30 Works

Data from: \"De novo assembly transcriptome for the rostrum dace (Leuciscus burdigalensis, Cyprinidae: fish) naturally infected by a copepod ectoparasite\" in Genomic Resources Notes accepted 1 December 2014 to 31 January 2015

Olivier Rey, Géraldine Loot, Olivier Bouchez, Simon Blanchet, Maria Jose Ruiz-Lopez, Nelson Ting, Paul D. Etter, Eric A. Johnson, Tony L. Goldberg, Colin A. Chapman, James H. Jones, Patrick A. Omeja & William M. Switzer
The emergence of pathogens represents substantial threats to public health, livestock, domesticated animals, and biodiversity. How wild populations respond to emerging pathogens has generated a lot of interest in the last two decades. With the recent advent of high-throughput sequencing technologies it is now possible to develop large transcriptomic resources for non-model organisms, hence allowing new research avenues on the immune responses of hosts from a large taxonomic spectra. We here focused on a wild...

Data from: Large wildlife removal drives immune defense increases in rodents

Hillary S. Young, Rodolfo Dirzo, Kristofer M. Helgen, Douglas J. McCauley, Charles L. Nunn, Paul Snyder, Kari E. Veblen, Serena Zhao & Vanessa O. Ezenwa
Anthropogenic disturbances involving land use change, climate disruption, pollution, and invasive species have been shown to impact immune function of wild animals. These immune changes have direct impacts on the fitness of impacted animals and, also, potentially indirect effects on other species and on ecological processes, notably involving the spread of infectious disease. Here, we investigate whether the selective loss of large wildlife can also drive changes in immune function of other consumer species. Using...

Data from: Genomic variation in recently collected maize landraces from Mexico

María Clara Arteaga, Alejandra Moreno-Letelier, Alicia Mastretta-Yanes, Alejandra Vázquez-Lobo, Alejandra Breña-Ochoa, Andrés Moreno-Estrada, Luis E. Eguiarte & Daniel Piñero
The present dataset comprises 36,931 SNPs genotyped in 46 maize landraces native to Mexico as well as the teosinte subspecies Zea maiz ssp. Parviglumis and ssp. Mexicana. These landraces were collected directly from farmers mostly between 2006 and 2010. We accompany these data with a short description of the variation within each landrace, as well as maps, principal component analyses and neighbor joining trees showing the distribution of the genetic diversity relative to landrace, geographical...

Data from: Characterizing driver-response relationships in marine pelagic ecosystems for improved ocean management

Mary E. Hunsicker, Carrie V. Kappel, Kimberly A. Selkoe, Benjamin S. Halpern, Courtney Scarborough, Lindley Mease & Alisan Amrhein
Scientists and resources managers often use methods and tools that assume ecosystem components respond linearly to environmental drivers and human stressor. However, a growing body of literature demonstrates that many relationships are non-linear, where small changes in a driver prompt a disproportionately large ecological response. Here we aim to provide a comprehensive assessment of the relationships between drivers and ecosystem components to identify where and when non-linearities are likely to occur. We focus our analyses...

Data from: Genomic sequencing reveals historical, demographic and selective factors associated with the diversification of the fire-associated fungus Neurospora discreta

Pierre Gladieux, Benjamin A. Wilson, Fanny Perraudeau, Liliam A. Montoya, David Kowbel, Christopher Hann-Soden, Monika Fischer, Iman Sylvain, David J. Jacobson & John W. Taylor
Delineating microbial populations, discovering ecologically relevant phenotypes and identifying migrants, hybrids or admixed individuals have long proved notoriously difficult, thereby limiting our understanding of the evolutionary forces at play during the diversification of microbial species. However, recent advances in sequencing and computational methods have enabled an unbiased approach whereby incipient species and the genetic correlates of speciation can be identified by examining patterns of genomic variation within and between lineages. We present here a population...

Data from: Effects of increased flight on the energetics and life history of the butterfly Speyeria mormonia

Kristjan Niitepõld & Carol L. Boggs
Movement uses resources that may otherwise be allocated to somatic maintenance or reproduction. How does increased energy expenditure affect resource allocation? Using the butterfly Speyeria mormonia, we tested whether experimentally increased flight affects fecundity, lifespan or flight capacity. We measured body mass (storage), resting metabolic rate and lifespan (repair and maintenance), flight metabolic rate (flight capacity), egg number and composition (reproduction), and food intake across the adult lifespan. The flight treatment did not affect body...

