictors and hormonal correlates

Laurence R. Gesquiere, Jeanne Altmann, Elizabeth A. Archie & Susan C. Alberts
Objectives: Interbirth intervals (IBIs) are a key metric of female reproductive success; understanding how they are regulated by environmental, social, and demographic factors can provide insight into sources of variance in female fitness. Materials and Methods: Using 36 years of reproductive data on 490 IBIs for 160 wild female baboons, we identified sources of variance in the duration of IBIs and of their component phases: postpartum amenorrhea (PPA), sexual cycling, and pregnancy. We also examined...

Data from: Limited genetic evidence for host plant-related differentiation in the Western cherry fruit fly Rhagoletis indifferens (Diptera: Tephritidae)

Gilbert Saint Jean, Glen R. Hood, Scott P. Egan, Thomas H.Q. Powell, Hannes Schuler, Meredith M. Doellman, Mary M. Glover, James J. Smith, Wee L. Yee, Robert B. Goughnour, Howard M.A. Thistlewood, Sheri A. Maxwell, Nusha Keyghobadi, Juan Rull, Martin Aluja, Jeffrey L. Feder & Thomas H. Q. Powell
The shift of the fruit fly Rhagoletis pomonella (Walsh) in the mid-1800s from downy hawthorn, Crataegus mollis (Torrey & Asa Gray) Scheele, to introduced domesticated apple, Malus domestica (Borkhausen), in the eastern USA is a model for ecological divergence with gene flow. A similar system may exist in the northwestern USA and British Columbia, Canada, where Rhagoletis indifferens Curran (Diptera: Tephritidae) attacks the native bitter cherry Prunus emarginata (Douglas ex Hooker) Eaton (Rosaceae). Populations of...

Data from: Mate choice strategies in a spatially-explicit model environment

Giordano B.S. Ferreira, Matthias Scheutz, Sunny K. Boyd & Giordano B. S. Ferreira
Decisions about the choice of a mate can greatly impact both individual fitness and selection processes. We developed a novel agent-based model to investigate two common mate choice rules that may be used by female gray treefrogs (Hyla versicolor). In this model environment, female agents using the minimum-threshold strategy found higher quality mates and traveled shorter distances on average, compared with female agents using the best-of-n strategy. Females using the minimum-threshold strategy, however, incur significant...

PresQT Needs Assessment

Donald Brower, Sandra Gesing, Brandon Greenawalt, Richard Johnson, Natalie Meyers, Jeffrey Spies & John Wang
PresQT Needs Assessment conducted Summer-Fall 2017

960 EBA from Base Rates to LASSO

Eric Youngstrom, Thu-Mai Christian & Amanda Gooch

PresQT May 1-2 , 2017 Workshop

Sandra Gesing, Richard Johnson, Natalie Meyers, John Wang & Noel Recla
PresQT May 1-2 , 2017 Workshop at University of Notre Dame

Data from: Standing geographic variation in eclosion time and the genomics of host race formation in Rhagoletis pomonella fruit flies

Meredith M. Doellman, Scott P. Egan, Gregory J. Ragland, Peter J. Meyers, Glen R. Hood, Thomas H.Q. Powell, Peter Lazorchak, Daniel A. Hahn, Stewart H. Berlocher, Patrik Nosil, Jeff L. Feder, Jeffrey L. Feder & Thomas H. Q. Powell
Taxa harboring high levels of standing variation may be more likely to adapt to rapid environmental shifts and experience ecological speciation. Here, we characterize geographic and host-related differentiation for 10,241 single nucleotide polymorphisms in Rhagoletis pomonella fruit flies to infer if standing genetic variation in adult eclosion time in the ancestral hawthorn (Crataegus spp.)-infesting host race, as opposed to new mutations, contributed substantially to its recent shift to earlier fruiting apple (Malus domestica). Allele frequency...

