58 Works

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: 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: 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: 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: 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: 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: 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...

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.

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...

Data from: Caenorhabditis elegans genes affecting interindividual variation in life-span biomarker gene expression

Alexander Mendenhall, Matthew M. Crane, Patricia M. Tedesco, Thomas E. Johnson & Roger Brent
Genetically identical organisms grown in homogenous environments differ in quantitative phenotypes. Differences in one such trait, expression of a single biomarker gene, can identify isogenic cells or organisms that later manifest different fates. For example, in isogenic populations of young adult Caenorhabditis elegans, differences in Green Fluorescent Protein (GFP) expressed from the hsp-16.2 promoter predict differences in life span. Thus, it is of interest to determine how interindividual differences in biomarker gene expression arise. Prior...

Data from: Range contraction and increasing isolation of a polar bear subpopulation in an era of sea-ice loss

Kristin L. Laidre, Erik W. Born, Stephen N. Atkinson, Øystein Wiig, Liselotte W. Andersen, Nicholas J. Lunn, Markus Dyck, Eric V. Regehr, Richard McGovern & Patrick Heagerty
Climate change is expected to result in range shifts and habitat fragmentation for many species. In the Arctic, loss of sea ice will reduce barriers to dispersal or eliminate movement corridors, resulting in increased connectivity or geographic isolation with sweeping implications for conservation. We used satellite telemetry, data from individually marked animals (research and harvest), and microsatellite genetic data to examine changes in geographic range, emigration, and interpopulation connectivity of the Baffin Bay (BB) polar...

Data from: The function and organization of the motor system controlling flight maneuvers in flies

Theodore H. Lindsay, Anne Sustar, Michael H. Dickinson, Theodore Lindsay & Michael Dickinson
Animals face the daunting task of controlling their limbs using a small set of highly constrained actuators. This problem is particularly demanding for insects such as Drosophila, which must adjust wing motion for both quick voluntary maneuvers and slow compensatory reflexes using only a dozen pairs of muscles. To identify strategies by which animals execute precise actions using sparse motor networks, we imaged the activity of a complete ensemble of wing control muscles in intact,...

Data from: A descending neuron correlated with the rapid steering maneuvers of flying Drosophila

Bettina Schnell, Ivo G. Ros & Michael H. Dickinson
To navigate through the world, animals must stabilize their path against disturbances and change direction to avoid obstacles and to search for resources. Locomotion is thus guided by sensory cues but also depends on intrinsic processes, such as motivation and physiological state. Flies, for example, turn with the direction of large-field rotatory motion, an optomotor reflex that is thought to help them fly straight. Occasionally, however, they execute fast turns, called body saccades, either spontaneously...

Data from: Neural evidence supports a dual sensory-motor role for insect wings

Brandon Pratt, Tanvi Deora, Thomas Mohren, Tom Daniel & Thomas Daniel
Flying insects use feedback from various sensory modalities including vision and mechanosensation to navigate through their environment. The rapid speed of mechanosensory information acquisition and processing compensates for the slower processing times associated with vision, particularly under low light conditions. While halteres in dipteran species are well known to provide such information for flight control, less is understood about the mechanosensory roles of their evolutionary antecedent, wings. The features that wing mechanosensory neurons (campaniform sensilla)...

Data from: Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae: Phrynosoma)

Christopher Blair, & Robert W. Bryson
Biodiversity reduction and loss continues to progress at an alarming rate, and thus there is widespread interest in utilizing rapid and efficient methods for quantifying and delimiting taxonomic diversity. Single-locus species-delimitation methods have become popular, in part due to the adoption of the DNA barcoding paradigm. These techniques can be broadly classified into tree-based and distance-based methods depending on whether species are delimited based on a constructed genealogy. Although the relative performance of these methods...

