59 Works

Salmon Creek radon data

Laurel Larsen & Cleo Woelfle-Erskine
This datafile contains results of 222Rn analysis of samples collected within the Salmon Creek Watershed in Sonoma County, Califonia. Please see Woelfle-Erskine et al. (2017) for site location details. The present dataset is provided in support of Larsen and Woelfle-Erskine (in review).The purpose of this dataset was to determine relative ages of water samples.Data were collected in 2016 in the Fay Creek and Tannery Creek watersheds, both second-order tributaries of Salmon Creek.For further information, please...

Salmon Creek Organic Geochemistry Chemometric Data

Laurel Larsen & Cleo Woelfle-Erskine
This datafile contains fluorescence indices and the results of a parallel factor analysis (PARAFAC) performed on samples collected within the Salmon Creek Watershed in Sonoma County, Califonia. Please see Woelfle-Erskine et al. (2017) for site location details. The present dataset is provided in support of Larsen and Woelfle-Erskine (in review). The purpose of this dataset was to develop a fluorescent fingerprint for purposes of differentiating between surface water, groundwater, and hyporheic water.

Data from: Body temperature distributions of active diurnal lizards in three deserts: skewed up or skewed down?

Raymond B. Huey & Eric R. Pianka
1. The performance of ectotherms integrated over time depends in part on the position and shape of the distribution of body temperatures (Tb) experienced during activity. For several complementary reasons, physiological ecologists have long expected that Tb distributions during activity should have a long left tail (left-skewed); but only infrequently have they quantified the magnitude and direction of Tb skewness in nature. 2. To evaluate whether left-skewed Tb distributions are general for diurnal desert lizards,...

Data from: Invasive seaweeds transform habitat structure and increase biodiversity of associated species

Jennifer A. Dijkstra, Larry G. Harris, Kristen Mello, Amber Littere, Christopher Wells, Colin Ware & Amber Litterer
The visual landscape of marine and terrestrial systems is changing as a result of anthropogenic factors. Often these shifts involve introduced species that are morphologically dissimilar to native species, creating a unique biogenic structure and habitat for associated species within the landscape. While community level changes as a result of introduced species have been documented in both terrestrial and marine systems, it is still unclear how long-term shifts in species composition will affect habitat complexity...

Data from: Identification of genomic regions associated with sex in Pacific halibut

Daniel P. Drinan, Timothy Loher & Lorenz Hauser
Understanding and identifying the genetic mechanisms responsible for sex-determination are important for species management, particularly in exploited fishes where sex biased harvest could have implications on population dynamics and long-term persistence. The Pacific halibut (Hippoglossus stenolepis) supports important fisheries in the North Pacific Ocean. The proportion of each sex in the annual harvest is currently estimated using growth curves, but genetic techniques may provide a more accurate method. We used restriction-site associated DNA (RAD) sequencing...

Data from: Epigenetic memory via concordant DNA methylation is inversely correlated to developmental potential of mammalian cells

Minseung Choi, Diane P. Genereux, Jamie Goodson, Haneen Al-Azzawi, Shannon Q. Allain, Noah Simon, Stan Palasek, Carol B. Ware, Chris Cavanaugh, Daniel G. Miller, Winslow C. Johnson, Kevin D. Sinclair, Reinhard Stöger & Charles D. Laird
In storing and transmitting epigenetic information, organisms must balance the need to maintain information about past conditions with the capacity to respond to information in their current and future environments. Some of this information is encoded by DNA methylation, which can be transmitted with variable fidelity from parent to daughter strand. High fidelity confers strong pattern matching between the strands of individual DNA molecules and thus pattern stability over rounds of DNA replication; lower fidelity...

Data from: A comparison of individual-based genetic distance metrics for landscape genetics

Andrew J. Shirk, Erin L. Landguth & Samuel A. Cushman
A major aim of landscape genetics is to understand how landscapes resist gene flow and thereby influence population genetic structure. An empirical understanding of this process provides a wealth of information that can be used to guide conservation and management of species in fragmented landscapes, and also to predict how landscape change may affect population viability. Statistical approaches to infer the true model among competing alternatives are based on the strength of the relationship between...

Data from: Temperature-dependent body size effects determine population responses to climate warming

Max Lindmark, Magnus Huss, Jan Ohlberger & Anna Gårdmark
Current understanding of animal population responses to rising temperatures is based on the assumption that biological rates such as metabolism, which governs fundamental ecological processes, scale independently with body size and temperature, despite empirical evidence for interactive effects. Here we investigate the consequences of interactive temperature- and size-scaling of vital rates for the dynamics of populations experiencing warming using a stage-structured consumer-resource model. We show that interactive scaling alters population and stage-specific responses to rising...

Data from: Taxonomic and functional assessment of mesopredator diversity across an estuarine habitat mosaic

Collin Gross, Cinde Donoghue, Casey Pruitt, Alan C. Trimble & Jennifer L. Ruesink
A long-standing rule in ecology is that structural complexity increases abundance and diversity of organisms, but this paradigm glosses over potential trait-specific benefits of habitat structure across different regional species pools. We tested this idea using multiple response variables emphasizing taxonomic and functional diversity in seagrass-vegetated, edge, and unvegetated habitats across three estuaries in Washington State (USA). We also used these variables in tandem to evaluate functional redundancy as a proxy for ecosystem resistance and...

