20 Works

An effective mutualism? The role of theoretical studies in ecology and evolution

Maria Servedio
Theoretical models often have fundamentally different goals than do empirical studies of the same topic. Models can test the logic of existing hypotheses, explore the plausibility of new hypotheses, provide expectations that can be tested with data, and address aspects of topics that are currently inaccessible empirically. Theoretical models are common in ecology and evolution, and are generally well-cited, but I show that many citations appearing in non-theoretical studies are general to topic and a...

Extinct plants of North America north of Mexico

Wesley Knapp, Anne Frances, Reed Noss, Robert Naczi, Alan Weakley, George Gann, Bruce Baldwin, James Miller, Patrick McIntyre, Brent Mishler, Gerry Moore, Richard Olmstead, Anna Strong, Daniel Gluesenkamp & Kathryn Kennedy
The recent study by Humphreys et al., reporting extinction of almost 600 plant species globally, represents a groundbreaking effort at compiling direct data on seed plants. We applaud Humphreys et al. for quantifying plant extinctions because they formulate an important and testable hypothesis. However, their study missed many extinctions and rediscoveries of seed plants in the United States and Canada. Our team of experts has been compiling a list of extinct plants of North America...

Data from: How stabilizing selection and nongenetic inheritance combine to shape the evolution of phenotypic plasticity

Nicholas A. Levis & David W. Pfennig
Relatively little is known about whether and how nongenetic inheritance interacts with selection to impact the evolution of phenotypic plasticity. Here, we empirically evaluated how stabilizing selection and a common form of nongenetic inheritance––maternal environmental effects––jointly influence the evolution of phenotypic plasticity in natural populations of spadefoot toads. We compared populations that previous field work has shown to have evolved conspicuous plasticity in resource-use phenotypes (‘resource polyphenism’) with those that, owing to stabilizing selection favouring...

Data from: Nitrogen transformations differentially affect nutrient-limited primary production in lakes of varying trophic state

J. Thad Scott, Mark J. McCarthy & Hans W. Paerl
The concept of lakes “evolving” phosphorus (P) limitation has persisted in limnology despite limited direct evidence. Here, we developed a simple model to broadly characterize nitrogen (N) surpluses and deficits relative to P in lakes, and compared the magnitude of this imbalance to estimates of N gains and losses through biological N transformations. The model suggested that approximately half of oligotrophic lakes in the US had a stoichiometric N deficit, but almost 90% of the...

Assessing the impact of product inhibition in a chromogenic assay

Michael Stobb, Karin Leiderman, Suzanne Sindi & Dougald Monroe
Chromogenic substrates (CS) are synthetic substrates used to monitor the activity of a target enzyme. It has been reported that some CSs display competitive product inhibition with their target enzyme. Thus, in assays where enzyme activity is continuously monitored over long periods of time, the product inhibition may significantly interfere with the reactions being monitored. Despite this knowledge, it is rare for CSs to be directly incorporated into mathematical models that simulate these assays. This...

United States National Lynching Data, 1883-1941

Charles Seguin & David Rigby
These data extend existing data on lynching victims to cover the 48 contiguous United States from 1883 to 1941. The data here cover 38 states not included in Tolney and Beck's (1995) original data, as well as 3 additional victims in the 10 states covered by Tolney and Beck. The authors confirmed 1,319 victims from previous data and found 15 additional victims not recorded in any prior data set.

Data from: Human endometrial transcriptome and progesterone receptor cistrome reveal important pathways and epithelial regulators

Ru-Pin Alicia Chi, Tianyuan Wang, Nyssa Adams, San-Pin Wu, Steven Young, Thomas Spencer & Francesco DeMayo
Context. Poor uterine receptivity is one major factor leading to pregnancy loss and infertility. Understanding the molecular events governing successful implantation is hence critical in combating infertility. Objective. To define PGR-regulated molecular mechanisms and epithelial roles in receptivity. Design. RNA-seq and PGR-ChIP-seq were conducted in parallel to identify PGR-regulated pathways during the WOI in endometrium of fertile women. Setting. Endometrial biopsies from the proliferative and mid-secretory phases were analyzed. Patients or Other Participants. Participants were...