Data from: Mapping polyclonal HIV-1 antibody responses via next-generation neutralization fingerprinting

Nicole A. Doria-Rose, Han R. Altae-Tran, Ryan S. Roark, Stephen D. Schmidt, Matthew S. Sutton, Mark K. Louder, Gwo-Yu Chuang, Robert T. Bailer, Valerie Cortez, Rui Kong, Krisha McKee, Sijy O'Dell, Felicia Wang, Salim S. Abdool Karim, James M. Binley, Mark Connors, Barton F. Haynes, Malcolm A. Martin, David C. Montefiori, Lynn Morris, Julie Overbaugh, Peter D. Kwong, John R. Mascola, Ivelin S. Georgiev & Sijy O’Dell
Computational neutralization fingerprinting, NFP, is an efficient and accurate method for predicting the epitope specificities of polyclonal antibody responses to HIV-1 infection. Here, we present next-generation NFP algorithms that substantially improve prediction accuracy for individual donors and enable serologic analysis for entire cohorts. Specifically, we developed algorithms for: (a) selection of optimized virus neutralization panels for NFP analysis, (b) estimation of NFP prediction confidence for each serum sample, and (c) identification of sera with potentially...

Data from: Graphics for relatedness research

Iván Galván-Femenía, Jan Graffelman & Carles Barceló-I-Vidal
Studies of relatedness have been crucial in molecular ecology over the last decades. Good evidence of this is the fact that studies of population structure, evolution of social behaviours, genetic diversity and quantitative genetics all involve relatedness research. The main aim of this article is to review the most common graphical methods used in allele sharing studies for detecting and identifying family relationships. Both IBS and IBD based allele sharing studies are considered. Furthermore, we...

Data from: Compensatory mutations improve general permissiveness to antibiotic resistance plasmids

Wesley Loftie-Eaton, Kelsie Bashford, Hannah Quinn, Kieran Dong, Jack Millstein, Samuel Hunter, Maureen K. Thomason, Houra Merrikh, Jose M. Ponciano & Eva M. Top
Horizontal gene transfer mediated by broad-host-range plasmids is an important mechanism of antibiotic resistance spread. While not all bacteria maintain plasmids equally well, plasmid persistence can improve over time, yet no general evolutionary mechanisms have emerged. Our goal was to identify these mechanisms, and to assess if adaptation to one plasmid affects the permissiveness to others. We experimentally evolved Pseudomonas sp. H2 containing multi-drug resistance plasmid RP4, determined plasmid persistence and cost using a joint...

Data from: Clearing muddied waters: capture of environmental DNA from turbid waters

Kelly E. Williams, Antoinette J. Piaggio & Kathryn P. Huyvaert
Understanding the differences in efficiencies of various methods to concentrate, extract, and amplify environmental DNA (eDNA) is vital for best performance of eDNA detection. Aquatic systems vary in characteristics such as turbidity, eDNA concentration, and inhibitor load, thus affecting eDNA capture efficiency. Application of eDNA techniques to the detection of terrestrial invasive or endangered species may require sampling at intermittent water sources that are used for drinking and cooling; these water bodies may often be...

Data from: Hemiparasites can transmit indirect effects from their host plants to herbivores

Nathan L. Haan, Jonathan D. Bakker & M. Deane Bowers
Parasitic plants can serve as critical intermediaries between their hosts and other organisms; however these relationships are not well understood. To investigate the relative importance of plant traits in such interactions, we studied the role of the root hemiparasite, Castilleja levisecta (Orobanchaceae), as a mediator of interactions between the host plants it parasitizes and the lepidopteran herbivore Euphydryas editha (Nymphalidae), whose caterpillars feed on Castilleja and sequester iridoid glycosides from it. We tested whether the...

Data from: Specialized specialists and the narrow niche fallacy: a tale of scale-feeding fishes

Matthew A. Kolmann, Jonathan M. Huie, Kory Evans & Adam P. Summers
Although rare within the context of 30,000 species of extant fishes, scale-feeding as an ecological strategy has evolved repeatedly across the teleost tree of life. Scale-feeding (lepidophagous) fishes are diverse in terms of their ecology, behavior, and specialized morphologies for grazing on scales and mucus of sympatric species. Despite this diversity, the underlying ontogenetic changes in functional and biomechanical properties of associated feeding morphologies in lepidophagous fishes are less understood. We examined the ontogeny of...

