61 Works

Data from: Species diversification and phylogenetically constrained symbiont switching generated high modularity in the lichen genus Peltigera

Pierre-Luc Chagnon, Nicolas Magain, Jolanta Miadlikowska & Francois Lutzoni
1. Ecological interactions range from purely specialized to extremely generalized in nature. Recent research has showed very high levels of specialization in the cyanolichens involving Peltigera (mycobionts) and their Nostoc photosynthetic partners (cyanobionts). Yet, little is known about the mechanisms contributing to the establishment and maintenance of such high specialization levels. 2. Here, we characterized interactions between Peltigera and Nostoc partners at a global scale, using more than one thousand thalli. We used tools from...

Data from: Genes, geology, and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host species

Laura E. Grieneisen, Marie J. E. Charpentier, Susan C. Alberts, Ran Blekhman, Gideon Bradburd, Jenny Tung & Elizabeth A. Archie
Gut microbiota in geographically isolated host populations are often distinct. These differences have been attributed to between-population differences in host behaviors, environments, genetics, and geographic distance. However, which factors are most important remains unknown. Here we fill this gap for baboons by leveraging information on 13 environmental variables from 14 baboon populations spanning a natural hybrid zone. Sampling across a hybrid zone allowed us to additionally test whether phylosymbiosis (codiversification between hosts and their microbiota)...

Data from: Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography

Yifu Ding, Daniel J Vanselow, Maksim A Yakovlev, Spencer R Katz, Alex Y Lin, Darin P Clark, Phillip Vargas, Xuying Xin, Jean E Copper, Victor A Canfield, Khai C Ang, Yuxin Wang, Xianghui Xiao, Francesco De Carlo, Damian B Van Rossum, Patrick La Riviere & Keith Cheng
Organismal phenotypes frequently involve multiple organ systems. Histology is a powerful way to detect cellular and tissue phenotypes, but is largely descriptive and subjective. To determine how synchrotron-based X-ray micro-tomography (micro-CT) can yield 3-dimensional whole-organism images suitable for quantitative histological phenotyping, we scanned whole zebrafish, a small vertebrate model with diverse tissues, at ~1 micron voxel resolutions. Using micro-CT optimized for cellular characterization (histo-tomography), brain nuclei can be computationally segmented and assigned to brain regions....

Biotic and anthropogenic forces rival climatic/abiotic factors in determining global plant population growth and fitness

William Morris
Multiple, simultaneous environmental changes, in climatic/abiotic factors, in interacting species, and in direct human influences, are impacting natural populations and thus biodiversity, ecosystem services, and evolutionary trajectories. Determining whether the magnitudes of the population impacts of abiotic, biotic, and anthropogenic drivers differ, accounting for their direct effects and effects mediated through other drivers, would allow us to better predict population fates and design mitigation strategies. We compiled 644 paired values of the population growth rate...

Supp_Figs_11_12_13_CELL-METABOLISM-D-19-00134_Williams_et_al

Timothy Koves
Uncropped Blots for CELL-METABOLISM-D-19-00134 Disruption of acetyl-lysine turnover in muscle mitochondria promotes insulin resistance and redox stress without overt respiratory dysfunction

Convergent evolution in lemur environmental niches

James Herrera
Aim: To test the hypothesis that adaptive convergent evolution of climate niches occurred in multiple independent lemur lineages. Location: Madagascar Taxon: Lemurs Methods: I collected climate and altitude data from WorldClim and summarized the niches of almost all living lemurs (83 species) into phylogenetically-controlled principal components. To test for convergent evolution, I searched for multiple, similar climate optima using multi-peak Ornstein-Uhlenbeck models (surface, l1-ou, bayou). I compared the observed level of climate convergence to that...

Data from: Comparative genomic analysis of the pheromone receptor Class 1 family (V1R) reveals extreme complexity in mouse lemurs (genus, Microcebus) and a chromosomal hotspot across mammals

Kelsie E Hunnicutt, George P Tiley, Rachel C Williams, Peter A Larsen, Marina B Blanco, Rodin M Rasoloarison, Christopher Ryan Campbell, Kevin Zhu, David W Weisrock, Hiroaki Matsunami & Anne D Yoder
Sensory gene families are of special interest, both for what they can tell us about molecular evolution, and for what they imply as mediators of social communication. The vomeronasal type-1 receptors (V1Rs) have often been hypothesized as playing a fundamental role in driving or maintaining species boundaries given their likely function as mediators of intraspecific mate choice, particularly in nocturnal mammals. Here, we employ a comparative genomic approach for revealing patterns of V1R evolution within...