Data from: The role of transcriptome resilience in resistance of corals to bleaching

Francois O. Seneca & Stephen R. Palumbi
Wild populations increasingly experience extreme conditions as climate change amplifies environmental variability. How individuals respond to environmental extremes determines the impact of climate change overall. The variability of response from individual to individual can represent the opportunity for natural selection to occur as a result of extreme conditions. Here, we experimentally replicated the natural exposure to extreme temperatures of the reef lagoon at Ofu Island (American Samoa), where corals can experience severe heat stress during...

Data from: \"Identification of SNP markers for the endangered Ugandan red colobus (Procolobus rufomitratus tephrosceles) using RAD sequencing\" in Genomic Resources Notes accepted 1 December 2014 to 31 January 2015

Maria Jose Ruiz Lopez, Tony L. Goldberg, Colin A. Chapman, Patrick A. Omeja, James H. Jones, William M. Switzer, Paul D. Etter, Eric A. Johnson & Nelson Ting
Despite dramatic growth in the field of primate genomics over the past decade, studies of primate population and conservation genomics in the wild have been hampered due to the difficulties inherent in studying non-model organisms and endangered species, such as lack of a reference genome and current challenges in de novo primate genome assembly. Here, we used Restriction-site Associated DNA (RAD) sequencing to develop a population-based SNP panel for the Ugandan red colobus (P. rufomitratus...

Data from: Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

Jesse A. Port, James L. O'Donnell, Ofelia C. Romero-Maraccini, Paul R. Leary, Steven Y. Litvin, Kerry J. Nickols, Kevan M. Yamahara & Ryan P. Kelly
Preserving biodiversity is a global challenge requiring data on species’ distribution and abundance over large geographic and temporal scales. However, traditional methods to survey mobile species’ distribution and abundance in marine environments are often inefficient, environmentally destructive, or resource-intensive. Metabarcoding of environmental DNA (eDNA) offers a new means to assess biodiversity and on much larger scales, but adoption of this approach for surveying whole animal communities in large, dynamic aquatic systems has been slowed by...

Data from: Isolation by resistance across a complex coral reef seascape

Luke Thomas, W. Jason Kennington, Michael Stat, Shaun P. Wilkinson, Jonathan T. Kool & Gary A. Kendrick
A detailed understanding of the genetic structure of populations and an accurate interpretation of processes driving contemporary patterns of gene flow are fundamental to successful spatial conservation management. The field of seascape genetics seeks to incorporate environmental variables and processes into analyses of population genetic data to improve our understanding of forces driving genetic divergence in the marine environment. Information about barriers to gene flow (such as ocean currents) is used to define a resistance...

Data from: In an age of open access to research policies: physician and public health NGO staff research use and policy awareness

Laura L. Moorhead, Cheryl Holzmeyer, Lauren A. Maggio, Ryan M. Steinberg, John M. Willinsky & John Willinsky
Introduction: Through funding agency and publisher policies, an increasing proportion of the health sciences literature is being made open access. Such an increase in access raises questions about the awareness and potential utilization of this literature by those working in health fields. Methods: A sample of physicians (N=336) and public health non-governmental organization (NGO) staff (N=92) were provided with relatively complete access to the research literature indexed in PubMed, as well as access to the...

Data from: Ecosystem response to interventions: lessons from restored and created wetland ecosystems

David Moreno-Mateos, Paula Meli, María Isabel Vara-Rodriguez & James Aronson
1. Current efforts to restore and create ecosystems require greater understanding of ecosystems’ responses to commonly used physical and biological intervention approaches to overcome ecological and technological limitations. 2. We estimated effect sizes from measurements of biotic assemblage structure and biogeochemical functions at 628 restored and created wetlands globally, in comparison with 499 reference wetlands. We studied the recovery trajectories of wetlands where different restoration or creation approaches were used under different environmental settings. 3....

Data from: Pervasive and strong effects of plants on soil chemistry: a meta-analysis of individual plant ‘Zinke’ effects

Bonnie G. Waring, Leonor Álvarez-Cansino, Kathryn E. Barry, Kristen K. Becklund, Sarah Dale, Maria G. Gei, Adrienne B. Keller, Omar R. Lopez, Lars Markesteijn, Scott Mangan, Charlotte E. Riggs, Maria Elizabeth Rodríguez-Ronderos, R. Max Segnitz, Stefan A. Schnitzer & Jennifer S. Powers
Plant species leave a chemical signature in the soils below them, generating fine-scale spatial variation that drives ecological processes. Since the publication of a seminal paper on plant-mediated soil heterogeneity by Paul Zinke in 1962, a robust literature has developed examining effects of individual plants on their local environments (individual plant effects). Here, we synthesize this work using meta-analysis to show that plant effects are strong and pervasive across ecosystems on six continents. Overall, soil...