Data from: Species discrimination of co-occurring small fossil mammals: a case study of the Cretaceous-Paleogene multituberculate genus Mesodma

Stephanie M. Smith & Gregory P. Wilson
The mammalian fossil record is largely composed of isolated teeth and tooth-bearing elements. In vertebrate microfossil assemblages with closely related, co-occurring species of mammals, it can be difficult to identify isolated teeth to species level because morphological differences among species may be slight and based on a single tooth position. Here we investigate the utility of the allegedly diagnostic lower fourth premolar (p4) for species-level identification in the genus Mesodma (Multituberculata, Neoplagiaulacidae). We conducted linear...

Data from: High human papillomavirus (HPV) prevalence in South African adolescents and young women encourages expanded HPV vaccination campaigns

Zizipho Z.A. Mbulawa, Cari Van Schalkwyk, Nai-Chung Hu, Tracy L. Meiring, Shaun Barnabas, Smritee Dabee, Heather Jaspan, Jean-MAri Kriek, Shameem Z. Jaumdally, Etienne Muller, Linda-Gail Bekker, David A. Lewis, Janan Dietrich, Glenda Gray, Jo-Ann S. Passmore, Anna-Lise Williamson & Zizipho Z. A. Mbulawa
Objectives: To investigate prevalence of cervical human papillomavirus (HPV) genotypes to inform HPV vaccination strategy in South Africa and to study factors associated with HPV prevalence. Methods: Sexually active, HIV-negative women, aged 16-22 years recruited from Soweto (n=143) and Cape Town (n=148) were tested for cervical HPV and other genital infections. Results: Overall HPV prevalence was 66.7% (194/291) in young women. Cape Town women were more likely to have multiple HPV infections than the Soweto...

Data from: Genetic mapping of molar size relations identifies inhibitory locus for third molars in mice

Nicolas Navarro & A. Murat Maga
Molar size in Mammals shows considerable disparity and exhibits variation similar to that predicted by the Inhibitory Cascade model. The importance of such developmental systems in favoring evolutionary trajectories is also underlined by the fact that this model can predict macroevolutionary patterns. Using backcross mice, we mapped QTL for molar sizes controlling for their sequential development. Genetic controls for upper and lower molars appear somewhat similar, and regions containing genes implied in dental defects drive...

Data from: Microbiome sharing between children, livestock and household surfaces in western Kenya

Emily Mosites, Matt Sammons, Elkanah Otiang, Alexander Eng, Ceclia Noecher, Ohad Manor, Sarah Hilton, Samuel M. Thmbi, Clayton Onyango, Gemina Garland-Lewis, Douglas R. Call, M. Kariuki Njenga, Judith N. Wasserheit, Jennifer A. Zambriski, Judd L. Walson, Guy H. Palmer, Joel Montgomery, Elhanan Borenstein, Richard Omore, Peter M. Rabinowitz, Samuel M. Thumbi & Cecilia Noecker
The gut microbiome community structure and development are associated with several health outcomes in young children. To determine the household influences of gut microbiome structure, we assessed microbial sharing within households in western Kenya by sequencing 16S rRNA libraries of fecal samples from children and cattle, cloacal swabs from chickens, and swabs of household surfaces. Among the 156 households studied, children within the same household significantly shared their gut microbiome with each other, although we...

Registration Year

  • 2017
    58

Resource Types

  • Dataset
    58

Affiliations

  • University of Washington
    58
  • University of Montana
    4
  • Oregon State University
    3
  • University of California, Berkeley
    3
  • United States Department of Agriculture
    3
  • Fred Hutchinson Cancer Research Center
    2
  • Burke Museum of Natural History and Culture
    2
  • Occidental College
    2
  • University of Colorado Boulder
    2
  • University of the Witwatersrand
    2