89 Works

Data from: Environmental resource deficit may drive the evolution of intraspecific trait variation in invasive plant populations

Shuangshuang Liu, Jared Streich, Justin O. Borevitz, Kevin J. Rice, Tingting Li, Bo Li & Kent J. Bradford
Intraspecific trait variation within natural populations (i.e. intra‐population trait variation, IPTV) is the basic source for selection and can have significant ecological consequences. Higher IPTV may increase a population's niche breath and benefit interspecies competition under a resource‐limited environment, thus affecting the ability of a species to move into novel habitats. However, the reciprocal influences of variation in environmental conditions and phenotypic trait expression in spreading plant populations are not clearly defined. We propose that...

Data from: Phylogenetic patterns of trait and trait plasticity evolution: Insights from amphibian embryos

Rick Relyea, Patrick R. Stephens, Lisa N. Barrow, Andrew Blaustein, Paul Bradley, Julia Buck, Ann Chang, Brian I Crother, James Collins, Julia Earl, Stephanie S. Gervasi, Jason T. Hoverman, Olliver Hyman, Emily Claire Moriarty Lemmon, Thomas Luhring, Moses Michelsohn, Christopher M. Murray, Steven Price, Raymond Semlitsch, Andy Sih, Aaron Stoler, Nick VandenBroek, Alexa Warwick, Greta Wengert, John Hammond … & Aaron B. Stoler
Environmental variation favors the evolution of phenotypic plasticity. For many species, we understand the costs and benefits of different phenotypes, but we lack a broad understanding of how plastic traits evolve across large clades. Using identical experiments conducted across North America, we examined prey responses to predator cues. We quantified five life history traits and the magnitude of their plasticity for 23 amphibian species/populations (spanning three families and five genera) when exposed to no cues,...

Data from: Loss of murine Paneth cell function alters the immature intestinal microbiome and mimics changes seen in neonatal necrotizing enterocolitis

Shiloh R. Lueschow, Jessica Stumphy, Huiyu Gong, Stacy L. Kern, Timothy G. Elgin, Mark A. Underwood, Karen M. Kalanetra, David A. Mills, Melissa H. Wong, David K. Meyerholz, Misty Good & Steven J. McElroy
Necrotizing enterocolitis (NEC) remains the leading cause of gastrointestinal morbidity and mortality in premature infants. Human and animal studies suggest a role for Paneth cells in NEC pathogenesis. Paneth cells play critical roles in host-microbial interactions and epithelial homeostasis. The ramifications of eliminating Paneth cell function on the immature host-microbial axis remains incomplete. Paneth cell function was depleted in the immature murine intestine using chemical and genetic models, which resulted in intestinal injury consistent with...

Data from: Teratological and behavioral screening of the National Toxicology Program 91-compound library in zebrafish (Danio rerio)

Katharina Dach, Bianca Yaghoobi, Martin R. Schmuck, Dennis R. Carty, Kelly M. Morales & Pamela J. Lein
To screen the tens of thousands of chemicals for which no toxicity data currently exists, it is necessary to move from in vivo rodent models to alternative models, such as zebrafish. Here, we used dechorionated Tropical 5D wildtype zebrafish embryos to screen a 91-compound library provided by the National Toxicology Program (NTP) for developmental toxicity. This library contained 86 unique chemicals that included negative controls, flame retardants, polycyclic aromatic hydrocarbons (PAHs), drugs, industrial chemicals and...

Data from: Experiments reveal limited top-down control of key herbivores in southern California kelp forests

Robert P. Dunn & Kevin A. Hovel
Predator responses to gradients in prey density have important implications for population regulation and are a potential structuring force for subtidal marine communities, particularly on rocky reefs where herbivorous sea urchins can drive community state shifts. On rocky reefs in southern California where predatory sea otters have been extirpated, top-down control of sea urchins by alternative predators has been hypothesized but rarely tested experimentally. In laboratory feeding assays, predatory spiny lobsters (Panulirus interruptus) demonstrated a...

Data from: Adaptive radiation in labrid fishes: a central role for functional innovations during 65 My of relentless diversification

Edward D. Burress & Peter C. Wainwright
Early burst patterns of diversification have become closely linked with concepts of adaptive radiation, reflecting interest in the role of ecological opportunity in modulating diversification. But, this model has not been widely explored on coral reefs, where biodiversity is exceptional, but many lineages have high dispersal capabilities and a pan-tropical distribution. We analyze adaptive radiation in labrid fishes, arguably the most ecologically dominant and diverse radiation of fishes on coral reefs. We test for time-dependent...

