54 Works

Data from: A newly identified left–right asymmetry in larval sea urchins

Jason Hodin, Keegan Lutek & Andreas Heyland
Directional asymmetry (DA) in body form is a widespread phenomenon in animals and plants alike, and a functional understanding of such asymmetries can offer insights into the ways in which ecology and development interface to drive evolution. Echinoids (sea urchins, sand dollars and their kin) with planktotrophic development have a bilaterally symmetrical feeding pluteus larva that undergoes a dramatic metamorphosis into a pentameral juvenile that enters the benthos at settlement. The earliest stage of this...

Data from: Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci

Ryan K. Waples, Wesley A. Larson & Robin S. Waples
Contemporary effective population size (Ne) can be estimated using linkage disequilibrium (LD) observed across pairs of loci presumed to be selectively neutral and unlinked. This method has been commonly applied to data sets containing 10–100 loci to inform conservation and study population demography. Performance of these Ne estimates could be improved by incorporating data from thousands of loci. However, these thousands of loci exist on a limited number of chromosomes, ensuring that some fraction will...

Data from: Climate modifies response of non-native and native species richness to nutrient enrichment

Habacuc Flores-Moreno, Peter B. Reich, Eric M. Lind, Lauren L. Sullivan, Eric W. Seabloom, Laura Yahdjian, Andrew S. MacDougall, Lara G. Reichmann, Juan Alberti, Selene Báez, Jonathan D. Bakker, Marc W. Cadotte, Maria C. Caldeira, Enrique J. Chaneton, Carla M. D'Antonio, Philip A. Fay, Jennifer Firn, Nicole Hagenah, W. Stanley Harpole, Oscar Iribarne, Kevin P. Kirkman, Johannes M. H. Knops, Kimberly J. La Pierre, Ramesh Laungani, Andrew D. B. Leakey … & Elizabeth T. Borer
Ecosystem eutrophication often increases domination by non-natives and causes displacement of native taxa. However, variation in environmental conditions may affect the outcome of interactions between native and non-native taxa in environments where nutrient supply is elevated. We examined the interactive effects of eutrophication, climate variability and climate average conditions on the success of native and non-native plant species using experimental nutrient manipulations replicated at 32 grassland sites on four continents. We hypothesized that effects of...

Data from: Whole organism lineage tracing by combinatorial and cumulative genome editing

Aaron McKenna, Gregory M. Findlay, James A. Gagnon, Marshall S. Horwitz, Alexander Franz Schier & Jay Shendure
Multicellular systems develop from single cells through distinct lineages. However, current lineage-tracing approaches scale poorly to whole, complex organisms. Here, we use genome editing to progressively introduce and accumulate diverse mutations in a DNA barcode over multiple rounds of cell division. The barcode, an array of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 target sites, marks cells and enables the elucidation of lineage relationships via the patterns of mutations shared between cells. In cell culture...

Data from: Genomic data reveal ancient microendemism in forest scorpions across the California Floristic Province

, Warren E. Savary, Amanda J. Zellmer, R. Bruce Bury, John E. McCormack & Robert W. Bryson
The California Floristic Province (CFP) in western North America is a globally significant biodiversity hotspot. Elucidating patterns of endemism and the historical drivers of this diversity has been an important challenge of comparative phylogeography for over two decades. We generated phylogenomic data using ddRADseq to examine genetic structure in Uroctonus forest scorpions, an ecologically restricted and dispersal-limited organism widely distributed across the CFP north to the Columbia River. We coupled our genetic data with species...

Data from: Using collision cones to assess biological deconfliction methods

Natalie L. Brace, Tyson L. Hedrick, Diane H. Theriault, Nathan W. Fuller, Zheng Wu, Margrit Betke, Julia K. Parrish, Daniel Grünbaum & Kristi A. Morgansen
Biological systems consistently outperform autonomous systems governed by engineered algorithms in their ability to reactively avoid collisions. To better understand this discrepancy, a collision avoidance algorithm was applied to frames of digitized video trajectory data from bats, swallows and fish (Myotis velifer, Petrochelidon pyrrhonota and Danio aequipinnatus). Information available from visual cues, specifically relative position and velocity, was provided to the algorithm which used this information to define collision cones that allowed the algorithm to...

