405 Works

Data from: Earth history and the passerine superradiation

Carl H. Oliveros, Daniel J. Field, Daniel T. Ksepka, F. Keith Barker, Alexandre Aleixo, Michael J. Andersen, Per Alström, Brett W. Benz, Edward L. Braun, Michael J. Braun, Gustavo A. Bravo, Robb T. Brumfield, R. Terry Chesser, Santiago Claramunt, Joel Cracraft, Andrés M. Cuervo, Elizabeth P. Derryberry, Travis C. Glenn, Michael G. Harvey, Peter A. Hosner, Leo Joseph, Rebecca T. Kimball, Andrew L. Mack, Colin M. Miskelly, A. Townsend Peterson … & Brant C. Faircloth
Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships...

Implications for evolutionary trends from the pairing frequencies among golden-winged and blue-winged warblers and their hybrids

John Confer, Cody Porter, Kyle Aldinger, Ronald Canterbury, Jeffery Larkin & Darin McNeil
Extensive range loss for the Golden-winged Warbler (Vermivora chrysoptera) has occurred in areas of intrusion by the Blue-winged Warbler (V. cyanoptera) potentially related to their close genetic relationship. We compiled data on social pairing from nine studies for 2,679 resident Vermivora to assess evolutionary divergence. Hybridization between pure phenotypes occurred with 1.2% of resident males for sympatric populations. Pairing success rates for Golden-winged Warblers was 83% and for Blue-winged Warblers was 77%. Pairing success for...

Does evolutionary relatedness predict ecological similarity?

Judith Sclafani, Curtis Congreve & Mark Patzkowsky
A fundamental question in paleobiology is whether ecology is correlated with evolutionary history. By combining time-calibrated phylogenetic trees with genus occurrence data through time, we can understand how environmental preferences are distributed on a tree and evaluate support for models of ecological similarity. Exploring parameters that lend support to each evolutionary model will help address questions that lie at the nexus of the evolutionary and ecological sciences. We calculated ecological difference and phylogenetic distance between...

Neurovascular coupling and bilateral connectivity during NREM and REM sleep

Patrick Drew, Kevin Turner, Kyle Gheres & Elizabeth Proctor
Hemodynamic signals in the brain are used as surrogates of neural activity, but how these hemodynamic signals depend on arousal state is poorly understood. Here, we monitored neural activity and hemodynamic signals in un-anesthetized, head-fixed mice to understand how sleep and awake states impact cerebral hemodynamics. In parallel with electrophysiological recordings, we used intrinsic optical signal imaging to measure bilateral changes in cerebral hemoglobin ([HbT]), and two-photon laser scanning microscopy (2PLSM) to measure dilations of...

Data from: Group density, disease, and season shape territory size and overlap of social carnivores

Ellen Brandell, Nicholas Fountain-Jones, Marie Gilbertson, Paul Cross, Peter Hudson, Douglas Smith, Daniel Stahler, Craig Packer & Meggan Craft
1. The spatial organization of a population can influence the spread of information, behaviour, and pathogens. Territory size and territory overlap, components of spatial organization, provide key information as these metrics may be indicators of habitat quality, resource dispersion, contact rates, and environmental risk (e.g., indirectly transmitted pathogens). Furthermore, sociality and behaviour can also shape space use, and subsequently, how space use and habitat quality together impact demography. 2. Our study aims to identify factors...

Supplemental data for article: DNA content variation and SNP diversity within a single population of asexual snails

Kara Million, Amrita Bhattacharya, Zoe Dinges, Sarah Montgomery, Eries Smith & Curtis Lively
A growing body of research suggests that many clonal populations maintain genetic diversity even without occasional sexual reproduction. The purpose of our study was to document variation in SNP diversity, DNA content, and pathogen susceptibility in clonal lineages of the New Zealand freshwater snail, Potamopyrgus antipodarum. We studied snails that were collected from multiple field sites around a single lake (Lake Alexandrina), as well as isofemale clonal lineages that had been isolated and maintained in...

