16 Works

Data from: Automated size selection for short cell-free DNA fragments enriches for circulating tumor DNA and improves error correction during next generation sequencing

Sabine Hellwig, David A. Nix, Keith M. Gligorich, John M. O'Shea, Alun Thomas, Carrie L. Fuertes, Preetida J. Bhetariya, Gabor T. Marth, Mary P. Bronner, Hunter R. Underhill & John M. O’Shea
Circulating tumor-derived cell-free DNA (ctDNA) enables non-invasive diagnosis, monitoring, and treatment susceptibility testing in human cancers. However, accurate detection of variant alleles, particularly during untargeted searches, remains a principal obstacle to widespread application of cell-free DNA in clinical oncology. In this study, isolation of short cell-free DNA fragments is shown to enrich for tumor variants and improve correction of PCR- and sequencing-associated errors. Subfractions of the mononucleosome of circulating cell-free DNA (ccfDNA) were isolated from...

Data from: Phoretic dispersal influences parasite population genetic structure

Emily DiBlasi, Kevin P. Johnson, Sydney A. Stringham, Angela N. Hansen, Andrew B. Beach, Dale H. Clayton & Sarah E. Bush
Dispersal is a fundamental component of the life history of most species. Dispersal influences fitness, population dynamics, gene flow, genetic drift, and population genetic structure. Even small differences in dispersal can alter ecological interactions and trigger an evolutionary cascade. Linking such ecological processes with evolutionary patterns is difficult, but can be done in the proper comparative context. Here we investigate how differences in phoretic dispersal influence the population genetic structure of two different parasites of...

Data from: Large birds travel farther in homogeneous environments

Marlee A. Tucker, Olga Alexandrou, , Keith L. Bildstein, Katrin Böhning-Gaese, Chloe Bracis, John N. Brzorad, Evan R. Buechley, David Cabot, Justin M. Calabrese, Carlos Carrapato, André Chiaradia, Lisa C. Davenport, Sarah C. Davidson, Mark Desholm, Christopher R. DeSorbo, Robert Domenech, Peter Enggist, William F. Fagan, Nina Farwig, Wolfgang Fiedler, Christen H. Fleming, Alastair Franke, John M. Fryxell, Clara García-Ripollés … & João Paulo Silva
Aim: Animal movement is an important determinant of individual survival, population dynamics, and ecosystem structure and function. Yet it is still unclear how local movements are related to resource availability and the spatial arrangement of resources. Using resident bird species and migratory bird species outside of the migratory period, we examined how the distribution of resources affect the movement patterns of both large terrestrial birds (e.g., raptors, bustards, hornbills) and waterbirds (e.g., cranes, storks, ducks,...

Data from: The spatial structure of phylogenetic and functional diversity in the United States and Canada: an example using the sedge family (Cyperaceae)

Daniel Spalink, Jocelyn Pender, Marcial Escudero, Andrew L. Hipp, Eric H. Roalson, Julian R. Starr, Marcia J. Waterway, Lynn Bohs & Kenneth J. Sytsma
Systematically quantifying diversity across landscapes is necessary to understand how clade history and ecological heterogeneity contribute to the origin, distribution, and maintenance of biodiversity. Here, we chart the spatial structure of diversity among all species in the sedge family (Cyperaceae) throughout the USA and Canada. We first identify areas of remarkable species richness, phylogenetic diversity, and functional trait diversity, and highlight regions of conservation priority. We then test predictions about the spatial structure of this...

Data from: Drought legacies are dependent on water table depth, wood anatomy, and drought timing across the eastern U.S.

Steven A. Kannenberg, Justin T. Maxwell, Neil Pederson, Loïc D'Orangeville, Darren L. Ficklin & Richard P. Phillips
Severe droughts can impart long-lasting legacies on forest ecosystems through lagged effects that hinder tree recovery and suppress whole-forest carbon uptake. However, the local climatic and edaphic factors that interact to affect drought legacies in temperate forests remain unknown. Here, we pair a dataset of 143 tree ring chronologies across the mesic forests of the eastern U.S. with historical climate and local soil properties. We found legacy effects to be widespread, the magnitude of which...