Data from: A comparison of regression methods for model selection in individual-based landscape genetic analysis

Andrew J. Shirk, Erin L. Landguth & Samuel A. Cushman
Anthropogenic migration barriers fragment many populations and limit the ability of species to respond to climate-induced biome shifts. Conservation actions designed to conserve habitat connectivity and mitigate barriers are needed to unite fragmented populations into larger, more viable metapopulations, and to allow species to track their climate envelope over time. Landscape genetic analysis provides an empirical means to infer landscape factors influencing gene flow, and thereby inform such conservation actions. However, there are currently many...

Data from: Harvesting wildlife affected by climate change: a modelling and management approach for polar bears

Eric V. Regehr, Ryan R. Wilson, Karyn D. Rode, Michael C. Runge & Harry L. Stern
The conservation of many wildlife species requires understanding the demographic effects of climate change, including interactions between climate change and harvest, which can provide cultural, nutritional or economic value to humans. We present a demographic model that is based on the polar bear Ursus maritimus life cycle and includes density-dependent relationships linking vital rates to environmental carrying capacity (K). Using this model, we develop a state-dependent management framework to calculate a harvest level that (i)...

Data from: Protein structure determination using metagenome sequence data

Sergey Ovchinnikov, Hahnbeom Park, Neha Varghese, Po-Ssu Huang, Georgios A. Pavlopoulos, David E. Kim, Hetunandan Kamisetty, Nikos C. Kyrpides & David Baker
Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families and that metagenome sequence data more than triple the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact-based structure matching, and Rosetta structure...

Data from: microCT-based phenomics in the zebrafish skeleton reveals virtues of deep phenotyping in a distributed organ system

Matthew Hur, Charlotte A. Gistelinck, Philippe Huber, Jane Lee, Marjorie H. Thompson, Adrian T. Monstad-Rios, Claire J. Watson, Sarah K. McMenamin, Andy Willaert, David M. Parichy, Paul Coucke & Ronald Y. Kwon
Phenomics, which ideally involves in-depth phenotyping at the whole-organism scale, may enhance our functional understanding of genetic variation. Here, we demonstrate methods to profile hundreds of phenotypic measures comprised of morphological and densitometric traits at a large number of sites within the axial skeleton of adult zebrafish. We show the potential for vertebral patterns to confer heightened sensitivity, with similar specificity, in discriminating mutant populations compared to analyzing individual vertebrae in isolation. We identify phenotypes...

Data from: Physiology at near-critical temperatures, but not critical limits, varies between two lizard species that partition the thermal environment

Rory S. Telemeco, Eric J. Gangloff, Gerardo A. Cordero, Rebecca L. Polich, Anne M. Bronikowski & Fredric J. Janzen
The mechanisms that mediate the interaction between the thermal environment and species’ ranges are generally uncertain. Thermal environments may directly restrict species when environments exceed tolerance limits (i.e. the fundamental niche). However, thermal environments might also differentially affect relative performance among species prior to fundamental tolerances being met (i.e. the realized niche). We examined stress physiology (plasma glucose and corticosterone), mitochondrial performance, and the muscle metabolome of congeneric lizards that naturally partition the thermal niche,...

Data from: Diet tracing in ecology: method comparison and selection

Jens M. Nielsen, Elizabeth L. Clare, Brian Hayden, Michael T. Brett & Pavel Kratina
1. Determining diet is a key prerequisite for understanding species interactions, food web structure and ecological dynamics. In recent years, there has been considerable development in both the methodology and application of novel and more traditional dietary tracing methods, yet there is no comprehensive synthesis that systematically and quantitatively compares among the different approaches. 2. Here we conceptualize diet tracing in ecology, provide recommendations for method selection, and illustrate the advantages of method integration. We...

Data from: Top predators constrain mesopredator distributions

Thomas M. Newsome, Aaron C. Greenville, Duško Ćirović, Christopher R. Dickman, Chris N. Johnson, Miha Krofel, Mike Letnic, William J. Ripple, Euan G. Ritchie, Stoyan Stoyanov & Aaron J. Wirsing
Top predators can suppress mesopredators by killing them, competing for resources and instilling fear, but it is unclear how suppression of mesopredators varies with the distribution and abundance of top predators at large spatial scales and among different ecological contexts. We suggest that suppression of mesopredators will be strongest where top predators occur at high densities over large areas. These conditions are more likely to occur in the core than on the margins of top...

Data from: Apex predators and the facilitation of resource partitioning among mesopredators

Kelly J. Sivy, Casey B. Pozzanghera, Kassidy E. Colson, Matthew A. Mumma & Laura R. Prugh
Apex predators may influence carnivore communities through the suppression of competitively dominant mesopredators, however they also provide carrion subsidies that could influence foraging and competition among sympatric mesopredators when small prey is scarce. We assessed coyote Canis latrans and red fox Vulpes vulpes winter diet overlap and composition from scats collected in two study areas with >3-fold difference in grey wolf Canis lupus density due to a wolf control program. We hypothesized that differences in...

