74 Works

Data related to: Open-system evolution of a crustal-scale magma column, Klamath Mountains, California

Calvin Barnes, Nolwenn Coint, Melanie Barnes, Ariel Strickland, John Cottle, O. Ramo, Kevin Chamberlain & John Valley
Granitic magmas commonly display evidence for some level of interaction with and/or origins from crustal rocks. There is fundamental debate in the community as to the processes that control the origins of these magmas and the potential for their contamination as they pass through the crust. One approach to addressing these issues involves a combination of detailed field mapping combined with geochemical analysis of bulk-rock samples and their constituent minerals. In particular, resolution of debates...

Genomic variation within the maize Stiff Stalk heterotic germplasm pool

Nolan Bornowski, Kathryn J. Michel, John P. Hamilton, Shujun Ou, Arun S. Seetharam, Jerry Jenkins, Jane Grimwood, Chris Plott, Shengqiang Shu, Jayson Talag, Megan Kennedy, Hope Hundley, Vasanth R. Singan, Kerrie Barry, Chris Daum, Yuko Yoshinaga, Jeremy Schmutz, Candice N. Hirsch, Matthew B. Hufford, Natalia De Leon, Shawn M. Kaeppler & C. Robin Buell
The Stiff Stalk heterotic group is an important source of inbreds used in U.S. commercial hybrid production. Founder inbreds B14, B37, B73, and to a lesser extent B84, are found in the pedigrees of a majority of commercial seed parent inbred lines. We created high-quality genome assemblies of B84 and four ex-Plant Variety Protection lines LH145 representing B14, NKH8431 of mixed descent, PHB47 representing B37, and PHJ40 which is a Pioneer Hi-Bred early Stiff Stalk...

A recovery network leads to the natural recolonization of an archipelago and a potential trailing edge refuge

Matthew Smith, Jonathan Gilbert, Erik Olson, Kim Scribner, Timothy Van Deelen, Julie Van Stappen, Bronwyn Williams, James Woodford & Jonathan Pauli
Rapid environmental change is reshaping ecosystems and driving species loss globally. Carnivore populations have declined and retracted rapidly and have been the target of numerous translocation projects. Success, however, is complicated when these efforts occur in novel ecosystems. Identifying refuges, locations that are resistant to environmental change, within a translocation framework should improve population recovery and persistence. American martens (Martes americana) are the most frequently translocated carnivore in North America. As elsewhere, martens were extirpated...

Chemosensory genes in Leptinotarsa decemlineata

Sean Schoville, Yolanda Chen, Zach Cohen, Michael Crossley, Patamarerk Engsontia & Robert Mitchell
Plants and plant-feeding insects comprise the majority of global species diversity, and their coevolutionary dynamics provide an important window into the mechanisms that mediate niche evolution. In particular, there is considerable interest in understanding the nature of genetic changes that allow host-plant shifts to occur and to determine whether functional genomic diversity varies predictably in relation to host-plant breadth. Insect chemosensory proteins play a central role in mediating insect-plant interactions, as they directly influence plant...

A high-quality carabid genome provides insights into beetle genome evolution and cold adaptation

Yi-Ming Weng, Charlotte Francoeur, Cameron Currie, David Kavanaugh & Sean Schoville
The hyper-diverse order Coleoptera comprises a staggering ~25% of known species on Earth. Despite recent breakthroughs in next generation sequencing, there remains a limited representation of beetle diversity in assembled genomes. Most notably, the ground beetle family Carabidae, comprising more than 40,000 described species, has not been studied in a comparative genomics framework using whole genome data. Here we generate a high-quality genome assembly for Nebria riversi, to examine sources of novelty in the genome...

Identifying mismatches between conservation area networks and vulnerable populations using spatial randomization

Laura A. Nunes, Christine A. Ribic & Benjamin Zuckerberg
Grassland birds are among the most globally threatened bird groups due to substantial degradation of native grassland habitats. However, the current network of grassland conservation areas may not be adequate for halting population declines and biodiversity loss. Here, we evaluate a network of grassland conservation areas within Wisconsin, U.S.A. that includes both large Focal Landscapes and smaller targeted conservation areas (e.g., Grassland Bird Conservation Areas or GBCAs) established within them. To date, this conservation network...