Data from: Extremely fast feeding strikes are powered by elastic recoil in a seahorse relative, the snipefish, Macroramphosus scolopax

Sarah J. Longo, Tyler Goodearly & Peter C. Wainwright
Among over 30,000 species of ray-finned fishes, seahorses and pipefishes have a unique feeding mechanism whereby the elastic recoil of tendons allows them to rotate their long snouts extremely rapidly in order to capture small elusive prey. To understand the evolutionary origins of this feeding mechanism, its phylogenetic distribution among closely related lineages must be assessed. We present evidence for elastic recoil powered feeding in the snipefish (Macroramphosus scolopax) from kinematics, dynamics, and morphology. High-speed...

Data from: Impacts of urbanization on insect herbivory and plant defences in oak trees

Xoaquín Moreira, Luis Abdala-Roberts, Jorge Berny Mier C. Y Terán, Felisa Covelo, Raúl De La Mata, Marta Francisco, Bess Hardwick, Ricardo M. Pires, Tomas Roslin, Dmitry S. Schigel, Jan P.J.G. Ten Hoopen, Bart G.H. Timmermans, Laura J.A. Van Dijk, Bastien Castagneyrol, Ayco J.M. Tack, Jorge C. Berny Mier Y Teran, Laura J. A. Van Dijk & Ayco J. M. Tack
Systematic comparisons of species interactions in urban vs. rural environments can improve our understanding of shifts in ecological processes due to urbanization. However, such studies are relatively uncommon and the mechanisms driving urbanization effects on species interactions (e.g., between plants and insect herbivores) remain elusive. Here we investigated the effects of urbanization on leaf herbivory by insect chewers and miners associated with the English oak (Quercus robur) by sampling trees in rural and urban areas...

Data from: Paleotropical diversification dominates the evolution of the hyperdiverse ant tribe Crematogastrini (Hymenoptera: Formicidae)

Bonnie B. Blaimer, Philip S. Ward, Ted R. Schultz, Brian L. Fisher & Seán G. Brady
Levels of diversity vary strikingly among different phylogenetic lineages of ants. Rapid radiations in early ant evolution have often proven difficult to resolve with traditional Sanger-sequencing data sets of modest size. We provide a phylogenomic perspective on the evolution of the hyperdiverse ant tribe Crematogastrini by analyzing sequence data for nearly 1800 ultraconserved element (UCE) loci from 153 species comprising 56 genera. We reconstruct a next-to-complete genus-level phylogeny using concatenated maximum-likelihood and species-tree approaches, estimate...

Data from: The dynamics of open populations: integration of top–down, bottom–up and supply‐side influences on intertidal oysters

David L. Kimbro, James Wilson White & Edwin D. Grosholz
Most communities are structured not by a single process but by some combination of top–down, bottom–up and supply‐side (i.e. juvenile recruitment) factors. However, establishing how multiple processes interact remains a fundamental challenge. For example, the recruitment, growth, and mortality of estuarine species can vary along the steep and numerous environmental and biological gradients typical of these habitats, but the relative importance of those gradients is generally unknown. We took a novel approach to this question...

Data from: How size and conspicuousness affect the efficacy of flash coloration

Sangryong Bae, Doyeon Kim, Thomas N. Sherratt, Tim Caro & Changku Kang
Some prey are cryptic at rest but expose conspicuous colors when in motion. Previous findings suggest that these “flash displays” deceive would-be predators by providing false information about the color of prey, tricking them into continuing to look for prey with the conspicuous color when the prey have actually returned to their cryptic resting state. These results raise questions about the properties of flash coloration that make it effective. Here, using humans as visual foragers...

Data from: Optimizing carbon storage and biodiversity co-benefits in reforested riparian zones

Kristen E. Dybala, Kristin Steger, Robert G. Walsh, David R. Smart, Thomas Gardali & Nathaniel E. Seavy
1. Climate change and biodiversity loss are two global challenges that can be addressed simultaneously through reforestation of previously cleared land. However, carbon markets can encourage reforestations that focus on maximizing carbon storage, potentially at the expense of biodiversity conservation. 2. To identify opportunities to optimize reforestation design and management to meet both goals, we examined the forest stand features associated with carbon stocks in biomass and soil as well as bird abundance and diversity...