Data from: A consensus method for ancestral recombination graphs

Mary K. Kuhner & Jon Yamato
We propose a consensus method for ancestral recombination graphs (ARGs) that generates a single ARG representing commonalities among a cloud of ARGs defined for the same genomic region and set of taxa. Our method, which we call “threshold consensus,” treats a genomic location as a potential recombination breakpoint only if the number of ARGs in the cloud possessing a breakpoint at that location exceeds a chosen threshold. The estimate is further refined by ignoring recombinations...

Data from: Fire catalyzed rapid ecological change in lowland coniferous forests of the Pacific Northwest over the past 14,000 years

Shelley D. Crausbay, Philip E. Higuera, Douglas G. Sprugel & Linda B. Brubaker
Disturbance can catalyze rapid ecological change by causing widespread mortality and initiating successional pathways, and during times of climate change, disturbance may contribute to ecosystem state changes by initiating a new successional pathway. In the Pacific Northwest of North America (PNW), disturbance by wildfires strongly shapes the composition and structure of lowland forests, but understanding the role of fire over periods of climate change is challenging, because fire-return intervals are long (e.g., millennia) and the...

Data from: Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens

Ethan B. Linck, Zachary R. Hanna, Anna Sellas & John P. Dumbacher
Laboratory techniques for high-throughput sequencing have enhanced our ability to generate DNA sequence data from millions of natural history specimens collected prior to the molecular era, but remain poorly tested at shallower evolutionary time scales. Hybridization capture using restriction site-associated DNA probes (hyRAD) is a recently developed method for population genomics with museum specimens. The hyRAD method employs fragments produced in a restriction site-associated double digestion as the basis for probes that capture orthologous loci...

Data from: Evidence for concerted movement of nuclear and mitochondrial clines in a lizard hybrid zone

Adam Leaché, Jared Grummer, Rebecca Harris & Ian Breckheimer
Moving hybrid zones provide compelling examples of evolution in action, yet long-term studies that test the assumptions of hybrid zone stability are rare. Using replicated transect samples collected over a 10 year interval from 2002 to 2012, we find evidence for concerted movement of genetic clines in a plateau fence lizard hybrid zone (Sceloporus tristichus) in Arizona. Cline-fitting analyses of SNP and mtDNA data both provide evidence that the hybrid zone shifted northward by approximately...

Data from: Human-mediated evolution in a threatened species? Juvenile life-history changes in Snake River salmon

Robin S. Waples, Anna Elz, Billy D. Arnsberg, James R. Faulkner, Jeffrey J. Hard, Emma Timmins-Schiffman & Linda K. Park
Evaluations of human impacts on Earth's ecosystems often ignore evolutionary changes in response to altered selective regimes. Freshwater habitats for Snake River fall Chinook salmon (SRFCS), a threatened species in the U.S., have been dramatically changed by hydropower development and other watershed modifications. Associated biological changes include a shift in juvenile life history: historically essentially 100% of juveniles migrated to sea as subyearlings, but a substantial fraction have migrated as yearlings in recent years. In...

Data from: Phylogenomic analysis of the Chilean clade of Liolaemus lizards (Squamata: Liolaemidae) based on sequence capture data

Alejandra Panzera, Adam D. Leaché, Guillermo D'Elía & Pedro F. Victoriano
The genus Liolaemus is one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless, Liolaemus lizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination...

Data from: Habitat risk assessment for regional ocean planning in the U.S. Northeast and Mid-Atlantic

Katherine H. Wyatt, Rob Griffin, Anne D. Guerry, Mary Ruckelshaus, Michael Fogarty, Katie K. Arkema & Robert Griffin
Coastal habitats provide important benefits to people, including habitat for species targeted by fisheries and opportunities for tourism and recreation. Yet, such human activities also can imperil these habitats and undermine the ecosystem services they provide to people. Cumulative risk assessment provides an analytical framework for synthesizing the influence of multiple stressors across habitats and decision-support for balancing human uses and ecosystem health. To explore cumulative risk to habitats in the U.S. Northeast and Mid-Atlantic...

United States Census Data, 1900: Public Use Sample

Robert L. Higgs & Samuel H. Preston
This study was conducted under the auspices of the Center for Studies in Demography and Ecology at the University of Washington. It is a nationally representative sample of the population of the United States in 1900, drawn from the manuscript returns of individuals enumerated in the 1900 United States Census. Household variables include region, state and county of household, size of household, and type and ownership of dwelling. Individual variables for each household member include...

Registration Year

  • 2017

Resource Types

  • Dataset


  • University of Washington
  • University of Montana
  • Oregon State University
  • University of California, Berkeley
  • United States Department of Agriculture
  • Fred Hutchinson Cancer Research Center
  • University of Pennsylvania
  • Burke Museum of Natural History and Culture
  • Occidental College
  • University of Colorado Boulder