Resource selection functions based on hierarchical generalized additive models provide new insights into individual animal variation and species distributions

Jennifer McCabe, John Clare, Tricia Miller, Todd Katzner, Jeff Cooper, Scott Somershoe, David Hanni, Christine Kelly, Robert Sargent, Eric Soehren, Carrie Threadgill, Mercedes Maddox, Jonathan Stober, Mark Martell, Thomas Salo, Andrew Berry, Michael Lanzone, Melissa Braham & Christopher McClure
Habitat selection studies are designed to generate predictions of species distributions or inference regarding general habitat associations and individual variation in habitat use. Such studies frequently involve either individually indexed locations gathered across limited spatial extents and analyzed using resource selection functions (RSF), or spatially extensive locational data without individual resolution typically analyzed using species distribution models. Both analytical methodologies have certain desirable features, but analyses that combine individual- and population-level inference with flexible non-linear...

Ruffed grouse stress-scape dataset

Amy Shipley
Context Variability in temperature and snow cover are characteristics of high-latitude environments that impose significant pressures on overwintering species. To cope with increased energetic demands and decreased resources, species occupying seasonal environments often seek out refugia that buffer them from inclement conditions. Ruffed grouse (Bonasa umbellus) roosting in the thermally stable microhabitat beneath deep snow are buffered from negative effects of cold temperatures on physiological stress (glucocorticoid hormone levels). Objective Despite physiological advantages of accessing...

Experimental evidence for the recovery of mercury-contaminated fish populations

Lee Hrenchuk, Paul Blanchfield, John Rudd, Marc Amyot, Christopher Babiarz, Ken Beaty, Drew Bodaly, Brian Branfireun, Cynthia Gilmour, Jennifer Graydon, Britt Hall, Reed Harris, Andrew Heyes, Holger Hintelmann, James Hurley, Carol Kelly, David Krabbenhoft, Steve Lindberg, Robert Mason, Michael Paterson, Cheryl Podemski, Ken Sandilands, George Southworth, Vincent St. Louis, Lori Tate … & Michael Tate
Anthropogenic releases of mercury (Hg) are a human health issue because the potent toxicant methylmercury (MeHg), formed primarily by microbial methylation of inorganic Hg in aquatic ecosystems, bioaccumulates to high concentrations in fish consumed by humans. Predicting the efficacy of Hg pollution controls on fish MeHg concentrations is complex because many factors influence the production and bioaccumulation of MeHg. Here we conducted a 15-year whole-ecosystem, single-factor experiment to determine the magnitude and timing of reductions...

Stigma shape shifting in sages (Salvia: Lamiaceae) – hummingbirds guided the evolution of New World floral features

Ricardo Kriebel, Bryan Drew, Jesús González-Gallegos, Ferhat Celep, Guilherme Antar, José Floriano Barêa Pastore & Kenneth Sytsma
A fundamental question in evolutionary biology is how clades of organisms exert influence on one another. The evolution of the flower and subsequent plant/pollinator coevolution are major innovations that have operated in flowering plants to promote species radiations at a variety of taxonomic levels in the Neotropics. Here we test the hypothesis that pollination by Neotropical endemic hummingbirds drove the evolution of two unique stigma traits in correlation with other floral traits in New World...

High rates of anticoagulant rodenticide exposure in California Barred Owls

Daniel Hofstadter
Pesticide use is pervasive and the exposure of non-target wildlife has been well documented over the past half century. Among pesticides, anticoagulant rodenticides (AR) have emerged as a particularly important threat in forests of the western United States, with exposure and mortality reported for several species of conservation concern. To further quantify this threat, we collected specimens of Barred Owls (Strix varia) and Barred Owl x Spotted Owl hybrids from the Klamath and Cascade Mountains...

MicroRNA quantitative RT-PCR analysis of CMT1A Plasma

John Svaren, Hongge Wang, Matthew Davison & Michael Shy
Objective: To determine if microRNA’s (miR) are elevated in the plasma of individuals affected by the inherited peripheral neuropathy Charcot-Marie-Tooth Disease, type 1A (CMT1A), miR profiling was employed to compare control and CMT1A plasma. Methods: We undertook a screen of CMT1A and control plasma samples to identify miRs that are elevated in CMT1A using a pilot screen of plasma miR by next generation sequencing, followed by validation of selected miRs by quantitative PCR, and correlation...