Data from: Competitively mediated changes in male toad calls can depend on call structure

Rebecca Stirman & Karin S. Pfennig
Many species of males aggregate in large groups where they signal to attract females. These large aggregations create intense competition for mates, and the simultaneous signaling by many individuals can impair any given male’s ability to attract females. In response to this situation, male signals can be modified, either evolutionarily or facultatively, such that the detectability of the signal is enhanced. The way in which signals are modified varies among even closely related species, yet...

Data from: Genomic scans reveal multiple mito‐nuclear incompatibilities in population crosses of the copepod Tigriopus californicus

Thiago G. Lima, Ronald S. Burton & Christopher Scott Willett
The evolution of intrinsic postzygotic isolation can be explained by the accumulation of Dobzhansky-Muller incompatibilities (DMI). Asymmetries in the levels of hybrid inviability and hybrid sterility are commonly observed between reciprocal crosses, a pattern that can result from the involvement of uniparentally inherited factors. The mitochondrial genome is one such factor that appears to participate in DMI in some crosses but the frequency of its involvement versus biparentally inherited factors is unclear. Here we assess...

Data from: Plasticity-led evolution: evaluating the key prediction of frequency-dependent adaptation

Nicholas A. Levis & David W. Pfennig
Plasticity-led evolution occurs when a change in the environment triggers a change in phenotype via phenotypic plasticity, and this pre-existing plasticity is subsequently refined by selection into an adaptive phenotype. A critical, but largely untested prediction of plasticity-led evolution (and evolution by natural selection generally) is that the rate and magnitude of evolutionary change should be positively associated with a phenotype’s frequency of expression in a population. Essentially, the more often a phenotype is expressed...

Rapid and predictable evolution of admixed populations between two Drosophila species pairs

Daniel Matute, Aaron Comeault, Eric Earley, Antonio Serrato-Capuchina, David Peede, Anaïs Monroy-Eklund, Wen Huang, Corbin Jones, Trudy Mackay & Jerry Coyne
The consequences of hybridization are varied, ranging from the origin of new lineages, introgression of some genes between species, to the extinction of one of the hybridizing species. We generated replicate admixed populations between two pairs of sister species of Drosophila: D. simulans and D. mauritiana; and D. yakuba and D. santomea. Each pair consisted of a continental species and an island endemic. The admixed populations were maintained by random mating in discrete generations for...

Data from: Transcriptional profiling of the murine airway response to acute ozone exposure

Adelaide Tovar, Gregory J. Smith, Joseph M. Thomas, Wesley L. Crouse, Jack R. Harkema & Samir N. P. Kelada
Ambient ozone (O3) exposure has serious consequences on respiratory health, including airway inflammation and injury. Decades of research have yielded thorough descriptions of these outcomes; however, less is known about the molecular processes that drive them. The aim of this study was to further describe the cellular and molecular responses to O3 exposure in murine airways, with a particular focus on transcriptional responses in two critical compartments: conducting airways (CA) and airway macrophages (AM). After...

Data from: The allometry of brain size in mammals

Joseph Robert Burger, Menshian Ashaki George, Claire Leadbetter & Farhin Shaikh
Why some animals have big brains and others do not has intrigued scholars for millennia. Yet, the taxonomic scope of brain size research is limited to a few mammal lineages. Here, we present a brain size dataset compiled from the literature for 1,552 species with representation from 28 extant taxonomic orders. The brain–body size allometry across all mammals is (Brain) = −1.26 (Body)^0.75. This relationship shows strong phylogenetic signal. Thus, we conducted additional allometries using...

Data from: A growth-defense trade-off is general across native and exotic grasses

Robert W. Heckman, Fletcher W. Halliday & Charles E. Mitchell
High-resource environments typically favor quick-growing, poorly-defended plants, while resource-poor environments typically favor slow-growing, well-defended plants. The prevailing hypothesis explaining this pattern states that, as resource availability increases, well-defended, slow-growing species are replaced by poorly defended, fast-growing species. A second hypothesis states that greater resource availability increases allocation to growth at the expense of defense, within species. Regardless of mechanism, if exotic species are released from enemies relative to natives, shifts in allocation to growth and...