Data from: Intrinsic and extrinsic drivers of source-sink dynamics

Julie A. Heinrichs, Joshua L. Lawler & Nathan H. Schumaker
Many factors affect the presence and exchange of individuals among subpopulations and influence not only the emergence, but the strength of ensuing source–sink dynamics within metapopulations. Yet their relative contributions remain largely unexplored. To help identify the characteristics of empirical systems that are likely to exhibit strong versus weak source–sink dynamics and inform their differential management, we compared the relative roles of influential factors in strengthening source–sink dynamics. In a series of controlled experiments within...

Data from: Population structure and phylogeography of the Gentoo Penguin (Pygoscelis papua) across the Scotia Arc

Hila Levy, Gemma V. Clucas, Alex D. Rogers, Adam D. Leaché, Kate L. Ciborowski, Michael J. Polito, Heather J. Lynch, Michael J. Dunn & Tom Hart
Climate change, fisheries pressure on penguin prey, and direct human disturbance of wildlife have all been implicated in causing large shifts in the abundance and distribution of penguins in the Southern Ocean. Without mark-recapture studies, understanding how colonies form and, by extension, how ranges shift is challenging. Genetic studies, particularly focused on newly established colonies, provide a snapshot of colonisation and can reveal the extent to which shifts in abundance and occupancy result from changes...

Data from: Relative importance of abiotic, biotic, and disturbance drivers of plant community structure in the sagebrush steppe

Rachel M. Mitchell, Jonathan D. Bakker, John B. Vincent & G. Matt Davies
Abiotic conditions, biotic factors, and disturbances can act as filters that control community structure and composition. Understanding the relative importance of these drivers would allow us to understand and predict the causes and consequences of changes in community structure. We used long-term data (1989-2002) from the sagebrush steppe in Washington state, USA, to ask three questions: 1) What are the key drivers of community-level metrics of community structure? 2) Do community-level metrics and functional groups...

Data from: Always chew your food: freshwater stingrays use mastication to process tough insect prey

Matthew A. Kolmann, Kenneth C. Welch, Adam P. Summers & Nathan R. Lovejoy
Chewing, characterized by shearing jaw motions and high-crowned molar teeth, is considered an evolutionary innovation that spurred dietary diversification and evolutionary radiation of mammals. Complex prey-processing behaviours have been thought to be lacking in fishes and other vertebrates, despite the fact that many of these animals feed on tough prey, like insects or even grasses. We investigated prey capture and processing in the insect-feeding freshwater stingray Potamotrygon motoro using high-speed videography. We find that Potamotrygon...

Data from: Modelling tooth–prey interactions in sharks: the importance of dynamic testing

Katherine A. Corn, Stacy C. Farina, Jeffrey Brash & Adam P. Summers
The shape of shark teeth varies among species, but traditional testing protocols have revealed no predictive relationship between shark tooth morphology and performance. We developed a dynamic testing device to quantify cutting performance of teeth. We mimicked head-shaking behaviour in feeding large sharks by attaching teeth to the blade of a reciprocating power saw fixed in a custom-built frame. We tested three tooth types at biologically relevant speeds and found differences in tooth cutting ability...

Data from: Hidden histories of gene flow in highland birds revealed with genomic markers

Eugenia Zarza, Brant C. Faircloth, Whitney L. E. Tsai, , John Klicka, John E. McCormack, Whitney L.E. Tsai & Robert W. Bryson
Genomic studies are revealing that divergence and speciation are marked by gene flow, but it is not clear whether gene flow has played a prominent role during the generation of biodiversity in species-rich regions of the world where vicariance is assumed to be the principal mode by which new species form. We revisit a well-studied organismal system in the Mexican Highlands, Aphelocoma jays, to test for gene flow among Mexican sierras. Prior results from mitochondrial...

Data from: A public database of memory and naive B-cell receptor sequences

William S. DeWitt, Paul Lindau, Thomas M. Snyder, Anna M. Sherwood, Marissa Vignali, Christopher S. Carlson, Philip D. Greenberg, Natalie Duerkopp, Ryan O. Emerson & Harlan S. Robins
The vast diversity of B-cell receptors (BCR) and secreted antibodies enables the recognition of, and response to, a wide range of epitopes, but this diversity has also limited our understanding of humoral immunity. We present a public database of more than 37 million unique BCR sequences from three healthy adult donors that is many fold deeper than any existing resource, together with a set of online tools designed to facilitate the visualization and analysis of...