Arresting the spread of invasive species in continental systems

Daniel Hofstadter, Nicholas Kryshak, Connor Wood, Brian Dotters, Kevin Roberts, Kevin Kelly, John Keane, Sarah Sawyer, Paula Shaklee, Anu Kramer, Rocky Gutiérrez & Zach Peery
Invasive species are a primary threat to biodiversity and are challenging to manage once populations become established. But removing them is further complicated when invasions occur in continental, mixed-ownership systems. We demonstrate a rare conservation success: the regional-scale removal of an invasive predator – the barred owl (Strix varia) – to benefit the spotted owl (S. occidentalis) in California, USA. Barred owl site occupancy declined six-fold from 0.19 to 0.03 following one year of removals,...

Biometric conversion factors as a unifying platform for comparative assessment of invasive freshwater bivalves

Neil Coughlan, Eoghan Cunningham, Ross Cuthbert, Patrick Joyce, Pedro Anastacio, Filipe Banha, Nicolás Bonel, Stephanie Bradbeer, Elizabeta Briski, Vincent Butitta, Zuzana Čadková, Jaimie Dick, Karel Douda, Lawrence Eagling, Noé Ferreira-Rodríguez, Leandro Hünicken, Mattias Johansson, Louise Kregting, Anna Labecka, Deliang Li, Florencia Liquin, Jonathan Marescaux, Todd Morris, Patrycja Nowakowska, Małgorzata Ożgo … & Francisco Sylvester
1. Invasive bivalves continue to spread and negatively impact freshwater ecosystems worldwide. As different metrics for body size and biomass are frequently used within the literature to standardise bivalve related ecological impacts (e.g. respiration and filtration rates), the lack of broadly applicable conversion equations currently hinders reliable comparison across bivalve populations. To facilitate improved comparative assessment amongst studies originating from disparate geographic locations, we report body size and biomass conversion equations for six invasive freshwater...

Hierarchical genetic structure and implications for conservation of the world’s largest salmonid, Hucho taimen

Lanie M. Galland, James B. Simmons, Joshua P. Jahner, Agusto R. Luzuriaga-Neira, Matthew R. Sloat, Sudeep Chandra, Zeb Hogan, Olaf P. Jensen & Thomas L. Parchman
Population genetic analyses can evaluate how evolutionary processes shape diversity and inform conservation and management of imperiled species. Taimen (Hucho taimen), the world’s largest freshwater salmonid, is threatened, endangered, or extirpated across much of its range due to anthropogenic activity including overfishing and habitat degradation. We generated genetic data using high throughput sequencing of reduced representation libraries for taimen from multiple drainages in Mongolia and Russia. Nucleotide diversity estimates were within the range documented in...

Disease or drought: Environmental fluctuations release zebra from a potential pathogen-triggered ecological trap

Yen-Hua Huang, Hendrina Joel, Martina Küsters, Zoe Barandongo, Claudine Cloete, Axel Hartmann, Pauline Kamath, Werner Kilian, John Mfune, Gabriel Shatumbu, Royi Zidon, Wayne Getz & Wendy Turner
When a transmission hotspot for an environmentally persistent pathogen establishes in otherwise high-quality habitat, the disease may exert a strong impact on a host population. However, fluctuating environmental conditions lead to heterogeneity in habitat quality and animal habitat preference, which may interrupt the overlap between selected and risky habitats. We evaluated spatiotemporal patterns in anthrax mortalities in a plains zebra (Equus quagga) population in Etosha National Park, Namibia, incorporating remote-sensing and host telemetry data. A...

Code for: A metapopulation model of social group dynamics and disease applied to Yellowstone wolves

Ellen E. Brandell
Abstract The population structure of social species has important consequences for both their demography and transmission of their pathogens. We develop a new form of metapopulation model that tracks two key components of a species’ social system: average group size and number of groups within a population. While the model is general, we parameterize it to mimic the dynamics of the Yellowstone wolf population and two associated pathogens: sarcoptic mange and canine distemper. In the...

Terrestrial lichen data for Saskatchewan, Canada

Jill Johnstone, Ruth Greuel, Sarah Hart, Alexandre Truchon-Savard & Philip McLoughlin
Increased fire activity due to climate change may impact the successional dynamics of boreal forests, with important consequences for caribou habitat. Early successional forests have been shown to support lower quantities of caribou forage lichens, but geographic variation in, and controls on, the rates of lichen recovery have been largely unexplored. In this study, we sampled across a broad region in northwestern Canada to compare lichen biomass accumulation in ecoprovinces, including the Saskatchewan Boreal Shield,...