Methods Synopsis

Laura Warmuth & David Gill

Folk Intuitions and the Conditional Ability to Do Otherwise

Thomas Nadelhoffer, Siyuan Yin & Rose Graves

Data from: Costs and drivers of helminth parasite infection in wild female baboons

Mercy Y. Akinyi, David Jansen, Bobby Habig, Laurence Gesquiere, Susan C. Alberts & Elizabeth A. Archie
1. Helminth parasites can have wide ranging, detrimental effects on host reproduction and survival. These effects are best documented in humans and domestic animals, while only a few studies in wild mammals have identified both the forces that drive helminth infection risk and their costs to individual fitness. 2. Working in a well-studied population of wild baboons (Papio cynocephalus) in the Amboseli ecosystem in Kenya, we pursued two goals, to: (i) examine the costs of...

NASPSPA/STORK Pre-Conference Workshop on Open Science Practices

Christopher Hill, Keith Lohse, John Mills & Zachary Zenko
Files and materials from the NASPSPA/STORK pre-conference workshop on open science practices.

Systematic review of public evaluations of the LENA (TM) software

Alejandrina Cristia, Federica Bulgarelli & Elika Bergelson

Presentations Given by COS

, , Hannah Moshontz, Briana Wade, Terry Foor, Mirka Dirzo, Brian J. Geiger, Olivia Miske, Blaine Butler, Andrew Tyner, Abram Booth, Zachary Loomas, Olivia Lowrey, Nicole Pfeiffer, Macie Daley, Huajin Wang, Doug Corell, Sarah Lynch, Fielding L. Grasty, Brian Pilati, Alexis Rice, David Thomas Mellor, Fitz Elliott, Marcy Reedy, Matthew Frazier … & Matt Clark
A collection of slides for virtually all presentations given by Center for Open Science staff since its founding in 2013.

Dissociating the freely-moving thought dimension of mind-wandering from the intentionality and task-unrelated thought dimensions

Kevin O'Neill, Anna Smith, Paul Seli & Daniel Smilek
The recently forwarded family-resemblances framework of mind-wandering argues that mind-wandering is a multidimensional construct consisting of a variety of exemplars. On this view, membership in the mind-wandering family is graded along various dimensions that define more or less prototypical instances of mind-wandering. In recent work, three dimensions that have played a prominent role in defining prototypicality within the mind-wandering family include: (a) task-relatedness (i.e., how related the content of a thought is to an ongoing...

New Needs, New Approaches: Libraries as Technology Collaborators

Susan Ivey
Presentation for NISO's "That Cutting Edge: Technology’s Impact on Scholarly Research Processes in the Library". October 24, 2018

Data from: Eulerian videography technology improves classification of sleep architecture in primates

Emilie M. Melvin, David R. Samson & Charles L. Nunn
Sleep is a critically important dimension of primate behavior, ecology, and evolution, yet primate sleep is under-studied because current methods of analyzing sleep are expensive, invasive, and time-consuming. In contrast to electroencephalography (EEG) and actigraphy, videography is a cost-effective and non-invasive method to study sleep architecture in animals. With video data, however, it is challenging to score subtle changes that occur in different sleep states, and technology has lagged behind innovations in EEG and actigraphy....

Social bonds fail to mediate the connection between early adversity and fecal glucocorticoids in wild baboons

Shuxi Zeng
Code scripts for "Social bonds fail to mediate the connection between early adversity and fecal glucocorticoids in wild baboons ".

Differential Return on Investment: Academic Growth based on Initial Performance

Karen Rambo-Hernandez, Matthew Makel & Scott Peters

Data from: Intestinal Serum Amyloid A suppresses systemic neutrophil activation and bactericidal activity in response to microbiota colonization

Caitlin Murdoch, Scott Espenschied, Molly Matty, Olaf Mueller, David Tobin & John Rawls
The intestinal microbiota influences the development and function of myeloid lineages such as neutrophils, but the underlying molecular mechanisms are unresolved. Using gnotobiotic zebrafish, we identified the immune effector Serum amyloid A (Saa) as one of the most highly induced transcripts in digestive tissues following microbiota colonization. Saa is a conserved secreted protein produced in the intestine and liver with described effects on neutrophils in vitro, however its in vivo functions remain poorly defined. We...