Data from: Pre-basic molt, feather quality and modulation of the adrenocortical response to stress in two populations of Rufous-collared sparrows, Zonotrichia capensis

Valentina Echeverria, Cristián F. Estades, Esteban Botero-Delgadillo, John C. Wingfield & Paulina L. Gonzalez-Gomez
Molt is an energetically expensive process in which birds may allocate 25% or more of their body protein mass to the production of new feathers. Stressful events can interfere with feather growth via the adrenal hormone corticosterone, which is released in response to environmental stress. Corticosterone release, in turn, regulates gluconeogenesis which could directly inhibit protein synthesis and deposition during molt when feathers are growing, which potentially could reduce feather quality dramatically. Thus, many species...

Data from: Complexity of possibly gapped histogram and analysis of histogram

Hsieh Fushing & Tania Roy
We demonstrate that gaps and distributional patterns embedded within real-valued measurements are inseparable biological and mechanistic information contents of the system. Such patterns are discovered through data-driven possibly gapped histogram, which further leads to the geometry-based analysis of histogram (ANOHT). Constructing a possibly gapped histogram is a complex problem of statistical mechanics due to the ensemble of candidate histograms being captured by a two-layer Ising model. This construction is also a distinctive problem of Information...

Data from: Predator-driven natural selection on risk-taking behavior in anole lizards

Oriol Lapiedra, Thomas W. Schoener, Manuel Leal, Jonathan B. Losos & Jason J. Kolbe
Biologists have long debated the role of behavior in evolution, yet understanding of its role as a driver of adaptation is hampered by the scarcity of experimental studies of natural selection on behavior in nature. After showing that individual Anolis sagrei lizards vary consistently in risk-taking behaviors, we experimentally established populations on eight small islands either with or without Leiocephalus carinatus, a major ground predator. We found that selection predictably favors different risk-taking behaviors under...

Data from: A conservation hatchery population of Delta Smelt shows evidence of genetic adaptation to captivity after 9 generations

Amanda Finger, Brian Mahardja, Kathleen M. Fisch, Alyssa Benjamin, Joan Lindberg, Luke Ellison, Tewdros Ghebremariam, Tien-Chieh Hung, Bernie May & Amanda J Finger
Genetic adaptation to captivity is a concern for threatened and endangered species held in conservation hatcheries. Here, we present evidence of genetic adaptation to captivity in a conservation hatchery for the endangered Delta Smelt (Fish Conservation and Culture Laboratory, University of California Davis; FCCL). The FCCL population is genetically managed with parentage analysis and the addition of wild fish each year. Molecular monitoring indicates little loss of genetic variation and low differentiation between the wild...

Water uptake, cloud condensation nuclei and surface tension: results from the MadFACTS campaign

Sara Forestieri, Sean Staudt, Thomas Kuborn, Christopher Ruehl, Timothy Bertram & Christopher Cappa
This data set is associated with the manuscript “Establishing the Impact of Model Surfactants on Cloud Condensation Nuclei Activity of Sea Spray Aerosols” by Forestieri et al. that has been submitted to Atmospheric Chemistry and Physics. The abstract to this manuscript is provided below. By reducing surface tension (σ), surfactants present in aerosols can increase their cloud condensation nuclei (CCN) activation efficiency. However, the importance of this effect is poorly constrained. Here we present estimates...

Data from: Prolific fruit output by the invader Bellucia pentamera (Melastomataceae) is enhanced by selective logging disturbance

Christopher Dillis, Andrew J. Marshall, Campbell O. Webb & Mark N. Grote
Selective logging in tropical rain forests may promote population growth of invasive plants. The ability of invaders to respond, specifically in reproductive traits, to increases in resource abundance may allow them to increase their presence in the seed rain of recipient communities. The invasive pioneer tree Bellucia pentamera (Melastomataceae) is currently spreading within Gunung Palung National Park in West Kalimantan, Indonesia. The park has also experienced periods of illegal, small-scale, selective logging that seem to...

Data from: Urbanization and anticoagulant poisons promote immune dysfunction in bobcats

Laurel E.K. Serieys, Amanda J. Lea, Marta Epeldegui, Tiffany C. Armenta, Joanne Moriarty, Sue Vandewoude, Scott Carver, Janet Foley, Robert K. Wayne, Seth P.D. Riley, Christel H. Uittenbogaart, Laurel E. K. Serieys & Seth P. D. Riley
Understanding how human activities influence immune response to environmental stressors can support biodiversity conservation across increasingly urbanizing landscapes. We studied a bobcat (Lynx rufus) population in urban southern California that experienced a rapid population decline from 2002–2005 due to notoedric mange. Because anticoagulant rodenticide (AR) exposure was an underlying complication in mange deaths, we aimed to understand sublethal contributions of urbanization and ARs on 65 biochemical markers of immune and organ function. Variance in immunological...

