76 Works

Rare missense functional variants at COL4A1 and COL4A2 in sporadic intracerebral hemorrhage

Jaeyoon Chung, Graham Hamilton, Minsup Kim, Sandro Marini, Bailey Montgomery, Jonathan Henry, Art Cho, Devin Brown, Bradford Worrall, James Meschia, Scott Silliman, Magdy Selim, David Tirschwell, Chelsea Kidwell, Brett Kissela, Steven Greenberg, Anand Viswanathan, Joshua Goldstein, Carl Langefeld, Kristiina Rannikmae, Catherine Sudlow, Neshika Samarasekera, Mark Rodrigues, Rustam Salman, James Prendergast … & Christopher Anderson
Objective To test the genetic contribution of rare missense variants in COL4A1 and COL4A2 in which common variants are genetically associated with sporadic intracerebral hemorrhage (ICH), we performed rare variant analysis in multiple sequencing data for the risk for sporadic ICH. Methods We performed sequencing across 559Kbp at 13q34 including COL4A1 and COL4A2 among 2,133 individuals (1,055 ICH cases; 1,078 controls) in US-based and 1,492 individuals (192 ICH cases; 1,300 controls) from Scotland-based cohorts, followed...

Deer GPS and animal-borne camera data showing effects of gray wolves on niche overlap between mule and white-tailed deer in eastern Washington state

Aaron Wirsing
Predators may alter niche overlap between prey species by eliciting divergent anti-predator behavior. Accordingly, we exploited heterogeneous gray wolf (Canis lupus) presence in Washington, USA, to contrast patterns of resource and dietary overlap between mule (Odocoileus hemionus) and white-tailed deer (O. virginianus) at sites with and without resident packs. Mule deer run (stot) in a way that is less effective as a means of fleeing from predators than the galloping gait of white-tailed deer. Consequently,...

Appendices interview formats

Una Cunningham, Aoife De Brún, Willgerodt Mayumi, Erin Blakeney & Eilish McAuliffe
Background: Literature on multi-disciplinary healthcare team interventions to improve quality and safety of care in acute hospital contexts tends to focus on evaluating the success of the intervention by assessing patient outcomes. In contrast, there is little focus on the team who delivered the intervention, how the team worked to deliver the intervention or the context in which it was delivered. In practice, there is a poor understanding of why some interventions work and are...

Data from: Functional genetic diversity in an exploited marine species and its relevance to fisheries management

Eleni L. Petrou
The timing of reproduction influences key evolutionary and ecological processes in wild populations. Variation in reproductive timing may be an especially important evolutionary driver in the marine environment, where the high mobility of many species and few physical barriers to migration provide limited opportunities for spatial divergence to arise, and where many species synchronize their reproduction to seasonal cycles of planktonic productivity. Using genomic data collected from spawning aggregations of Pacific herring (Clupea pallasii) across...

Comparing diversification rates in lakes, rivers, and the sea

Elizabeth Miller
The diversity of species inhabiting freshwater relative to marine habitats is striking, given that freshwater habitats encompass <1% of Earth’s water. The most commonly proposed explanation for this pattern is that freshwater habitats are more fragmented than marine habitats, allowing more opportunities for allopatric speciation and thus increased diversification rates in freshwater. However, speciation may be generally faster in sympatry than in allopatry, as illustrated by lacustrine radiations such as African cichlids. Differences between rivers...

Resource allocation to a structural biomaterial: induced production of byssal threads decreases growth of a marine mussel

Emily Roberts, Laura Newcomb, Michelle McCartha, Katie Harrington, Sam LaFramboise, Emily Carrington & Kenneth Sebens
1. Specialized mechanical structures produced by organisms provide crucial fitness advantages. The energetic cost associated with producing these structural materials and the resulting energetic trade-off with growth, however, is rarely quantified. We evaluate resource allocation to structural material production within the context of an energetic framework by combining an experimental manipulation with an energetic model. 2. Mytilid bivalves produce byssus, a network of collagen-like threads that tethers individuals to hard substrate. We hypothesized that a...