Data from: Post-dispersal seed recovery by animals: is it a plant- or an animal-driven process?

Ramón Perea, Rodolfo Dirzo, Alfonso San Miguel & Luis Gil
The ability of animals to find and consume hoarded seeds (i.e. seed recovery) is a key stage within the seed dispersal process. However, the ecology of seed recovery is still poorly understood. Here, we analyze the factors controlling seed recovery by scatter-hoarding rodents in an oak-dominated temperate forest. We examined the relative importance of intrinsic seed traits (i.e. plant-driven) and extrinsic seed factors (i.e. animal-driven) on the probability of seed recovery. We found that seed...

Data from: Transcriptome dynamics of the stomatal lineage: birth, amplification, and termination of a self-renewing population

Jessika Adrian, Jessica Chang, Catherine E. Ballenger, Bastiaan O. R. Bargmann, Julien Alassimone, Kelli A. Davies, On Sun Lau, Juliana L. Matos, Charles Hachez, Amy Lanctot, Anne Vatén, Kenneth D. Birnbaum & Dominique C. Bergmann
Developmental transitions can be described in terms of morphology and the roles of individual genes, but also in terms of global transcriptional and epigenetic changes. Temporal dissections of transcriptome changes, however, are rare for intact, developing tissues. We used RNA sequencing and microarray platforms to quantify gene expression from labeled cells isolated by fluorescence-activated cell sorting to generate cell-type-specific transcriptomes during development of an adult stem-cell lineage in the Arabidopsis leaf. We show that regulatory...

Data from: Forage species in predator diets: synthesis of data from the California Current

Amber I. Szoboszlai, Julie A. Thayer, Spencer A. Wood, William J. Sydeman & Laura E. Koehn
Characterization of the diets of upper-trophic pelagic predators that consume forage species is a key ingredient in the development of ecosystem-based fishery management plans, conservation of marine predators, and ecological and economic modeling of trophic interactions. Here we present the California Current Predator Diet Database (CCPDD) for the California Current region of the Pacific Ocean over the past century, assimilating over 190 published records of predator food habits for over 100 predator species and 32...

Data from: Comparative population genomics of latitudinal variation in D. simulans and D. melanogaster

Heather E. Machado, Alan O. Bergland, Emily L. Behrman, Katherine R. O'Brien, Paul S. Schmidt & Dmitri A. Petrov
Examples of clinal variation in phenotypes and genotypes across latitudinal transects have served as important models for understanding how spatially varying selection and demographic forces shape variation within species. Here we examine the selective and demographic contributions to latitudinal variation through the largest comparative genomic study to date of Drosophila simulans and D. melanogaster, with genomic sequence data from 382 individual fruit flies, collected across a spatial transect of 19 degrees latitude and at multiple...

Data from: Fungal specificity and selectivity for algae play a major role in determining lichen partnerships across diverse ecogeographic regions in the lichen-forming family Parmeliaceae

Steven D. Leavitt, Ekaphan Kraichak, Matthew P. Nelsen, Susanne Altermann, Pradeep K. Divakar, David Alors, Theodore L. Esslinger, Ana Crespo, H. Thorsten Lumbsch & Thorsten Lumbsch
Microbial symbionts are instrumental to the ecological and long-term evolutionary success of their hosts, and the central role of symbiotic interactions is increasingly recognized across the vast majority of life. Lichens provide an iconic group for investigating patterns in species interactions; however, relationships among lichen symbionts are often masked by uncertain species boundaries or an inability to reliably identify symbionts. The species-rich lichen-forming fungal family Parmeliaceae provides a diverse group for assessing patterns of interactions...

Data from: Adapting environmental management to uncertain but inevitable change

Sam C. Nicol, Richard A. Fuller, Takuya Iwamura, Iadine Chades & S. Nicol
Implementation of adaptation actions to protect biodiversity is limited by uncertainty about the future. One reason for this is the fear of making the wrong decisions caused by the myriad future scenarios presented to decision-makers. We propose an adaptive management (AM) method for optimally managing a population under uncertain and changing habitat conditions. Our approach incorporates multiple future scenarios and continually learns the best management strategy from observations, even as conditions change. We demonstrate the...

