70 Works

Data from: Differential patterns of floristic phylogenetic diversity across a post‐glacial landscape

Ida M. Mienna, James D.M. Speed, Mika Bendiksby, Andrew H. Thornhill, Brent D. Mishler & Michael D. Martin
Aim In this study, we explored spatial patterns of phylogenetic diversity (PD) and endemism in the flora of Norway and tested hypothesized post‐glacial environmental drivers of PD, including temperature, precipitation, edaphic factors and time since glacial retreat. Location Norway. Taxon Vascular plants (Trachaeophyta). Methods We produced a multi‐locus maximum‐likelihood (ML) phylogeny using a combination of newly produced DNA sequences from herbarium specimens and sequences available from public repositories. We combined the phylogeny with species occurrence...

Data from: Species richness, endemism, and abundance patterns: tests of two fractal models in a serpentine grassland

Jessica Green, John Harte & Annette Ostling
From Ecology Letters: Although scaling relationships that characterize fractal species distributions offer an exciting potential for unification in biogeography, empirical support for fractal theory remains the subject of debate. We synthesize and test multiple predictions of two interrelated fractal models and a null model of random placement using Californian serpentine grassland data describing the spatial location of over 37 000 individually identified plants. The endemics–area relationship and species‐abundance distribution recently derived from a community‐level fractal...

Kinesin and dynein use distinct mechanisms to bypass obstacles

Luke S Ferro, Ahmet Yildiz, Sinan Can, Meghan A Turner & Mohamed M ElShenawy
Kinesin-1 and cytoplasmic dynein are microtubule (MT) motors that transport intracellular cargos. It remains unclear how these motors move along MTs densely coated with obstacles of various sizes in the cytoplasm. Here, we tested the ability of single and multiple motors to bypass synthetic obstacles on MTs in vitro. Contrary to previous reports, we found that mammalian dynein is highly capable of bypassing obstacles. Human kinesin-1 motors fail to avoid obstacles, consistent with their inability...

The many population genetic and demographic routes to islands of genomic divergence

Claudio Quilodrán, Kristen Ruegg, Ashley Sendell-Price, Eric Anderson, Tim Coulson & Sonya Clegg
The way that organisms diverge into reproductively isolated species is a major question in biology. The recent accumulation of genomic data provides promising opportunities to understand the genomic landscape of divergence, which describes the distribution of differences across genomes. Genomic areas of unusually high differentiation have been called genomic islands of divergence. Their formation has been attributed to a variety of mechanisms, but a prominent hypothesis is that they result from divergent selection over a...

Data from: Genome-wide epigenetic isolation by environment in a widespread Anolis lizard

Ian Wang, Guinevere Wogan, Michael Yuan & D. Luke Mahler
Epigenetic changes can provide a pathway for organisms to respond to local environmental conditions by influencing gene expression. However, we still know little about the spatial distribution of epigenetic variation in natural systems, how it relates to the distribution of genetic variation and the environmental structure of the landscape, and the processes that generate and maintain it. Studies examining spatial patterns of genetic and epigenetic variation can provide valuable insights into how ecological and population...

Supplementary information for: Deterministic assembly of arrays of lithographically defined WS_2 and MoS_2 monolayer features directly from multilayer sources into van der Waals heterostructures

Hayden Taylor, Vu Nguyen, Hannah Gramling, Clarissa Towle, Wan Li, Der-Hsien Lien, Hyungjin Kim, Daryl Chrzan, Ali Javey, Ke Xu & Joel Ager
One of the major challenges in the van der Waals (vdW) integration of 2D materials is achieving high-yield and high-throughput assembly of pre-defined sequences of monolayers into heterostructure arrays. Mechanical exfoliation has recently been studied as a promising technique to transfer monolayers from a multilayer source synthesized by other techniques, allowing the deposition of a wide variety of 2D materials without exposing the target substrate to harsh synthesis conditions. Although a variety of processes have...