Long-term change in the parasite burden of shore crabs (Hemigrapsus oregonensis and H. nudus) on the northwestern Pacific coast of North America

Jessica Quinn, Sarah Lee, Duncan Greeley, Alyssa Gehman, Armand Kuris & Chelsea Wood
The abundances of free-living species have changed dramatically in recent decades, but little is known about change in the abundance of parasitic species. We investigated whether populations of several parasites have shifted over time in two shore crab hosts, Hemigrapsus oregonensis and H. nudus, by comparing the prevalence and abundance of three parasite taxa in a historical dataset (1969–1970) to contemporary parasite abundance (2018–2020) for hosts collected from 11 intertidal sites located from Oregon, USA...

Heterogeneous genetic basis of age at maturity in salmonid fishes

Charles Waters, Anthony Clemento, Tutku Aykanat, John Garza, Kerry-Ann Naish, Shawn Narum & Craig Primmer
Understanding the genetic basis of repeated evolution of the same phenotype across taxa is a fundamental aim in evolutionary biology and has applications to conservation and management. However, the extent to which interspecific life-history trait polymorphisms share evolutionary pathways remains under-explored. We address this gap by studying the genetic basis of a key life-history trait, age at maturity, in four species of Pacific salmon (genus Oncorhynchus) that exhibit intra- and interspecific variation in this trait...

Supplemental Tables for Heal et al: Marine community metabolomes carry fingerprints of phytoplankton community composition

Katherine Heal
Phytoplankton transform inorganic carbon into thousands of biomolecules that represent an important pool of fixed carbon, nitrogen, and sulfur in the surface ocean. Metabolite production differs between phytoplankton, and the flux of these molecules through the microbial food web depends on compound-specific bioavailability to members of a wider microbial community. Yet relatively little is known about the diversity or concentration of metabolites within marine plankton. Here we compare 313 polar metabolites in 21 cultured phytoplankton...

COMSOL models of fluid flow in the sarcomere

Sage Malingen, Kaitlyn Hood, Eric Lauga, Anette Hosoi & Thomas Daniel
A highly organized and densely packed lattice of molecular machinery within the sarcomeres of muscle cells powers contraction. Although many of the proteins that drive contraction have been studied extensively, the mechanical impact of fluid shearing within the lattice of molecular machinery has received minimal attention. It was recently proposed that fluid flow augments substrate transport in the sarcomere, however, this analysis used analytical models of fluid flow in the molecular machinery that could not...

Phylogeny of Citharexyleae

Laura Frost, Nataly O'Leary, Laura Lagomarsino, David Tank & Richard Olmstead
As a family of Neotropical origin and primarily Neotropical distribution, the Verbenaceae are a good but understudied system with which to understand Neotropical evolution. Tribe Citharexyleae comprises three genera: Baillonia, Citharexylum—one of the largest genera in Verbenaceae—and Rehdera. A molecular phylogenetic approach was taken to resolve intergeneric relationships in Citharexyleae and infrageneric relationships in Citharexylum. The phylogeny is used to elucidate character evolution in a widespread, morphologically diverse Neotropical genus. Seven plastid regions, two nuclear...

Data from: Latitudinal embryonic thermal tolerance and plasticity shape the vulnerability of oviparous species to climate change

Bao-Jun Sun, Liang Ma, Yang Wang, Chun-Rong Mi, Lauren Buckley, Ofir Levy, Hong-Liang Lu & Wei-Guo Du
Heat tolerance at the immobile embryonic stage is expected to be critical in determining species vulnerability to climate change. However, how the mean and developmental plasticity of embryonic heat tolerance vary geographically, and how these geographic variations affect species’ vulnerability under climate change remain unknown. We experimentally determined the mean and developmental plasticity of embryonic acute heat tolerance (EAHT, i.e., heat shock temperature at which embryonic heartbeats ceased) for three latitudinally-distributed populations of an oviparous...