Serological dataset and R code for: Patterns and processes of pathogen exposure in gray wolves across North America

Ellen E Brandell
The presence of many pathogens varies in a predictable manner with latitude, with infections decreasing from the equator towards the poles. We investigated the geographic trends of pathogens infecting a widely distributed carnivore: the gray wolf (Canis lupus). We compiled a large serological dataset of nearly 2000 wolves from 17 study areas, spanning 80º longitude and 50º latitude. Generalized linear mixed models were constructed to predict the probability of seropositivity of four important viruses: canine...

Mesophyll photosynthetic sensitivity to leaf water potential in Eucalyptus: A new dimension of plant adaptation to native moisture supply

Amanda Salvi, Duncan Smith, Mark Adams, Katherine McCulloh & Thomas J. Givnish
Photosynthetic sensitivity to drought is a fundamental constraint on land-plant evolution and ecosystem function. However, little is known about how the sensitivity of photosynthesis to non-stomatal limitations varies among species in the context of phylogenetic relationships. Using saplings of 10 Eucalyptus species, we measured maximum CO2-saturated photosynthesis using A-ci curves at several different leaf water potentials (PSIleaf) to quantify mesophyll photosynthetic sensitivity to PSIleaf (MPS), a measure of how rapidly non-stomatal limitations to carbon uptake...

Selection on convergent functional traits drives compositional divergence in a tallgrass prairie restoration experiment

Nisa Karimi & Andrew Hipp
1. Plant biodiversity is often partitioned into taxonomic diversity (species composition and abundance), phylogenetic diversity (breadth of evolutionary lineages) and functional diversity (resource‐use strategies or physical traits). Evaluating the effects and interplay of these dimensions can provide insights into how assembly processes drive compositional changes in plant communities. However, teasing apart the effects of different biodiversity dimensions is challenging in observational studies or retrospective analyses. 2. To evaluate how plant phylogenetic and trait history shape...

Positive associations of soil organic matter and crop yields across a regional network of working farms

Emily Oldfield, Mark Bradford, Abigail Augarten, Eric Cooley, Amber Radatz, Timothy Radatz & Matthew Ruark
The amount of soil organic matter (SOM) is considered a key indicator of soil properties associated with higher fertility. Despite the ubiquity of assumptions surrounding SOM’s contributions to soil functioning, we lack quantitative relationships between SOM and yield outcomes on working farms. We quantified the relationship between SOM and yields of corn (Zea mays L.) and silage for a dataset of 170 fields arrayed across 49 farms in a network of growers based in Wisconsin...

Taxonomic sampling and rare genomic changes overcome long-branch attraction in the phylogenetic placement of pseudoscorpions

Andrew Ontano, Guilherme Gainett, Shlomi Aharon, Jesús Balesteros, Ligia Benavides, Kevin Corbett, Efrat Gavish-Regev, Mark Harvey, Scott Monsma, Carlos Santibáñez-López, Emily Setton, Jakob Zehms, Jeanne Zeh, David Zeh & Prashant Sharma
Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with LBA artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale datasets. Pseudoscorpion placement is particularly variable across datasets and analytical frameworks, with this group either clustering with other long-branch...

Maternal and neonatal outcomes of repeated antepartum bleeding in 493 placenta previa cases: a retrospective study

Shiyun Huang, Qing Zuo, Tianjun Wang, Xiaotong Tang, Zhiping Ge, Hongmei Lu, Xin Zhou & Ziyan Jiang
To explore the effect of antepartum bleeding caused by PP on pregnancy outcomes. We retrospectively analyzed 493 pregnant women complicated with PP. Patients were divided into antepartum repeated bleeding and non-bleeding groups. Maternal characteristics and pregnancy outcomes were compared. The risk of antepartum hemorrhage was 2.038 times higher when gravidity was 5 (95% CI 1.104–3.760, p = .023). Pregnant women with a history of more than three intrauterine procedures had a 1.968 times higher risk...

Registration Year

  • 2021

Resource Types

  • Dataset


  • University of Wisconsin-Madison
  • University of Wisconsin–Madison
  • University of Minnesota
  • University of California, Berkeley
  • California Academy of Sciences
  • University of Florida
  • Chinese Academy of Sciences
  • United States Geological Survey
  • Sun Yat-sen University
  • University of Washington