Direct mapping of curve-crossing dynamics in IBr by attosecond transient absorption spectroscopy

Yuki Kobayashi, Kristina Chang, Tao Zeng, Daniel Neumark & Stephen Leone
Herein is the experimental data set for the publication titled "Direct mapping of curve-crossing dynamics in IBr by attosecond transient absorption spectroscopy." The abstract of the paper is as follows: The electronic character of photoexcited molecules can abruptly change at avoided crossings and conical intersections. Here, we report direct mapping of the coupled interplay between electrons and nuclei in a prototype molecule, iodine monobromide (IBr), using attosecond transient absorption spectroscopy. A few-femtosecond visible pulse resonantly...

As the Wind Blows: The Effects of Long-Term Exposure to Air Pollution on Mortality

Replication files for "As the Wind Blows: The Effects of Long-Term Exposure to Air Pollution on Mortality", published in the Journal of the European Economic Association.

Contrasting impacts of a novel specialist vector on multi-host viral pathogen epidemiology in wild and managed bees

Robyn Manley, Ben Temperton, Mike Boots & Wilfert Lena
Typically pathogens infect multiple host species. Such multi-host pathogens can show considerable variation in their degree of infection and transmission specificity, which has important implications for potential disease emergence. Transmission of multi-host pathogens can be driven by key host species and changes in such transmission networks can lead to disease emergence. We study two viruses that show contrasting patterns of prevalence and specificity in managed honeybees and wild bumblebees, black queen cell virus (BQCV) and...

Data from: Introduced parasite changes host phenotype, mating signal and hybridisation risk: Philornis downsi effects on Darwin’s finch song

Sonia Kleindorfer, Georgina Custance, Katharina Peters & Frank J. Sulloway
Introduced parasites that alter their host’s mating signal can change the evolutionary trajectory of a species through sexual selection. Darwin’s Camarhynchus finches are threatened by the introduced fly Philornis downsi that is thought to have accidentally arrived on the Galapagos Islands during the 1960s. The P. downsi larvae feed on the blood and tissue of developing finches causing on average ~55 % in-nest mortality and enlarged naris size in survivors. Here we test if enlarged...

Data from: Megaphylogeny resolves global patterns of mushroom evolution

Torda Varga, Krisztina Krizsán, Csenge Földi, Bálint Dima, Marisol Sánchez-García, Santiago Sánchez-Ramírez, Gergely J. Szöllősi, János G. Szarkándi, Viktor Papp, László Albert, William Andreopoulos, Claudio Angelini, Vladimír Antonín, Kerrie W. Barry, Neale L. Bougher, Peter Buchanan, Bart Buyck, Viktória Bense, Pam Catcheside, Mansi Chovatia, Jerry Cooper, Wolfgang Dämon, Dennis Desjardin, Péter Finy, József Geml … & László G. Nagy
Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfill diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree...

Data from: Harvest selection on multiple traits in the wild revealed by aquatic animal telemetry

Even Moland, Stephanie M. Carlson, David Villegas-Rios, Jørgen Ree Wiig & Esben Moland Olsen
Harvesting can have profound impacts on the ecology and evolution of marine populations. However, little is known about the strength and direction of fisheries-induced selection acting on multiple traits in the wild. Here, we used acoustic telemetry to directly monitor individual behavior and fate in an intensively harvested species, the European lobster (Homarus gammarus, n = 100), in southern Norway. Overall, 24% of the tracked lobsters survived the two-month harvest season within the study area....

Videos of Gold Nanorods Etching in Graphene Liquid Cell Transmission Electron Microscopy- 28 mM FeCl3

Matthew Hauwiller, Justin Ondry & A. Paul Alivisatos
Premade gold nanorods were etched in a graphene liquid cell and imaged using Transmission Electron Microscopy (TEM). An aqueous solution of gold nanorods, Tris Buffer-HCl, and FeCl3 was encapsulated between graphene sheets. The final concentration of FeCl3 was 28mM. Through a combination of the electron beam-generated radiolysis products and the FeCl3, the nanorods underwent non-equilibrium etching. See associated papers for more details.

