146 Works

Opposing dominance within a color gene block is associated with maladaptive hybrid signal discordance

Silu Wang
Color divergence is increasingly recognized as important for speciation in songbirds through its influence on social dynamics. However, the behavioral mechanisms underlying the eco-evolutionary feedback that acts across species boundaries is poorly understood. The hybrid zone between Setophaga occidentalis (SOCC) and S. townsendi (STOW) in the Cascade mountain ranges provides a natural observatory to test the interplay between genetics and social behaviour in maintaining species boundaries. Recently, we found that selection within a gene block...

Perceptual restoration fails to recover unconscious processing for smooth eye movements after occipital stroke

Sunwoo Kwon, Jude Mitchell & Krystel Huxlin
Visual pathways that guide actions do not necessarily mediate conscious perception. Patients with primary visual cortex (V1) damage lose conscious perception but often retain unconscious abilities (e.g. blindsight). Here, we asked if saccade accuracy and post-saccadic following responses (PFRs) that automatically track target motion upon saccade landing are retained when conscious perception is lost. We contrasted these behaviors in the blind and intact fields of 8 chronic V1-stroke patients, and in 8 visually-intact controls. Saccade...

PSP FIELDS Fluxgate Magnetometer (MAG) Magnetic Field Vectors, Spacecraft, SC, Coordinates, 4 samples/cycle, Level 2 (L2), 3.413 ms Data

Stuart D. Bale, Robert J. MacDowall, Andriy Koval, Marc Pulupa, Timothy Quinn & Peter Schroeder
Parker Solar Probe FIELDS Instrument Suite Fluxgate Magnetometer, MAG, Data: The time resolution of the MAG time series data varies with instrument mode ranging from 2.289 samples/s to 292.9 samples/s. These two data sampling rates corresponding to 2 samples or 256 samples per 0.874 s where 0.874 s is equal to 2^25 divided 38.4 MHz. The Magnetometer has four ranges: ±1024 nT, ±4096 nT, ±16,384 nT, and ±65,536 nT. The Magnetometer Range is selected by...

Parker Solar Probe, FIELDS Radio Frequency Spectrometer, RFS, Low Frequency Receiver, LFR, Spectra, Level 2 (L2), 7 s and 56 s Data

Stuart D. Bale, Marc Pulupa, Peter R. Harvey, Timothy Quinn & Peter Schroeder
PSP FIELDS Radio Frequency Spectrometer, RFS, Low Frequency Receiver, LFR, Data: The RFS is the high frequency component of the FIELDS experiment on the Parker Solar Probe spacecraft. The RFS produces auto and cross spectral data products in two frequency ranges, the Low Frequency Reciever range and the High Frequency Receiver range. Telemetered spectral data products for both HFR and LFR contain 64 frequency bins, with the LFR typically covering a frequency range from 10.5...

PSP FIELDS Digital Fields Board (DFB) AC-coupled Searchcoil Magnetometer, SCM, Spectra, Low Frequency, High Gain, e-component, Sensor coordinates, Level 2 (L2), 0.873813 s Data

Stuart D. Bale, Thierry Dudok de Wit, David M. Malaspina, Katherine A. Goodrich, Marc Pulupa, Timothy Quinn & Peter Schroeder
PSP FIELDS Digital Fields Board, DFB, SCMdlfhg data: The DFB is the low frequency, less than 75 kHz, component of the FIELDS experiment on the Parker Solar Probe spacecraft. For a full description of the FIELDS experiment. DFB AC spectra data consist of power spectral densities as a function of frequency and time. These spectra are averaged over both frequency and time. The Level 2 data products contained in this data file have been calibrated...

PSP FIELDS Digital Fields Board (DFB) AC-coupled V5 Antenna Voltage, Monopole Mode, Auto Spectra, High Gain, Sensor coordinates, Level 2 (L2), 0.873813 s Data

Stuart D. Bale, David M. Malaspina, Katherine A. Goodrich, Marc Pulupa, Timothy Quinn & Peter Schroeder
PSP FIELDS Digital Fields Board, DFB, V5 data: The DFB is the low frequency, less than 75 kHz, component of the FIELDS experiment on the Parker Solar Probe spacecraft. For a full description of the FIELDS experiment. DFB AC spectra data consist of power spectral densities as a function of frequency and time. These spectra are averaged over both frequency and time. The Level 2 data products contained in this data file have been calibrated...