Data from: Climate-mediated hybrid zone movement revealed with genomics, museum collection and simulation modeling

Sean F. Ryan, Jillian M. Deines, J. Mark Scriber, Michael E. Pfrender, Stuart E. Jones, Scott J. Emrich & Jessica J. Hellmann
Climate-mediated changes in hybridization will dramatically alter the genetic diversity, adaptive capacity and evolutionary trajectory of interbreeding species. Our ability to predict the consequences of such changes will be key to future conservation and management decisions. Here we tested through simulations how recent warming (over a 32-year period) is affecting the geographic extent of a climate-mediated developmental threshold implicated in maintaining a butterfly hybrid zone (Papilio glaucus and Papilio canadensis; Lepidoptera: Papilionidae). These simulations predict...

How Notre Dame Researchers Use Open Source Tools to Facilitate Collaboration

Natalie Meyers
An RDAP webinar presentation Jan 23, 2018 for a panel on How Researchers Use Open Source Tools to Facilitate Collaboration


Eric Youngstrom & Joshua Langfus
Teaching materials for Receiver Operating Characteristic (ROC) analyses and naive Bayesian applications

Open Science Framework for Reproducible Research AGU Data FAIR Workshop

Natalie Meyers
A presentation on Open Science Framework for Reproducible Research delivered at the AGU Data FAIR Workshop Dec 12 at AGU Fall meeting 2018

PresQT Sept 18, 2017 Workshop

Sandra Gesing, Richard Johnson, Natalie Meyers, John Wang & Noel Recla
Workshop Info for PresQT Workshop II collocated at RDA 10th Plenary in Montreal

PresQT Use Cases

Donald Brower, Sandra Gesing, Richard Johnson, Markus Krusche, Natalie Meyers, Jeffrey Spies, Miranda VanNevel, John Wang & Noel Recla

Data from: Genomic differentiation during speciation-with-gene-flow: comparing geographic and host-related variation in divergent life history adaptation in Rhagoletis pomonella

Meredith M. Doellman, Gregory J. Ragland, Glen R. Hood, Peter J. Meyers, Scott P. Egan, Thomas H.Q. Powell, Peter Lazorchak, Mary M. Glover, Cheyenne Tait, Hannes Schuler, Daniel A. Hahn, Stewart H. Berlocher, James J. Smith, Patrik Nosil, Jeffrey L. Feder, Daniel Hahn, Stewart Berlocher, Peter Meyers, Scott Egan, Jeffrey Feder, Glen Hood, Thomas Powell & Gregory Ragland
A major goal of evolutionary biology is to understand how variation within populations gets partitioned into differences between reproductively isolated species. Here, we examine the degree to which diapause life history timing, a critical adaptation promoting population divergence, explains geographic and host-related genetic variation in ancestral hawthorn and recently derived apple-infesting races of Rhagoletis pomonella. Our strategy involved combining experiments on two different aspects of diapause (initial diapause intensity and adult eclosion time) with a...

Women in Science Conference - OSF 101

Natalie Meyers
A presentation delivered to the Women in Science Conference (WISC 2018) at University of Notre Dame

Implementation Phase Technical Project Plan Resources

Donald Brower, Sandra Gesing, Markus Krusche, Richard Johnson, Natalie Meyers, Miranda VanNevel, John Wang & Noel Recla

Data from: Natural selection and the predictability of evolution in Timema stick insects

Patrik Nosil, Romain Villoutreix, Clarissa F. De Carvalho, Tim E. Farkas, Victor Soria-Carrasco, Jeff L. Feder, Bernard J. Crespi & Zachariah Gompert
Predicting evolution remains difficult. We studied the evolution of cryptic body coloration and pattern in a stick insect using 25 years of field data, experiments, and genomics. We found that evolution is more difficult to predict when it involves a balance between multiple selective factors and uncertainty in environmental conditions than when it involves feedback loops that cause consistent back-and-forth fluctuations. Specifically, changes in color-morph frequencies are modestly predictable through time (r2 = 0.14) and...

Registration Year

  • 2018

Resource Types

  • Text
  • Dataset


  • University of Notre Dame
  • Center For Open Science
  • Notre Dame University
  • University of North Carolina at Chapel Hill
  • University of Sheffield
  • Michigan State University
  • Rice University
  • Utah State University
  • Johns Hopkins University
  • United States Department of Agriculture