Videos of Gold Nanorods Etching in Graphene Liquid Cell Transmission Electron Microscopy- 34 mM FeCl3

Matthew Hauwiller, Justin Ondry & A. Paul Alivisatos
Premade gold nanorods were etched in a graphene liquid cell and imaged using Transmission Electron Microscopy (TEM). An aqueous solution of gold nanorods, Tris Buffer-HCl, and FeCl3 was encapsulated between graphene sheets. The final concentration of FeCl3 was 34 mM. Through a combination of the electron beam-generated radiolysis products and the FeCl3, the nanorods underwent non-equilibrium etching. See associated papers for more details.

Data from: The effects of microhabitat specialization on mating communication in a wolf spider

Malcolm F. Rosenthal, Eileen A. Hebets, Benji Kessler, Rowan McGinley & Damian O. Elias
Animal signals experience selection for detectability, which is determined in large part by the signal transmission properties of the habitat. Understanding the ecological context in which communication takes place is therefore critical to understanding selection on the form of communication signals. In order to determine the influence of environmental heterogeneity on signal transmission, we focus on a wolf spider species native to central Florida, Schizocosa floridana, in which males court females using a substrate-borne vibratory...

Data from: Comparative landscape genetics reveals the evolution of viviparity reduces genetic connectivity in fire salamanders

André Lourenço, João Gonçalves, Filipe Carvalho, Ian J Wang & Guillermo Velo Antón
Evolutionary changes in reproductive mode may affect co-evolving traits, such as dispersal, though this subject remains largely underexplored. The shift from aquatic oviparous or larviparous reproduction to terrestrial viviparous reproduction in some amphibians entails skipping the aquatic larval stage and, thus, greater independence from water. Accordingly, amphibians exhibiting terrestrial viviparous reproduction may potentially disperse across a wider variety of sub-optimal habitats and increase population connectivity in fragmented landscapes compared to aquatic-breeding species. We investigated this...

Videos of Gold Nanorods Etching in Graphene Liquid Cell Transmission Electron Microscopy- 42 mM FeCl3

Matthew Hauwiller, Justin Ondry & A. Paul Alivisatos
Premade gold nanorods were etched in a graphene liquid cell and imaged using Transmission Electron Microscopy (TEM). An aqueous solution of gold nanorods, Tris Buffer-HCl, and FeCl3 was encapsulated between graphene sheets. The final concentration of FeCl3 was 42 mM. Through a combination of the electron beam-generated radiolysis products and the FeCl3, the nanorods underwent non-equilibrium etching. See associated papers for more details.

ArXiV Archive

R.Stuart Geiger
This is a full archive of metadata about papers on arxiv.org from 1993-2018, including abstracts. Data is tidy and packed in TSV files, in two different collections of the total dataset: per year (all categories) and per primary category (all years). This archive also includes Jupyter notebooks for unpacking and analyzing it in python. See the README.md file and https://github.com/staeiou/arxiv_archive for more information.

Synthetic Log-Conductivity

Bradley Harken
This dataset contains the baseline fields for the case study described in the manuscript Hydrogeological Modeling and Water Resources Management: Improving the Link between Data, Prediction, and Decision-Making (Water Resources Research, under review). The data are described in the files readme.txt and example_code.R.

Temporal Inflection Points in Decorated Pottery: a Bayesian Refinement of the Late Formative Chronology in the Southern Lake Titicaca Basin, Bolivia

Christine Hastorf, Erik Marsh, Andrew Roddick, Maria Bruno, Scott Smith & John Janusek
The Late Formative Period immediately precedes the emergence of Tiwanaku, one of the earliest South American states, yet is one of the most poorly understood periods in the southern Lake Titicaca Basin (Bolivia). In this paper, we refine this period’s ceramic chronology with large sets of dates from eight sites, focusing on temporal inflection points in decorated ceramic styles. These points, estimated here by Bayesian models, index specific moments of change: (1) cal AD 140...