Data from: Cough frequency during treatment associated with baseline cavitary volume and proximity to the airway in pulmonary TB

Alvaro Proaño, David P. Bui, José W. López, Nancy M. Vu, Marjory A. Bravard, Gwenyth O. Lee, Brian H. Tracey, Ziyue Xu, Germán Comina, Eduardo Ticona, Daniel J. Mollura, Jon S. Friedland, David A. J. Moore, Carlton A. Evans, Philip Caligiuri, Robert H. Gilman & Tuberculosis Working Group In Peru
Background: Cough frequency, and its duration, is a lab-free biomarker that can be used in low-resource settings and has been associated with transmission and treatment response. Radiological characteristics associated with increased cough frequency may be important in understanding transmission. The relationship between cough frequency and cavitary lung disease has never been studied. Methods: We analyzed 41 human immunodeficiency virus-negative adults with culture-confirmed, drug-susceptible pulmonary tuberculosis throughout treatment. Cough recordings were based on the Cayetano Cough...

A local and global sensitivity analysis of a mathematical model of coagulation and platelet deposition under flow

Kathryn Link, Michael Stobb, Jorge Di Paola, Keith Neeves, Aaron Fogelson, Suzanne Sindi & Karin Leiderman
The hemostatic response involves blood coagulation and platelet aggregation to stop blood loss from an injured blood vessel. The complexity of these processes make it difficult to intuit the overall hemostatic response without quantitative methods. Mathematical models aim to address this challenge but are often accompanied by numerous parameters choices and thus need to be analyzed for sensitivity to such choices. Here we use local and global sensitivity analyses to study a model of coagulation...

Data from: Tracking of host defenses and phylogeny during the radiation of Neotropical Inga-Feeding sawflies (Hymenoptera; Argidae)

María-José Endara, James A. Nicholls, Phyllis D. Coley, Dale L. Forrister, Gordon C. Younkin, Kyle G. Dexter, Catherine A. Kidner, R. Toby Pennington, Graham N. Stone & Thomas A. Kursar
Coevolutionary theory has long predicted that the arms race between plants and herbivores is a major driver of host selection and diversification. At a local scale, plant defenses contribute significantly to the structure of herbivore assemblages and the high alpha diversity of plants in tropical rain forests. However, the general importance of plant defenses in host associations and divergence at regional scales remains unclear. Here, we examine the role of plant defensive traits and phylogeny...

Data from: The truncated bell: an enigmatic but pervasive elevational diversity pattern in Middle American ants

John T. Longino & Michael G. Branstetter
Studies on elevation gradients in Panama and Costa Rica have shown that leaf-litter ants exhibit a mid-elevation peak in diversity. This diversity pattern has been observed in other groups and regions, but uncertainty remains as to just how pervasive it is and what might explain it. Here we examine the robustness of the mid-elevation peak in ant diversity across the entire Middle American corridor, from Veracruz, Mexico, to Costa Rica. We sampled 56 sites distributed...

Data from: Phytochemical changes in milkweed induced by elevated CO2 alter wing morphology but not toxin sequestration in monarch butterflies

Leslie E. Decker, Abrianna J. Soule, Jacobus C. De Roode & Mark D. Hunter
1. Environmental change has the potential to influence trophic interactions by altering the defensive phenotype of prey. 2. Here, we examine the effects of a pervasive environmental change driver, elevated atmospheric concentrations of CO2 (eCO2), on toxin sequestration and flight morphology of a specialist herbivore. 3. We fed monarch butterfly larvae, Danaus plexippus, foliage from four milkweed, Asclepias, species of varying chemical defense profiles grown under either ambient or eCO2. We also infected a subset...

Data from: Evolution of the latitudinal gradient in the hyperdiverse ant genus Pheidole

Evan P. Economo, Jen-Pan Huang, Georg Fischer, Eli M. Sarnat, Nitish Narula, Milan Janda, Benoit Guénard, John T. Longino & L. Lacey Knowles
Aim: The latitudinal diversity gradient is the dominant pattern of life on Earth, but a consensus understanding of its origins has remained elusive. The analysis of recently diverged, hyper-rich invertebrate groups provides an opportunity to investigate latitudinal patterns with the statistical power of large trees while minimizing potentially confounding variation in ecology and history. Here, we synthesize global phylogenetic and macroecological data on a hyperdiverse (>1100 species) ant radiation, Pheidole, and test predictions of three...