PSP FIELDS Digital Fields Board (DFB) DC-coupled Searchcoil Magnetometer, SCM, Spectra, Low Frequency, High Gain, v-component, Sensor coordinates, Level 2 (L2), 6.99054 s Data

Stuart D Bale, Thierry Dudok de Wit, David M. Malaspina, Katherine A. Goodrich, Marc Pulupa, Timothy Quinn & Peter Schroeder
PSP FIELDS Digital Fields Board, DFB, SCMvlfhg data: The DFB is the low frequency, less than 75 kHz, component of the FIELDS experiment on the Parker Solar Probe spacecraft. For a full description of the FIELDS experiment. DFB DC spectra data consist of power spectral densities as a function of frequency and time. These spectra are averaged over both frequency and time. The Level 2 data products contained in this data file have been calibrated...

Data from: Drivers of site fidelity in ungulates

Thomas Morrison, Jerod Merkel, J. Grant Hopcraft, Ellen Aikens, Jeffrey Beck, Randall Boone, Alyson Courtemanch, Samantha Dwinnell, Sue Fairbanks, Brad Griffith, Arthur Middleton, Kevin Monteith, Brendan Oates, Louise Riotte-Lambert, Hall Sawyer, Kurt Smith, Jared Stabach, Kaitlyn Taylor & Matthew Kauffman
While the tendency to return to previously visited locations – termed ‘site fidelity’ – is common in animals, the cause of this behaviour is not well understood. One hypothesis is that site fidelity is shaped by an animal’s environment, such that animals living in landscapes with predictable resources have stronger site fidelity. Site fidelity may also be conditional on the success of animals’ recent visits to that location, and it may become stronger with age...

Reconstructing squamate biogeography in Afro-Arabia reveals the influence of a complex and dynamic geologic past

Héctor Tejero-Cicuéndez, Austin H. Patton, Daniel S. Caetano, Jiří Šmíd, Luke J. Harmon & Salvador Carranza
The geographic distribution of biodiversity is central to understanding evolutionary biology. Paleogeographic and paleoclimatic histories often help to explain how biogeographic patterns unfold through time. However, such patterns are also influenced by a variety of other factors, such as lineage diversification, that may affect the probability of certain types of biogeographic events. The complex and well-known geologic and climatic history of Afro-Arabia, together with the extensive research on reptile systematics in the region, makes Afro-Arabian...

Indoor temperature - office work performance database

Jose Ali Porras-Salazar, Stefano Schiavon, Pawel Wargocki, Toby Cheung & Kwok Wai Tham
The objective of developing this database was to summarise all relevant published studies that have linked the thermal environment to office work performance within the most representative temperature range for office buildings (20 °C to 30 °C). We conducted a comprehensive literature review and collected the relevant published data into our database. A variety of combinations of keywords including temperature, thermal sensation, work, cognitive, and task performance, and office and commercial buildings, were used. In...

Data for: Nitrous oxide formation by corona discharge: Isotopic composition measurements and atmospheric applications

Mica C. Smith, Julia M. Carlstad, P. Quinby Hunter, John Randazzo & Kristie A. Boering
Agricultural practices have led to a greater use of nitrogen-containing fertilizers and an increase in N2O, an important greenhouse gas and ozone-depleting substance. Isotopic measurements can be used to differentiate sources of N2O in the atmosphere, and the data presented here explore the isotopic composition of N2O formed in a low-temperature plasma, similar to some forms of lightning in the atmosphere. A corona discharge was used to generate N2O under flowing and static conditions, at...

Data from: Biogeographic history and habitat specialisation shape floristic and phylogenetic composition across Amazonian forests

Christopher Baraloto, Jason Vleminckx, Julien Engel, Pascal Petronelli, Nállarett Dávila, Marcos Ríos, Elvis Harry Valderrama Sandoval, Italo Mesones, Juan Ernesto Guevara Andino, Claire Fortunel, Elodie Allie, C. E. Timothy Paine, Aurélie Dourdain, Jean-Yves Goret, Oscar J. Valverde-Barrantes, Freddie Draper & Paul V. A. Fine
A major challenge remains to understand the relative contributions of history, dispersal and environmental filtering to the assembly of hyperdiverse communities across spatial scales. Here, we examine the extent to which biogeographical history and habitat specialization have generated turnover among and within lineages of Amazonian trees across broad geographic and environmental gradients. We replicated standardised tree inventories in 102 0.1-ha plots located in two distant regions - the western Amazon and the eastern Guiana shield....

Why aren’t rabbits and hares larger?