Data from: The environmental determinants of total evaporative water loss in birds at multiple temperatures

Soorim Song & Steven Beissinger
Endotherms dissipate heat to the environment to maintain a stable body temperature at high ambient temperatures, which requires them to maintain a balance between heat dissipation and water conservation. Birds are relatively small, contain a large amount of metabolically expensive tissue, and are mostly diurnal, making them susceptible to physiological challenges related to water balance and heat dissipation. We compiled total evaporative water loss (TEWL) measurements for 172 species of birds exposed to different temperatures...

Multiple sequence alignment for the native Norwegian vascular plant phylogeny

Ida M. Mienna, James D.M. Speed, Mika Bendiksby, Andrew H. Thornhill, Brent D. Mishler & Michael D. Martin
Methods: We produced a multi-locus Maximum Likelihood (ML) phylogeny using a combination of newly produced DNA sequences from herbarium specimens and sequences available from public repositories. We combined the phylogeny with species occurrence data to estimate phylogenetic diversity and phylogenetic endemism across Norway, using a spatial randomization to judge statistical significance. We used multiple-model inference to identify environmental variables that contributed the most to the patterns of phylogenetic diversity. Finally, we estimated phylogenetic turnover and...

Data from: A small yet occasional meal: predatory drill holes in Paleocene ostracods from Argentina and methods to infer predation intensity

Jorge Villegas-Martín, Daiane Ceolin, Gerson Fauth & Adiël Klompmaker
Ostracods are common yet understudied prey in the fossil record. We document drill holes in Paleocene (Danian) ostracods from central Argentina using 9025 specimens representing 66 species. While the assemblage-level drilling percentage is only 2.3%, considerable variation exists within species (0.3–25%), suggesting prey preference by the drillers. This preference is not determined by abundance because no significant correlation is found between species abundance and drilling percentages. Seven methods were used, some of which are new,...

Data from: Do genomics and sex predict migration in a partially migratory salmonid fish, Oncorhynchus mykiss?

Suzanne J. Kelson, Michael R. Miller, Tasha Q. Thompson, Sean M. O'Rourke & Stephanie M. Carlson
Partial migration is a common phenomenon wherein populations include migratory and resident individuals. Whether an individual migrates or not has important ecological and management implications, particularly within protected populations. Within partially migratory populations of O. mykiss, migration is highly correlated with a specific genomic region, but it is unclear how well this region predicts migration at the individual level. Here, we relate sex and life history genotype, determined using >400 SNPs on the migratory-linked genomic...

Data from: Global patterns in fine root decomposition: climate, chemistry, mycorrhizal association, and woodiness

Craig R. See, Michael Luke McCormack, Sarah E. Hobbie, Habacuc Flores-Moreno, Whendee L. Silver & Peter G. Kennedy
Fine root decomposition constitutes a critical yet poorly understood flux of carbon and nutrients in terrestrial ecosystems. Here, we present the first large‐scale synthesis of species trait effects on the early stages of fine root decomposition at both global and local scales. Based on decomposition rates for 279 plant species across 105 studies and 176 sites, we found that mycorrhizal association and woodiness are the best categorical traits for predicting rates of fine root decomposition....

Registration Year

  • 2019
    70

Resource Types

  • Dataset
    70

Affiliations

  • University of California, Berkeley
    70
  • University of Minnesota
    2
  • United States Department of Agriculture
    2
  • Lawrence Berkeley National Laboratory
    2
  • University of Toronto
    2
  • Technical University of Madrid
    2
  • University of Exeter
    2
  • Worcester Polytechnic Institute
    2
  • University of California, Davis
    2
  • Norwegian University of Science and Technology
    2