Unprecedented heat mortality of Magellanic penguins

Katie Holt & P. Dee Boersma
Extreme weather events are becoming more frequent and severe, leading to an increase in direct, adverse thermoregulatory impacts to wildlife. Here we document an unprecedented, single day, heat-related mortality event of Magellanic penguins ( Spheniscus magellanicus ) at Punta Tombo, Chubut Province, Argentina, one of the largest breeding colonies for this species. We found 264 dead adults and 90 dead chicks in the breeding colony and along the beaches after recording the highest temperature in...

Diverse arsenic-containing lipids in the surface ocean

Katherine Heal, Ashley Maloney, Anitra Ingalls & Randelle Bundy
Arsenic is present at nanomolar levels throughout the ocean, and microbes assimilate this potentially toxic element due to its similarity to inorganic phosphorus. Although dissolved arsenic has been a focus of several oceanographic studies, the size and chemical character of the particulate arsenic pool is poorly understood. We measured particulate arsenic in five samples from the open ocean and determined the contribution of arsenic-containing lipids to this pool. Here we show that the accumulation of...

Longitudinal variation in the nutritional quality of basal food sources and its effect on invertebrates and fish in subalpine rivers

Fen Guo, Nadine Ebm, Stuart Bunn, Michael Brett, Hannes Hager & Martin Kainz
1. There is growing recognition of the importance of food quality over quantity for aquatic consumers. In streams and rivers, most previous studies considered this primarily in terms of the quality of terrestrial leaf litter and importance of microbial conditioning. However, many recent studies suggest that algae are a more nutritional food source for riverine consumers than leaf litter. To date, few studies have quantified longitudinal shifts in the nutritional quality of basal food resources...

Scaling and structural properties of juvenile bull kelp (Nereocystis luetkeana) Data

Stephanie Crofts & Katie Dobkowski
Bull kelp (Nereocystis luetkeana), the only canopy-forming kelp in the Salish Sea, provides primary production in the nearshore subtidal environment and serves as important habitat for economically and ecologically important species. An annual species, each year juvenile bull kelp sporophytes must grow from the hydrodynamically more benign benthos to the water column, where they experience substantial drag at the surface. Because of the differences in morphology and ecology across life stages, and the fact that...

Optimal test-assisted quarantine strategies for COVID-19

Bo Peng, Wen Zhou, Rowland Pettit, Patrick Yu, Peter Matos, Alexander Greninger, Julie McCashin & Christopher Amos
Objective: To evaluate the effectiveness of SARS-CoV-2 testing on shortening the duration of quarantines for COVID-19 and to identify the most effective choices of testing schedules. Design: We performed extensive simulations to evaluate the performance of quarantine strategies when one or more SARS-CoV-2 tests were administered during the quarantine. Simulations were based on statistical models for the transmissibility and viral loads of SARS-CoV-2 infections and the sensitivities of available testing methods. Sensitivity analyses were performed...

Size-driven preservational and macroecological biases in the latest Maastrichtian terrestrial vertebrate assemblages of North America

Caleb Brown, Nicolas Campione, Gregory Wilson Mantilla & David Evans
The end-Cretaceous (K/Pg) mass-extinction event is the most recent and well-understood of the “Big Five” and triggered establishment of modern terrestrial ecosystem structure. Despite the depth of research into this event, our knowledge of upper Maastrichtian terrestrial deposits globally relies primarily on assemblage-level data limited to a few well-sampled formations in North America, the Hell Creek and Lance formations. These assemblages disproportionally affect our interpretations of this important interval. Multiple investigations have quantified diversity patterns...

Data from: A burning issue: Savanna fire management can generate enough carbon revenue to help restore Africa’s rangelands and fill protected area funding gaps

Timothy Tear, Nicholas Wolff, Geoffrey Lipsett-Moore, Mark Ritchie, Natasha Ribeiro, Lisanne Petracca, Peter Lindsey, Luke Hunter, Andrew Loveridge & Franziska Steinbruch
Many savanna-dependent species in Africa including large herbivores and apex predators are at increasing risk of extinction. Achieving effective management of protected areas (PAs) in Africa where lions live will cost an estimated USD >$1-2 B/year in new funding. We explored the potential for fire management-based carbon-financing programs to fill this funding gap and benefit degrading savanna ecosystems. We demonstrated how introducing early dry season fire management programs could produce potential carbon revenues (PCR) from...