Code and data from: Evolution of sexual cooperation from sexual conflict

Maria R Servedio, John M Powers, Russell Lande & Trevor D Price
This C code conducts deterministic iterations of the exact recursion equations presented in the Model section of "Evolution of sexual cooperation from sexual conflict" by Servedio, Powers, Lande and Price. The code produces a two-dimensional grid with any parameters of choice on the x and y axis. Examples can be found in Figures 2c, 3c and 4 of the main text as well as many similar figures in the Supplementary Material. A sample parameter file...

Data from: Dragonflies use underdamped pursuit to chase conspecifics

Amanda C. Lohmann, Aaron J. Corcoran & Tyson L. Hedrick
Pursuit is a common behavior exhibited by animals chasing prey, competitors, and potential mates. Because of their speed and maneuverability, dragonflies are frequently studied as a model system for biological pursuit. Most quantitative studies have focused on prey pursuits in captive environments. To determine whether a different pursuit strategy is used when chasing conspecifics of nearly equal speed and agility, we recorded 3D flight trajectories from nine territorial chases between male Erythemis simplicicollis dragonflies in...

Data from: Identification of candidate risk factor genes for human idelalisib toxicity using a collaborative cross approach

Merrie Mosedale, Yanwei Cai, J. Scott Eaddy, Robert Corty, Manisha Nautiyal, Paul B. Watkins & William Valdar
Idelalisib is a phosphatidylinositol 3-kinase inhibitor highly selective for the delta isoform that has shown good efficacy in treating chronic lymphocytic leukemia and follicular lymphoma. In clinical trials, however, idelalisib was associated with rare, but potentially serious liver and lung toxicities. In this study, we used the Collaborative Cross (CC) mouse population to identify genetic factors associated with the drug response that may inform risk management strategies for idelalisib in humans. Eight (8) male mice...

Data from: A logical model of homology for comparative biology

Paula Mabee, James Balhoff, Wasila Dahdul, Hilmar Lapp, Christopher Mungall & Todd Vision
There is a growing body of research on the evolution of anatomy in a wide variety of organisms. Discoveries in this field could be greatly accelerated by computational methods and resources that enable these findings to be compared across different studies and different organisms and linked with the genes responsible for anatomical modifications. Homology is a key concept in comparative anatomy; two important types are historical homology (the similarity of organisms due to common ancestry)...

Data from: Randomized phase 2 study of FcRn antagonist efgartigimod in generalized myasthenia gravis

James F. Howard, Vera Bril, Ted M. Burns, Renato Mantegazza, Malgorzata Bilinska, Andrzej Szczudlik, Said Beydoun, Francisco Javier Rodriguez De Rivera Garrido, Fredrik Piehl, Mariarosa Rottoli, Philip Van Damme, Tuan Vu, Amelia Evoli, Miriam Freimer, Tahseen Mozaffar, E. Sally Ward, Torsten Dreier, Peter Ulrichts, Katrien Verschueren, Antonio Guglietta, Hans De Haard, Nicolas Leupin & Jan J. G. M. Verschuuren
Objective: To investigate safety and explore efficacy of efgartigimod (ARGX-113), an anti-neonatal Fc receptor immunoglobulin G1 Fc fragment, in patients with generalized myasthenia gravis (gMG) with a history of anti-acetylcholine receptor (AChR) autoantibodies, who were on stable standard-of-care myasthenia gravis (MG) treatment. Methods: A phase 2, exploratory, randomized, double-blind, placebo-controlled, 15-center study is described. Eligible patients were randomly assigned (1:1) to receive 4 doses over a 3-week period of either 10 mg/kg IV efgartigimod or...

Unique bacterial composition and assembly in a parasitic plant

Connor Fitzpatrick & Adam Schneider
How plant-associated microbiota are shaped by, and potentially contribute to the unique ecology and heterotrophic life history of parasitic plants is relatively unknown. Here, we investigate the leaf and root bacterial communities associated with the root holoparasite Orobanche hederae and its host plant Hedera spp. We sequenced the V4 region of the 16S rRNA gene from DNA extracted from leaf and root samples of naturally growing populations of Orobanche and infected and uninfected Hedera. Root...

Registration Year

  • 2019

Resource Types

  • Dataset


  • University of North Carolina
  • University of North Carolina at Chapel Hill
  • University of Chicago
  • University of California, Irvine
  • Michigan State University
  • University of South Dakota
  • Baylor University
  • Bangor University
  • University of Washington
  • University of California, Merced