Data from: The comparative hydrodynamics of rapid rotation by predatory appendages

Mathew J. McHenry, Philip S. L. Anderson, Sam Van Wassenbergh, David Matthews, Adam Summers & S. N. Patek
Countless aquatic animals rotate appendages through the water, yet fluid forces are typically modeled with translational motion. To elucidate the hydrodynamics of rotation, we analyzed the raptorial appendages of mantis shrimp (Stomatopoda) using a combination of flume experiments, mathematical modeling and phylogenetic comparative analyses. We found that computationally efficient blade-element models offered an accurate first-order approximation of drag, when compared with a more elaborate computational fluid-dynamic model. Taking advantage of this efficiency, we compared the...

Data from: Indexed PCR primers induce template-specific bias in large-scale DNA sequencing studies

James L. O'Donnell, Ryan P. Kelly, Jesse A. Port, Natalie C. Lowell & James L. O’Donnell
Massively parallel sequencing is rapidly emerging as an efficient way to quantify biodiversity at all levels, from genetic variation and expression to ecological community assemblage. However, the number of reads produced per sequencing run far exceeds the number required per sample for many applications, compelling researchers to sequence multiple samples per run in order to maximize efficiency. For studies that include a PCR step, this can be accomplished using primers that include an index sequence...

Data from: Estimation of a killer whale (Orcinus orca) population’s diet using sequencing analysis of DNA from feces

Michael J. Ford, Jennifer Hempelmann, M. Bradley Hanson, Katherine L. Ayres, Robin W. Baird, Candice K. Emmons, Jessica I. Lundin, Gregory S. Schorr, Samuel K. Wasser & Linda K. Park
Estimating diet composition is important for understanding interactions between predators and prey and thus illuminating ecosystem function. The diet of many species, however, is difficult to observe directly. Genetic analysis of fecal material collected in the field is therefore a useful tool for gaining insight into wild animal diets. In this study, we used high-throughput DNA sequencing to quantitatively estimate the diet composition of an endangered population of wild killer whales (Orcinus orca) in their...

Data from: Physiological plasticity and local adaptation to elevated pCO2 in calcareous algae: an ontogenetic and geographic approach

Jacqueline L. Padilla-Gamiño, Juan D. Gaitán-Espitia, Morgan W. Kelly & Gretchen E. Hofmann
To project how ocean acidification will impact biological communities in the future, it is critical to understand the potential for local adaptation and the physiological plasticity of marine organisms throughout their entire life cycle, as some stages may be more vulnerable than others. Coralline algae are ecosystem engineers that play significant functional roles in oceans worldwide, and are considered vulnerable to ocean acidification. Using different stages of coralline algae, we tested the hypothesis that populations...

Data from: Neonatal activation of the xenobiotic-sensors PXR and CAR results in acute and persistent down-regulation of PPARα-signaling in mouse liver

Cindy Yanfei Li, Sunny Lihua Cheng, Theo K. Bammler & Julia Yue Cui
Safety concerns have emerged regarding the potential long-lasting effects due to developmental exposure to xenobiotics. The pregnane X receptor (PXR) and constitutive androstane receptor (CAR) are critical xenobiotic-sensing nuclear receptors that are highly expressed in liver. The goal of this study was to test our hypothesis that neonatal exposure to PXR- or CAR-activators not only acutely but also persistently regulates the expression of drug-processing genes (DPGs). A single dose of the PXR-ligand PCN (75 mg/kg),...

Data from: A transmission-virulence evolutionary trade-off explains attenuation of HIV-1 in Uganda

François Blanquart, Mary Kate Grabowski, Joshua Herbeck, Fred Nalugoda, David Serwadda, Michael A. Eller, Merlin L. Robb, Ronald Gray, Godfrey Kigozi, Oliver Laeyendecker, Katrina A. Lythgoe, Gertrude Nakigozi, Thomas C. Quinn, Steven J. Reynolds, Maria J. Wawer & Christophe Fraser
Evolutionary theory hypothesizes that intermediate virulence maximizes pathogen fitness as a result of a trade-off between virulence and transmission, but empirical evidence remains scarce. We bridge this gap using data from a large and long-standing HIV-1 prospective cohort, in Uganda. We use an epidemiological-evolutionary model parameterised with this data to derive evolutionary predictions based on analysis and detailed individual-based simulations. We robustly predict stabilising selection towards a low level of virulence, and rapid attenuation of...