Site fidelity and behavioral plasticity regulate an ungulate’s response to extreme disturbance

Samantha Kreling, Kaitlyn Gaynor, Alex McInturff, Kendall Calhoun & Justin Brashares
1. With rapid global change, the frequency and severity of extreme disturbance events are increasing worldwide. The ability of animal populations to survive these stochastic events depends on how individual animals respond to their altered environments, yet our understanding of the immediate and short-term responses of animals to acute disturbances remains poor. 2. We focused on animal responses to the environmental disturbance created by megafire. Specifically, we explored the effects of the 2018 Mendocino Complex...

HadCM3 and HadGEM3 LIG model outputs: A sea ice-free Arctic

Maria Vittoria Guarino & Louise Sime
The HadGEM3 (HadGEM3-GC3.1 or HadGEM3-GC3.1-N96ORCA1) PI simulation was initialized using the standard CMIP6 protocol using constant 1850 GHGs, ozone, solar, tropospheric aerosol, stratospheric volcanic aerosol and land-use forcing. The PI spin-up was 700 model-years, which allowed the land and oceanic masses to attain approximate steady state. The HadGEM3 LIG (Last Interglacial) simulation was initialized from the end of the spin-up phase of the equivalent pre-industrial (PI) simulation. After initialization, the LIG was run for 350...

Wind Tunnel Mosquito Trajectory Data

Jeff Riffell
Mosquitoes track odors, locate hosts, and find mates visually. The color of a food resource, such as a flower or warm-blooded host, can be dominated by long wavelengths of the visible light spectrum (green to red for humans) and is likely important for object recognition and localization. However, little is known about the hues that attract mosquitoes or how odor affects mosquito visual search behaviors. We use a real-time 3D tracking system and wind tunnel...

Genotypes for herring samples collected from Chinook salmon gut contents

Eleni Petrou, Joshua Chamberlin, Will Duguid, Russel Barsh, Francis Juanes, Jessica Qualley & Lorenz Hauser
Dynamic prey resources influence foraging opportunities for consumers. In coastal food webs, forage fish abundance and seasonal reproduction mediate foraging opportunities for mobile consumers. Recent declines in Chinook salmon productivity have prompted efforts to determine whether poormarine survival is caused by limited feeding opportunities. To establish the importance of phenological diversity in Pacific herring for Chinook salmon, we used genetic stock identification to assign individual herring collected from the guts of juvenile and adult Chinook...

Data from: New approaches to ceramic use and discard: cooking pottery from the Peruvian Andes in ethnoarchaeological perspective

John A. Hildebrand & Melissa B. Hagstrum
Ethnoarchaeological data from contemporary Wanka villages in the Mantaro Valley of the Peruvian Andes provide new perspectives on the use and discard of ceramic cooking vessels. We present a regional survey of ceramic vessel use and discard with household consumption as the focus of study. A mathematical model determines vessel uselife from the age distribution of in-use vessels. We examine the number of vessels per household, their volume, their uselife, and their reported discard. A...

Flatfish exon-capture

Calder Atta
This dataset contains alignments used to study phylogenetic relationships of flatfishes based on exon-capture data. The samples in this dataset represent 89 species: 86 flatfishes and 3 outgroup Carangidae. 57 samples were extracted and assembled from tissues collected for this project, while 39 were sourced from previously assembled data that were prepared as part of the FishLife project. For this study we targeted 4,434 markers developed by Jiang et al. (2019) for capture efficiency in...

Registration Year

  • 2021

Resource Types

  • Dataset


  • University of Washington
  • Stanford University
  • University of Cambridge
  • University of California, Berkeley
  • University of California, Santa Barbara
  • University of British Columbia
  • The Nature Conservancy
  • University of Glasgow
  • The University of Texas at Arlington
  • Occidental College