Data from: Genomic signatures of GPCR expansions reveal functional transitions in the evolution of cephalopod signal transduction

Elena A. Ritschard, Robert R. Fitak, Oleg Simakov & Sönke Johnsen
Coleoid cephalopods show unique morphological and neural novelties, such as arms with tactile and chemosensory suckers and a large complex nervous system. The evolution of such cephalopod novelties has been attributed at a genomic level to independent gene family expansions, yet the exact association and the evolutionary timing remain unclear. In the octopus genome, one such expansion occurred in the G-protein coupled receptors (GPCRs) repertoire, a superfamily of proteins that mediate signal transduction. Here we...

Data from: Statistical structure of locomotion and its modulation by odors

Liangyu Tao, Siddhi Ozarkar, Jeffrey M. Beck & Vikas Bhandawat
Most behaviors such as making tea are not stereotypical but have an obvious structure. However, analytical methods to objectively extract structure from non-stereotyped behaviors are immature. In this study, we analyze the locomotion of fruit flies and show that this non-stereotyped behavior is well-described by a Hierarchical Hidden Markov Model (HHMM). HHMM shows that a fly's locomotion can be decomposed into a few locomotor features, and odors modulate locomotion by altering the time a fly...

Resource-use optimization across the age gap: Older adults less effectively modulate their mind-wandering than young

Paul Seli & Kevin O'Neill
Preregistration, data, and materials used in Seli et al.'s paper entitled: " Resource-use optimization across the age gap: Older adults less effectively modulate their mind-wandering than young"

Data from: Male-mediated prenatal loss: functions and mechanisms

Matthew Zipple, Eila K. Roberts, Susan C. Alberts & Jacinta C. Beehner
Sexually selected infanticide has been the subject of intense empirical and theoretical study for decades; a related phenomenon, male-mediated prenatal loss, has received much less attention in evolutionary studies. Male-mediated prenatal loss occurs when inseminated or pregnant females terminate reproductive effort following exposure to a non-sire male, either through implantation failure or pregnancy termination. Male-mediated prenatal loss encompasses two sub-phenomena: sexually selected feticide and the Bruce effect. In this review, we lay out a framework...

Maternal pre-pregnancy obesity, offspring cord blood DNA methylation, and offspring cardiometabolic health in early childhood: an epigenome-wide association study

Chantel L. Martin, Dereje Jima, Gemma C. Sharp, Lauren E. McCullough, Sarah S. Park, Kymberly M. Gowdy, David Skaar, Michael Cowley, Rachel L. Maguire, Bernard Fuemmeler, David Collier, Caroline L. Relton, Susan K. Murphy & Cathrine Hoyo
Pre-pregnancy obesity is an established risk factor for adverse sex-specific cardiometabolic health in offspring. Epigenetic alterations, such as in DNA methylation (DNAm), are a hypothesized link; however, sex-specific epigenomic targets remain unclear. Leveraging data from the Newborn Epigenetics Study (NEST) cohort, linear regression models were used to identify CpG sites in cord blood leukocytes associated with pre-pregnancy obesity in 187 mother-female and 173 mother-male offsprings. DNAm in cord blood was measured using the Illumina HumanMethylation450k...

Data from: Phylogenomic delineation of Physcomitrium (Bryophyta: Funariaceae) based on targeted sequencing of nuclear exons and their flanking regions rejects the retention of Physcomitrella, Physcomitridium and Aphanorrhegma

Rafael Medina, Matthew G. Johnson, Yang Liu, Norman J. Wickett, A. Jonathan Shaw & Bernard Goffinet
Selection on spore dispersal mechanisms in mosses is thought to shape the transformation of the sporophyte. The majority of extant mosses develop a sporangium that dehisces through the loss of an operculum, and regulates spore release through the movement of articulate teeth, the peristome, lining the capsule mouth. Such complexity was acquired by the Mesozoic Era, but was lost in some groups during subsequent diversification events, challenging the resolution of the affinities for taxa with...

Registration Year

  • 2019
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Affiliations

  • Duke University
    61
  • University of Notre Dame
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  • The University of Texas Southwestern Medical Center
    3
  • University of Minnesota
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  • University of Chicago
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  • University of Connecticut
    2
  • Michigan State University
    2
  • University of South Dakota
    1
  • University of Liège
    1
  • The Nature Conservancy
    1