83 Works

Reproducible Social Work Research

Daniel Dunleavy
Syllabus to be presented at Research Reproducibility 2020.

Audio Stroop

Jonathan Ryan & A. Threadgill

Data from: Bee phenology is predicted by climatic variation and functional traits

Michael Stemkovski, Will Pearse, Sean Griffin, Gabriella Pardee, Jason Gibbs, Terry Griswold, John Neff, Ryan Oram, Molly RightMyer, Cory Sheffield, Karen Wright, Brian Inouye, David Inouye & Rebecca Irwin
Climate change is shifting the environmental cues that determine the phenology of interacting species. Plant-pollinator systems may be susceptible to temporal mismatch if bees and flowering plants differ in their phenological responses to warming temperatures. While the cues that trigger flowering are well-understood, little is known about what determines bee phenology. Using Generalized Additive Models, we analyzed time-series data representing 67 bee species collected over nine years in the Colorado Rocky Mountains to perform the...

Data from: Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus)

Robert Alexander Pyron, Kyle A. O'Connell, Emily Moriarty Lemmon, Alan R. Lemmon & David A. Beamer
Gene flow between evolutionarily distinct lineages is increasingly recognized as a common occurrence. Such processes distort our ability to diagnose and delimit species, as well as confound attempts to estimate phylogenetic relationships. A conspicuous example is Dusky Salamanders (Desmognathus), a common model-system for ecology, evolution, and behavior. Only 22 species are described; 7 in the last 40 years. However, mitochondrial datasets indicate the presence of up to 45 “candidate species” presenting a complex history of...

Developing small worlds of e-science: using quantum mechanics, biological science, and oceanography for education and outreach strategies for engaging research communities within a university

Plato Smith
The paper provides an introductory and exploratory research method for developing a data management plan strategy through the experimental approach of developing and preserving small worlds of e-science of grey literature from the physics, biological, and oceanographic research disciplines at Florida State University. The paper opted for an experimental approach of digitization, cataloging, and resource discovery in a digital content management system (DigiTool), online public access catalog (OPAC) in Aleph and OCLC WorldCat, and preservation...

Data from: Evolutionary and plastic phenotypic change can be just as fast as changes in population densities

Michael Cortez & Guenchik Grosklos
Evolution and plasticity can drive population-level phenotypic change (e.g., changes in the mean phenotype) on time scales comparable to changes in population densities. However, it is unclear if phenotypic change has the potential to be just as fast as changes in densities, or if comparable rates of change only occur when densities are changing slow enough for phenotypes to keep pace. Moreover, it is unclear if this depends on the mode of adaptation. Using scaling...

Data from: Congruence and conflict in the higher-level phylogenetics of squamate reptiles: an expanded phylogenomic perspective

Sonal Singhal, Timothy Colston, Maggie Grundler, Stephen Smith, Gabriel Costa, Guarino Colli, Craig Moritz, Alexander Pyron & Daniel Rabosky
Genome-scale data have the potential to clarify phylogenetic relationships across the tree of life, but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger datasets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflict is important for accurate reconstruction of evolutionary history. We explore this paradox in squamate reptiles, the vertebrate clade comprising lizards, snakes, and amphisbaenians. We collected an average of 5103 loci for 91 species...

Cohesin depleted cells rebuild functional nuclear compartments after endomitosis

Marion Cremer, Katharina Brandstetter, Andreas Maiser, Suhas S P Rao, Volker Schmid, Miguel Guirao-Ortiz, Namita Mitra, Stefania Mamberti, Kyle N Klein, David Gilbert, Heinrich Leonhardt, Maria Cristina Cardoso, Erez Lieberman Aiden, Hartmann Harz & Thomas Cremer
Cohesin plays an essential role in chromatin loop extrusion, but its impact on a compartmentalized nuclear architecture is debatable. Using live-cell and super-resolved 3D microscopy, we demonstrate that cohesin-depleted cells pass through an endomitosis and rebuild a single multilobulated nucleus (MLN) with chromosome territories (CTs) pervaded by interchromatin channels. CTs contain chromatin domain clusters with a zonal organization of repressed chromatin domains in the interior and transcriptionally competent domains located at the periphery. Splicing speckles...

Data from: Comparing the indirect effects between exploiters in predator-prey and host-pathogen systems

Michael H. Cortez & Meghan Duffy
DataS1 These files are Maple and Matlab scripts for analyzing the predator-prey and host-pathogen models in "Comparing the indirect effects between exploiters in predator-prey and host-pathogen systems" and generating the figures in that study.

The perfect storm: Gene tree estimation error, incomplete lineage sorting, and ancient gene flow explain the most recalcitrant ancient angiosperm clade, Malpighiales

Liming Cai, Zhenxiang Xi, Emily Lemmon, Alan Lemmon, Austin Mast, Christopher Buddenhagen, Liang Liu & Charles Davis
The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent (MSC) model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data...