nNOS-expressing interneurons control basal and behaviorally-evoked arterial dilation in somatosensory cortex of mice

Patrick Drew, Christina Echagarruga, Kyle Gheres & Jordan Norwood
Cortical neural activity is coupled to local arterial diameter and blood flow. However, which neurons control the dynamics of cerebral arteries is not well understood. We dissected the cellular mechanisms controlling the basal diameter and evoked dilation in cortical arteries in awake, head-fixed mice. Locomotion drove robust arterial dilation, increases in gamma band power in the local field potential (LFP), and increases calcium signals in pyramidal and neuronal nitric oxide synthase (nNOS)-expressing neurons. Chemogenetic or...

Bumble bees in landscapes with abundant floral resources have lower pathogen loads

Darin McNeil, Elyse McCormick, Ashley C. Heimann, Melanie Kammerer, Margaret R. Douglas, Sarah C. Goslee, Christina M. Grozinger & Heather M. Hines
AbstractThe pollination services provided by bees are essential for supporting natural and agricultural ecosystems. However, bee population declines have been documented across the world. Many of the factors known to undermine bee health (e.g., poor nutrition) can decrease immunocompetence and, thereby, increase bees’ susceptibility to diseases. Given the myriad of stressors that can exacerbate disease in wild bee populations, assessments of the relative impact of landscape habitat conditions on bee pathogen prevalence are needed to...

Cryptic diversity on cliffs: Aster sanqingensis, a new species of Asteraceae from Eastern China

Guojin Zhang, Jiahao Shen, Bohan Jiao, Guohao Niu, Fanghua Zhong, Guo Li & Tiangang Gao
It is generally believed that cliffs bear low biodiversity because of its harsh habitats. However, another reason, i.e. insufficient investigation caused by the inaccessibility of the cliffs, could not be excluded. In the genus Aster, two cliff species, Aster fanjingshanicus and Aster tianmenshanensis, respectively growing on the slate and limestone cliffs, were established. During our extensive field investigations, the third cliff species of Aster growing on granite cliffs from Eastern China was found. Based on...

Stone Valley Stem Mapped

E.K. Zenner & J.E. Peck
To permit forest structure analyses, two 2.25 ha permanent plots were established in mature (ca. 110 yr old) mixed stratified Eastern Hardwoods forest on the Stone Valley Experimental Forest in 2007. The species, diameter at breast height (DBH), and spatial position of all trees = 5 cm DBH were recorded.

Effects of the macroalga Asparagopsis taxiformis and oregano leaves on methane emission, rumen fermentation, and lactational performance of dairy cows

H.A. Stefenoni, S.E. Räisänen, S.F. Cueva, D.E. Wasson, C.F.A. Lage, A. Melgar, M.E. Fetter, P. Smith, M. Hennessy, B. Vecchiarelli, J. Bender, D. Pitta, C.L. Cantrell, C. Yarish & A.N. Hristov
Asparagopsis taxiformis (AT) is a source of multiple halogenated compounds and, in a limited number of studies, has been shown to decrease enteric CH4 production in vitro and in vivo. Similarly, oregano has also been suggested as a potential CH4 mitigating agent. This study consisted of 2 in vitro and 2 in vivo experiments. Experiment 1 (Exp. 1) was aimed at establishing the effect of AT on total gas production and CH4 emission in vitro....

Electrical Discharges Produce Prodigious Amounts of Hydroxyl and Hydroperoxyl Radicals

J.M. Jenkins & W.H. Brune
Reaction with the hydroxyl radical (OH) is often the first step in the removal of many atmospheric pollutants. The nitrogen oxides (NOx) generated by lightning can increase the amount of HOx (HOx = OH + HO2) present in the atmosphere, but direct HOx production from lightning has never been investigated in the laboratory. In this laboratory study, prodigious amounts of HOx were generated by both visible and subvisible electrical discharges over ranges of pressure and...