Data from: GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown roots systems

Ruben Rellán-Álvarez, Guillaume Lobet, Heike Lindner, Pierre-Luc Pradier, Jose Sebastian, Muh-Ching Yee, Yu Geng, Charlotte Trontin, Therese LaRue, Amanda Schrager-Lavelle, Cara H. Haney, Rita Nieu, Julin Maloof, John P. Vogel & José R. Dinneny
Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that...

Data from: Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster

Alan O. Bergland, Ray Tobler, Josefa Gonzalez, Paul Schmidt, Dimitri A. Petrov & Dmitri Petrov
Populations arrayed along broad latitudinal gradients often show patterns of clinal variation in phenotype and genotype. Such population differentiation can be generated and maintained by both historical demographic events and local adaptation. These evolutionary forces are not mutually exclusive and can in some cases produce nearly identical patterns of genetic differentiation among populations. Here, we investigate the evolutionary forces that generated and maintain clinal variation genome-wide among populations of Drosophila melanogaster sampled in North America...

Data from: Allogeneic HY antibodies detected 3 months after female-to-male HCT predict chronic GVHD and nonrelapse mortality in humans

Hideki Nakasone, Lu Tian, Bita Sahaf, Takakazu Kawase, Kelsi Schoenrock, Spenser Perloff, Christine E. Ryan, Jed Paul, Rakesh Popli, Fang Wu, Joanne M. Otani, John Coller, & David B. Miklos
Allogeneic antibodies against minor histocompatibility antigens encoded on the Y chromosome (HY-Abs) develop after hematopoietic cell transplant (HCT) of male recipients with female donors (F→M). However, the temporal association between HY-Ab development and chronic graft-versus-host disease (cGVHD) has yet to be elucidated. We studied 136 adult F→M HCT patients, with plasma prospectively collected through 3 years posttransplant, and measured immunoglobulin G against 6 H-Y antigens. Multiple HY-Abs were frequently detected beginning at 3 months posttransplant:...

Data from: Point process models for presence-only analysis

Ian W. Renner, Jane Elith, Adrian Baddeley, William Fithian, Trevor Hastie, Steven Phillips, Gordana Popovic & David I. Warton
1. Presence-only data are widely used for species distribution modelling, and point process regression models are a exible tool that has considerable potential for this problem, when data arise as point events. 2. In this paper we review point process models, some of their advantages, and some common methods of fitting them to presence-only data. 3. Advantages include (and are not limited to): clarification of what the response variable is that is modelled; a framework...

Data from: Genetic isolation between two recently diverged populations of a symbiotic fungus

Sara Branco, Pierre Gladieux, Christopher E. Ellison, Alan Kuo, Kurt LaButii, Anna Lipzen, Igor V. Grigoriev, Hui-Ling Liao, Rytas Vilgalys, Kabir G. Peay, John W. Taylor, Thomas D. Bruns & Kurt LaButti
Fungi are an omnipresent and highly diverse group of organisms, making up a significant part of eukaryotic diversity. Little is currently known about the drivers of fungal population differentiation and subsequent divergence of species, particularly in symbiotic, mycorrhizal fungi. Here, we investigate the population structure and environmental adaptation in Suillus brevipes (Peck) Kuntze, a wind-dispersed soil fungus that is symbiotic with pine trees. We assembled and annotated the reference genome for Su. brevipes and resequenced...

Data from: Tradeoffs between three forest ecosystem services across the state of New Hampshire, USA: timber, carbon, and albedo

David A. Lutz, Elizabeth A. Burakowski, Mackenzie B. Murphy, Mark E. Borsuk, Rebecca M. Niemiec & Richard B. Howarth
Forests are more frequently being managed to store and sequester carbon for the purposes of climate change mitigation. Generally, this practice involves long-term conservation of intact mature forests and/or reductions in the frequency and intensity of timber harvests. However, incorporating the influence of forest surface albedo often suggests that long rotation lengths may not always be optimal in mitigating climate change in forests characterized by frequent snowfall. To address this, we investigated tradeoffs between three...

Registration Year

  • 2015
    30

Resource Types

  • Dataset
    30

Affiliations

  • Stanford University
    30
  • McGill University
    4
  • University of Washington
    3
  • French National Centre for Scientific Research
    3
  • Curtin University
    3
  • Fred Hutchinson Cancer Research Center
    2
  • University of Pennsylvania
    2
  • Field Museum of Natural History
    2
  • Duke University
    2
  • Stanford University School of Medicine
    2