Data from: Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment

David Gray, David Weissman, Jeffrey Cole, Emily Lemmon & Alan Lemmon
We present the first comprehensive molecular phylogeny of Gryllus field cricket species found in the United States and Canada, select additional named Gryllus species found in Mexico and the Bahamas, plus the European field cricket G. campestris Linnaeus and the Afro-Eurasian cricket G. bimaculatus De Geer. Acheta, Teleogryllus, and Nigrogryllus were used as outgroups. Anchored hybrid enrichment was used to generate 492,531 base pairs of DNA sequence from 563 loci. RAxML analysis of concatenated sequence...

Data from: Are you more than the sum of your parents’ genes? phenotypic plasticity in a clonal vertebrate and F1 hybrids of its parental species

Amber M. Makowicz & Joseph Travis
All known vertebrate clones have originated from hybridization events and some have produced distinct evolutionary lineages via hybrid speciation. Amazon mollies (Poecilia formosa) present an excellent study system to investigate how clonal species have adapted to heterogeneous environments because they are the product of a single hybridization event between male sailfin mollies (P. latipinna) and female Atlantic mollies (P. mexicana). Here we ask whether the hybrid species differs from the combination of its parental species’...

Data from: Environmental change, if unaccounted, prevents detection of cryptic evolution in a wild population

Tomos Potter, Ronald D. Bassar, Paul Bentzen, Emily W. Ruell, Julián Torres-Dowdall, Corey A. Handelsman, Cameron K. Ghalambor, Joseph Travis, David N. Reznick & Tim Coulson
Detecting contemporary evolution requires demonstrating that genetic change has occurred. Mixed-effects models allow estimation of quantitative genetic parameters and are widely used to study evolution in wild populations. However, predictions of evolution based on these parameters frequently fail to match observations. Furthermore, such studies often lack an independent measure of evolutionary change against which to verify predictions. Here, we applied three commonly used quantitative genetic approaches to predict the evolution of size at maturity in...

Phylogenomics, biogeography and taxonomic revision of New Guinean pythons (Pythonidae, Leiopython) harvested for international trade

Damien Esquerre, Daniel J. D. Natusch, Jessica A. Lyons, Amir Hamidy, Alan R. Lemmon, Emily M. Lemmon, Awal Riyanto, J. Scott Keogh & Stephen Donnellan
The large and enigmatic New Guinean pythons in the genus Leiopython are harvested from the wild to supply the international trade in pets. Six species are currently recognized (albertisii, biakensis, fredparkeri, huonensis, meridionalis, montanus) but the taxonomy of this group has been controversial. We combined analysis of 421 nuclear loci and complete mitochondrial genomes with morphological data to construct a detailed phylogeny of this group, understand their biogeographic patterns and establish the systematic diversity of...

Data from: When does growth rate influence fitness in a colonial marine invertebrate?

Scott Burgess & Marília Bueno
Growth rate affects body size, and larger body sizes are often associated with the capacity to produce more surviving offspring. However, the assumption that growth rate should positively relate to fitness is rarely tested, especially in colonial marine invertebrates where size and age can be decoupled. We measured growth, survival, and reproduction through repeated census of 97 colonies from two populations of a marine bryozoan in the field from settlement to the end of their...

P17944_Advances in Asphaltene Petroleomics. Part 1: Asphaltenes Are Composed of Abundant Island and Archipelago Structural Motifs

Amy Mckenna, Martha Chacon-Patino & Ryan Rodgers

P17944_Microfluidic Study of the Deposition Dynamics of Asphaltene Subfractions Enriched with Island and Archipelago Motifs

Amy Mckenna & Martha Chacon-Patino
The publication can be found at: https://pubs.acs.org/doi/10.1021/acs.energyfuels.8b03835 Acknowledgments: We thank Patrick Gilliam and Zhuqing Zhang for their technical assistance and Nalco Champion for financial support.

Data from: Mating preference for novel phenotypes can be explained by general neophilia in female guppies

Mitchel J. Daniel, Laura Koffinas & Kimberly Hughes
Understanding how genetic variation is maintained in ecologically-important traits is a fundamental question in evolutionary biology. Male Trinidadian guppies (Poecilia reticulata) exhibit extreme genetic diversity in color patterns within populations, which is believed to be promoted by a female mating preference for rare or novel patterns. However, the origins of this preference remain unclear. Here, we test the hypothesis that mating preference for novel phenotypes is a by-product of general neophilia that evolved in response...

Integrating top-down and bottom-up effects of local density across scales and a complex life cycle

Jessie Mutz, Nora Underwood & Brian Inouye
Effects of group size (local conspecific density) on individual performance can be substantial, yet it is unclear how these translate to larger-scale and longer-term outcomes. Effects of group size can be mediated by both top-down and bottom-up interactions, can change in type or direction across the life cycle, and can depend on the spatial scale at which group size is assessed. Only by determining how these different processes combine can we make predictions about how...

Registration Year

  • 2020

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  • Florida State University
  • National High Magnetic Field Laboratory
  • University of Minnesota
  • Michigan Technological University
  • Sixth Affiliated Hospital of Sun Yat-sen University
  • West China Hospital of Sichuan University
  • Zhejiang University
  • Jiangxi Agricultural University
  • Air Force Medical University
  • Huazhong University of Science and Technology