Wild bumble bee colony abundance, scaled by field size, predicts pollination services

Shelby Fleischer, James Strange, Margarita Lopez-Uribe & Carley McGrady
Although bee visitation rate to flowers is often used to assess both pollination services and bee abundance, the abundance of social species needs to be assessed by quantifying the number of colonies instead of the number of foraging individuals. Because accurately quantifying the number of wild bee colonies can be difficult, the relationship of visitation rates provided by foragers and the abundance of colonies contributing those foragers from the surrounding landscape is poorly documented for...

Habitat suitability modeling to predict the spatial distribution of cold-water coral communities affected by the Deepwater Horizon oil spill

Samuel Georgian, Kody Kramer, Miles Saunders, William Shedd, Harry Roberts, Christopher Lewis, Chuck Fisher & Erik Cordes
Aim: The Deepwater Horizon disaster resulted in the largest accidental marine oil spill in history and caused extensive injury to deep-sea habitats, including cold-water coral communities dominated by Paramuricea species. One of the primary difficulties in assessing the full extent of the injury to cold-water coral ecosystems is the extreme paucity of observational data and the subsequent lack of knowledge of their distribution within the affected region. The aim of this study was to use...

Lactational performance, rumen fermentation and enteric methane emission of dairy cows fed high-amylase corn silage.

S.F. Cueva, H.A. Stefenoni, A. Melgar, S.E. Räisänen, C.F.A. Lage, D.E. Wasson, M.E. Fetter & A.N. Hristov
The current study investigated the effect of a high-amylase corn silage on lactational performance, enteric methane (CH4) emission, and rumen fermentation of lactating dairy cows. Following a 2-wk covariate period, 48 Holstein cows were blocked based on parity, days-in-milk, milk yield (MY), and CH4 emission. Cows were randomly assigned to 1 of 2 treatments in an 8-wk randomized complete block design experiment: (1) control corn silage (CON) from an isogenic corn without a-amylase trait and...

Data from: Broad geographic sampling reveals predictable, pervasive, and strong seasonal adaptation in Drosophila

Heather E. Machado, Alan O. Bergland, Ryan Taylor, Susanne Tilk, Emily Behrman, Kelly Dyer, Daniel K. Fabian, Thomas Flatt, Josefa González, Talia L. Karasov, Iryna Kozeretska, Brian P. Lazzaro, Thomas JS Merritt, John E. Pool, Katherine O’Brien, Subhash Rajpurohit, Paula R. Roy, Stephen W. Schaeffer, Svitlana Serga, Paul Schmidt, Dmitri Petrov & Bernard Kim
To advance our understanding of adaptation to temporally varying selection pressures, we identified signatures of seasonal adaptation occurring in parallel among Drosophila melanogaster populations. Specifically, we estimated allele frequencies genome-wide from flies sampled early and late in the growing season from 20 widely dispersed populations. We identified parallel seasonal allele frequency shifts across North America and Europe, demonstrating that seasonal adaptation is a general phenomenon of temperate fly populations. Seasonally fluctuating polymorphisms are enriched at...

Subroutines to Calculate the Deposition Coefficients for Ice Crystal Vapor Growth.

J.Y. Harrington, G. Sokolowsky & H. Morrison
This code uses fitting coefficients to calculate supersaturation-dependent deposition coefficients for numerical models. The code takes as input the ambient supersaturation, temperature, and atmospheric pressure, along with the size of the crystal. If the crystal shape is unknown an equivalent volume sphere may be used. The subroutines calculate and return the deposition coefficients.

Shale Network database – A snapshot of the Entire Shale Network database as of March 2021

S.L. Brantley & T. Wen
This data set is a snapshot copy of the entire Shale Network database (https://doi.org/10.4211/his-data-shalenetwork) as of March 3rd, 2021. The Shale Network (http://www.shalenetwork.org/) is a project funded by the National Science Foundation to help scientists and other stakeholders store data for water resources that may be affected by gas exploitation in shale in the U.S.A. Our primary focus currently is the northeastern U.S.A. We want to enable the generation of knowledge from water chemistry and...