Data from: Moving in the Anthropocene: global reductions in terrestrial mammalian movements

Marlee A. Tucker, Katrin Böhning-Gaese, William F. Fagan, John M. Fryxell, Bram Van Moorter, Susan C. Alberts, Abdullahi H. Ali, Andrew M. Allen, Nina Attias, Tal Avgar, Hattie Bartlam-Brooks, Buuveibaatar Bayarbaatar, Jerrold L. Belant, Alessandra Bertassoni, Dean Beyer, Laura Bidner, Floris M. Van Beest, Stephen Blake, Niels Blaum, Chloe Bracis, Danielle Brown, P. J. Nico De Bruyn, Francesca Cagnacci, Justin M. Calabrese, Constança Camilo-Alves … & Thomas Mueller
Animal movement is fundamental for ecosystem functioning and species survival, yet the effects of the anthropogenic footprint on animal movements have not been estimated across species. Using a unique GPS-tracking database of 803 individuals across 57 species, we found that movements of mammals in areas with a comparatively high human footprint were on average one-half to one-third the extent of their movements in areas with a low human footprint. We attribute this reduction to behavioral...

Data from: The spectre of too many species

Adam D. Leache, Tianqi Zhu, Bruce Rannala & Ziheng Yang
Recent simulation studies examining the performance of Bayesian species delimitation as implemented in the BPP program have suggested that BPP may detect population splits but not species divergences and that it tends to over-split when data of many loci are analyzed. Here we confirm these results and provide the mathematical justifications. We point out that the distinction between population and species splits made in the protracted speciation model has no influence on the generation of...

Evolution of SSR diversity from wild types to U.S. advanced cultivars in the Andean and Mesoamerican domestications of common bean (Phaseolus vulgaris)

Paul Gepts
Progress in common bean breeding requires the exploitation of genetic variation among market classes, races and gene pools. The present study was conducted to determine the amount of genetic variation and the degree of relatedness among 192 selected common bean advanced cultivars using 58 simple-sequence-repeat markers (SSR) evenly distributed along the 11 linkage groups of the Phaseolus reference map. All the lines belonged to commercial seed type classes that are widely grown in the USA...

Data from: Verbalizing phylogenomic conflict: representation of node congruence across competing reconstructions of the neoavian explosion

Nico M. Franz, Lukas J. Musher, Joseph W. Brown, Yu Shizhuo & Bertram Ludäscher
Phylogenomic research is accelerating the publication of landmark studies that aim to resolve deep divergences of major organismal groups. Meanwhile, systems for identifying and integrating the products of phylogenomic inference–such as newly supported clade concepts–have not kept pace. However, the ability to verbalize node concept congruence and conflict across multiple, in effect simultaneously endorsed phylogenomic hypotheses, is a prerequisite for building synthetic data environments for biological systematics and other domains impacted by these conflicting inferences....

Data from: The telomere bouquet is a hub where meiotic double-strand breaks, synapsis, and stable homolog juxtaposition are coordinated in the zebrafish, Danio rerio

Yana P. Blokhina, An D. Nguyen, Bruce W. Draper & Sean M. Burgess
Meiosis is a cellular program that generates haploid gametes for sexual reproduction. While chromosome events that contribute to reducing ploidy (homologous chromosome pairing, synapsis, and recombination) are well conserved, their execution varies across species and even between sexes of the same species. The telomere bouquet is a conserved feature of meiosis that was first described nearly a century ago, yet its role is still debated. Here we took advantage of the prominent telomere bouquet in...

Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia

Cassandra Ettinger, Laetitia Wilkins, Guillaume Jospin & Jonathan Eisen
Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refined, corrected and revolutionized understanding of the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and...

Registration Year

  • 2018
    89

Resource Types

  • Dataset
    89

Affiliations

  • University of California, Davis
    89
  • Duke University
    4
  • University of Wyoming
    3
  • Michigan State University
    3
  • Max Planck Institute for Ornithology
    2
  • University of Washington
    2
  • University of Michigan-Ann Arbor
    2
  • University of California System
    2
  • Université Paul-Valéry Montpellier
    2
  • The Ohio State University
    2