Data from: Elevational changes in the avian community of a Mesoamerican cloud forest park

Montague H. C. Neate-Clegg, Samuel E. I. Jones, Oliver Burdekin, Merlijn Jocque & Çağan Hakkı Şekercioğlu.
Harboring many range-restricted and specialized species, high elevation tropical cloud forests are diverse habitats represented in many protected areas. Despite this, many such areas receive little practical protection from deforestation and land conversion. Moreover, montane species may be more sensitive to climate change owing to various factors affecting community assembly across elevational gradients. Few studies have used annual monitoring to assess how biological communities in cloud forests may be shifting in response to habitat or...

Data from: Experimental manipulation of population-level MHC diversity controls pathogen virulence evolution in Mus musculus

Douglas H. Cornwall, Jason L. Kubinak, Elisabeth Zachary, Derek L. Stark, Dustan Seipel & Wayne K. Potts
The virulence levels attained by serial passage of pathogens through similar host genotypes are much higher than observed in natural systems, however, it is unknown what keeps natural virulence levels below these empirically demonstrated maximum levels. One hypothesis suggests that host diversity impedes pathogen virulence, because adaptation to one host genotype carries tradeoffs in the ability to replicate and cause disease in other host genotypes. To test this hypothesis, with the simplest level of population...

Data from: Incorporating non-equilibrium dynamics into demographic history inferences of a migratory marine species

Emma L. Carroll, Rachael Alderman, John L. Bannister, Martine Bérubé, Peter B. Best, Laura Boren, C. Scott Baker, Rochelle Constantine, Ken Findlay, Robert Harcourt, Louisiane Lemaire, Per J. Palsbøll, Nathalie J. Patenaude, Victoria J. Rowntree, Jon Seger, Debbie Steel, Luciano O. Valenzuela, Mandy Watson & Oscar E. Gaggiotti
Understanding how dispersal and gene flow link geographically separated populations over evolutionary history is challenging, particularly in migratory marine species. In southern right whales (SRWs, Eubalaena australis), patterns of genetic diversity are likely influenced by the glacial climate cycle and recent history of whaling. Here we use a dataset of mitochondrial DNA (mtDNA) sequences (n=1,327) and nuclear markers (17 microsatellite loci, n=222) from major wintering grounds to investigate circumpolar population structure, historical demography, and effective...

Data from: Phylogenomics and the evolution of hemipteroid insects

Kevin P. Johnson, Christopher H. Dietrich, Frank Friedrich, Rolf G. Beutel, Benjamin Wipfler, Ralph S. Peters, Julie M. Allen, Malte Petersen, Alexander Donath, Kimberly K. O. Walden, Alexey M. Kozlov, Lars Podsiadlowski, Christoph Mayer, Karen Meusemann, Alexandros Vasilikopoulos, Robert M. Waterhouse, Stephen L. Cameron, Christiane Weirauch, Daniel R. Swanson, Diana M. Percy, Nate B. Hardy, Irene Terry, Shanlin Liu, Xin Zhou, Bernhard Misof … & Kazunori Yoshizawa
Hemipteroid insects (Paraneoptera), with over 10% of all known insect diversity, are a major component of terrestrial and aquatic ecosystems. Previous phylogenetic analyses have not consistently resolved the relationships among major hemipteroid lineages. We provide maximum likelihood-based phylogenomic analyses of a taxonomically comprehensive dataset comprising sequences of 2,395 single-copy, protein-coding genes for 193 samples of hemipteroid insects and outgroups. These analyses yield a well-supported phylogeny for hemipteroid insects. Monophyly of each of the three hemipteroid...

Data from: Functional biogeography of dietary strategies in birds

Jean-Yves Barnagaud, Nathan Mazet, François Munoz, Matthias Grenié, Pierre Denelle, Mar Sobral, W. Daniel Kissling, Çağan H. Sekercioglu & Cyrille Violle
Aim: Diet is key to understanding species’ resource use, relationships with their environment and biotic interactions. We aimed to identify the major strategies that shape birds’ diet space, and to investigate their spatial distributions in association with biogeographic, bioclimatic and anthropogenic drivers. Location: Global Time period: Current Major taxa studied: Birds Methods: We analysed score-based assessments of eight diet categories for 8937 out of 10964 extant bird species. We constructed a multivariate diet space by...

Registration Year

  • 2018

Resource Types

  • Dataset


  • University of Utah
  • University of Michigan-Ann Arbor
  • Max Planck Institute for Ornithology
  • Friends University
  • University of Twente
  • National University of San Marcos
  • Newport (United States)
  • University of California, Merced
  • Biodiversity Research Institute
  • Stanford University