Data from: Crop pests and predators exhibit inconsistent responses to surrounding landscape composition

Daniel S. Karp, Rebecca Chaplin-Kramer, Timothy D. Meehan, Emily A. Martin, Fabrice DeClerck, Heather Grab, Claudio Gratton, Lauren Hunt, Ashley E. Larsen, Alejandra Martínez-Salinas, Megan E. O’Rourke, Adrien Rusch, Katja Poveda, Mattias Jonsson, Jay A. Rosenheim, Nancy A. Schellhorn, Teja Tscharntke, Stephen D. Wratten, Wei Zhang, Aaron L. Iverson, Lynn S. Adler, Matthias Albrecht, Audrey Alignier, Gina M. Angelella, Muhammad Zubair Anjum … & Yi Zou
The idea that noncrop habitat enhances pest control and represents a win–win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are...

Impacts of COVID-19 on the U.S. Restaurant Industry from the Global Perspective

Seoki Lee, Hyoungju Song, Michael S. Lin & Amit Sharma

Supplementary data, code, validation statistics, and other information for ‘Proxy-based reconstructions of hemispheric and global surface temperature variations over the past two millennia’ (PNAS, Mann et al. 2008)

M.E. Mann, Z. Zhang, M.K. Hughes, R.S. Bradley, S.K. Miller, S. Rutherford & F. Ni
Following the suggestions of a recent National Research Council report [NRC (National Research Council) (2006) Surface Temperature Reconstructions for the Last 2,000 Years (Natl Acad Press, Washington, DC).], we reconstruct surface temperature at hemispheric and global scale for much of the last 2,000 years using a greatly expanded set of proxy data for decadal-to-centennial climate changes, recently updated instrumental data, and complementary methods that have been thoroughly tested and validated with model simulation experiments. Our...

Supplementary data, code, and information for ‘Projected changes in persistent extreme summer weather events: The role of quasi-resonant amplification’ (Science Advances, Mann et al. 2018)

M.E. Mann, S.E. Räisänen, K. Kornhuber, B.A. Steinman, S.K. Miller, S. Petri & D. Coumou
Persistent episodes of extreme weather in the Northern Hemisphere summer have been associated with highamplitude quasi-stationary atmospheric Rossby waves, with zonal wave numbers 6 to 8 resulting from the phenomenon of quasi-resonant amplification (QRA). A fingerprint for the occurrence of QRA can be defined in terms of the zonally averaged surface temperature field. Examining state-of-the-art [Coupled Model Intercomparison Project Phase 5 (CMIP5)] climate model projections, we find that QRA events are likely to increase by...

Supplementary data, code, and information for ‘The likelihood of recent warmth’ (Nature Scientific Reports, Mann et al. 2016)

M.E. Mann, S. Rahmstorf, B.A. Steinman, M. Tingley & S.K. Miller
2014 was nominally the warmest year on record for both the globe and northern hemisphere based on historical records spanning the past one and a half centuries. It was the latest in a recent run of record temperatures spanning the past decade and a half. Press accounts reported odds as low as one-in-650 million that the observed run of global temperature records would be expected to occur in the absence of human-caused global warming. Press...

Supplementary data, code, and information for ‘On forced temperature changes, internal variability, and the AMO’ (Geophysical Research Letters, Mann et al. 2014)

M.E. Mann, B.A. Steinman & S.K. Miller
We estimate the low-frequency internal variability of Northern Hemisphere (NH) mean temperature using observed temperature variations, which include both forced and internal variability components, and several alternative model simulations of the (natural + anthropogenic) forced component alone. We then generate an ensemble of alternative historical temperature histories based on the statistics of the estimated internal variability. Using this ensemble, we show, first, that recent NH mean temperatures fall within the range of expected multidecadal variability....

Intersecting Identities: A Trioethnographic Exploration of How Disability Studies Informs Our Work as Artists, Educators, and Researchers

Alexandra Allen, Timothy Smith & Amanda Newman-Godfrey

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