Data from: Disparities in influenza mortality and transmission related to sociodemographic factors within Chicago in the pandemic of 1918

Kyra H. Grantz, Madhura S. Rane, Henrik Salje, Gregory E. Glass, Stephen E. Schachterle & Derek A. T. Cummings
Social factors have been shown to create differential burden of influenza across different geographic areas. We explored the relationship between potential aggregate-level social determinants and mortality during the 1918 influenza pandemic in Chicago using a historical dataset of 7,971 influenza and pneumonia deaths. Census tract-level social factors, including rates of illiteracy, homeownership, population, and unemployment, were assessed as predictors of pandemic mortality in Chicago. Poisson models fit with generalized estimating equations (GEEs) were used to...

Data from: Biodiversity-ecosystem functioning relationships in long-term time series and palaeoecological records: deep sea as a test bed

Moriaki Yasuhara, Hideyuki Doi, Chih-Lin Wei, Roberto Danovaro & Sarah E. Myhre
The link between biodiversity and ecosystem functioning (BEF) over long temporal scales is poorly understood. Here, we investigate biological monitoring and palaeoecological records on decadal, centennial and millennial time scales from a BEF framework, by using deep-sea, soft-sediment environments as a test bed. Results generally show positive BEF relationships, in agreement with BEF studies based on present-day spatial analyses and short-term manipulative experiments. However, the deep-sea BEF relationship is much noisier across longer time scales...

Data from: Quantifying thermal extremes and biological variation to predict evolutionary responses to changing climate

Joel G. Kingsolver & Lauren B. Buckley
Central ideas from thermal biology, including thermal performance curves and tolerances, have been widely used to evaluate how changes in environmental means and variances generate changes in fitness, selection and microevolution in response to climate change. We summarize the opportunities and challenges for extending this approach to understanding the consequences of extreme climatic events. Using statistical tools from extreme value theory, we show how distributions of thermal extremes vary with latitude, time scale and climate...

Data from: Long-term, high frequency in situ measurements of intertidal mussel bed temperatures using biomimetic sensors

Brian Helmuth, Francis Choi, Allison Matzelle, Jessica L. Torossian, Scott L. Morella, K. A. S. Mislan, Lauren Yamane, Denise Strickland, P. Lauren Szathmary, Sarah Gilman, Alyson Tockstein, Thomas J. Hilbish, Michael T. Burrows, Anne Marie Power, Elizabeth Gosling, Nova Mieszkowska, Christopher D. G. Harley, Michael Nishizaki, Emily Carrington, Bruce Menge, Laura Petes, Melissa M. Foley, Angela Johnson, Megan Poole, Mae M. Noble … & Gerardo Zardi
At a proximal level, the physiological impacts of global climate change on ectothermic organisms are manifest as changes in body temperatures. Especially for plants and animals exposed to direct solar radiation, body temperatures can be substantially different from air temperatures. We deployed biomimetic sensors that approximate the thermal characteristics of intertidal mussels at 71 sites worldwide, from 1998-present. Loggers recorded temperatures at 10–30 min intervals nearly continuously at multiple intertidal elevations. Comparisons against direct measurements...

Data from: Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping by sequencing data from natural populations

Garrett J. McKinney, Ryan K. Waples, Lisa W. Seeb & James E. Seeb
Whole genome duplications have occurred in the recent ancestors of many plants, fish, and amphibians, resulting in a pervasiveness of paralogous loci and the potential for both disomic and tetrasomic inheritance in the same genome. Paralogs can be difficult to reliably genotype and are often excluded from genotyping-by-sequencing (GBS) analyses; however, removal requires paralogs to be identified which is difficult without a reference genome. We present a method for identifying paralogs in natural populations by...

Data from: Global test of Eltonian niche conservatism of nonnative freshwater fish species between their native and introduced ranges

Lise Comte, Julien Cucherousset & Julian D. Olden
Despite growing evidence that biotic interactions limit the distribution of species and their potential redistribution under climate change, the recent surge of interest in niche conservatism has predominantly focused on the Grinellian (abiotic) niche, whereas few studies have attempted to quantify potential lability in the Eltonian (biotic or trophic) niche. Here, we test for conservatism in the Eltonian niche of 32 freshwater fish species between their introduced and native ranges from 435 populations across the...

Registration Year

  • 2016

Resource Types

  • Dataset


  • University of Washington
  • Stanford University
  • Duke University
  • Oregon State University
  • Occidental College
  • University of California, Santa Barbara
  • University of Oxford
  • Northwest Fisheries Science Center
  • University of North Carolina
  • Australian National University