Susumu Tomiya & Lauren K. Miller
Macroevolutionary consequences of competition among large clades have long been sought in patterns of lineage diversification. However, mechanistically clear examples of such effects remain elusive. Here we postulated that the limited phenotypic diversity and insular gigantism in lagomorphs could be explained at least in part by an evolutionary constraint placed on them by potentially-competing ungulate-type herbivores (UTHs). Our analyses yielded three independent lines of evidence supporting this hypothesis: (1) the minimum UTH body mass is...

Data from: Towards eradicating the nuisance of Numts and noise in molecular biodiversity assessment

Natalie Graham
DNA metabarcoding is a popular methodology for biodiversity assessment and increasingly used for community level analysis of intraspecific genetic diversity. The evolutionary history of hundreds of specimens can be captured in a single collection vial. However, the method is not without pitfalls, which may inflate or misrepresent recovered diversity metrics. Numts, nuclear pseudogene copies of mitochondrial DNA, have been particularly difficult to control because they can evolve rapidly and appear deceptively similar to true mitochondrial...

Data from: Structure of microhabitats used by Microcebus rufus across a heterogeneous landscape

Veronarindra Ramananjato & Onja Razafindratsima
Microhabitat preference among primates, which provides them with the niche they need to survive, often conditions primate diversity, abundance, and coexistence. Vegetation alteration and recovery have built heterogeneous forest landscapes that may influence primates’ microhabitat preference. We compared the diversity and size of trees/shrubs and the presence of lianas in 132 sites where we captured the rufous mouse lemur (Microcebus rufus), with that of 240 sites where we did not capture this species, to investigate...

Data from: Gentle topography increases vertical transport of coarse dust by orders of magnitude

Michael Heisel, Bicheng Chen, Jasper Kok & Marcelo Chamecki
The presence of coarse mineral dust in the atmosphere has been substantiated in several recent measurement campaigns, which include observations of particles up to and above 100 micrometer in diameter. Yet, atmospheric dust models either do not include particles larger than 20 micrometer or severely underestimate their concentrations. One possibility for the underestimated concentrations is that models do not represent enhancements of particle transport due to subgrid-scale topography. Here, large-eddy simulations are used in combination...

Joint effects of genes underlying a temperature specialization tradeoff in yeast

Faisal AlZaben, Rachel Brem, Julie Chuong & Melanie Abrams
A central goal of evolutionary genetics is to understand, at the molecular level, how organisms adapt to their environments. For a given trait, the answer often involves the acquisition of variants at unlinked sites across the genome. Genomic methods have achieved landmark successes in pinpointing adaptive loci. To figure out how a suite of adaptive alleles work together, and to what extent they can reconstitute the phenotype of interest, requires their transfer into an exogenous...

Parental population range expansion before secondary contact promotes heterosis

Ailene MacPherson, Silu Wang, Ryo Yamaguchi, Loren Rieseberg & Sarah Otto
Population genomic analysis of hybrid zones is instrumental to our understanding of the evolution of reproductive isolation. Many temperate hybrid zones are formed by the secondary contact between two parental populations that have undergone post-glacial range expansion. Here we show that explicitly accounting for historical parental isolation followed by range expansion prior to secondary contact is fundamental for explaining genetic and fitness patterns in these hybrid zones. Specifically, ancestral population expansion can result in allele...

Phenotypic and genomic diversification with isolation by environment along elevational gradients in a neotropical treefrog

Ricardo Medina, Ella Vázquez-Domínguez, Guinevere O.U. Wogan, Ke Bi, Flavia Termignoni-García, Manuel Hernando Bernal, Juan P. Jaramillo-Correa & Ian J. Wang
Understanding how geographic and environmental heterogeneity drive local patterns of genetic variation is a major goal of ecological genomics and a key question in evolutionary biology. The tropical Andes and inter-Andean valleys are shaped by markedly heterogeneous landscapes, where species experience strong selective processes. We examined genome-wide SNP data together with behavioral and ecological traits (mating calls and body size) known to contribute to genetic isolation in anurans in the emerald-eyed treefrog, Boana platanera, distributed...

Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts

Kristen LeGault
Bacteriophage predation selects for diverse anti-phage systems that frequently cluster on mobilizable defense islands in bacterial genomes. However, there remains a lack of molecular insight into the reciprocal dynamics of phage-bacterial adaptations in nature, particularly in clinical contexts where there is need to inform phage therapy efforts and understand how phages drive pathogen evolution. Here, we used time-shift assays to evaluate whether clinical Vibrio cholerae isolates were susceptible to infection by phage from past, future...

Single-nucleus RNA-sequencing in pre-cellularization Drosophila melanogaster embryos

Ashley Albright
Using 10x Genomics Single-Cell Gene Expression (v3 chemistry) and the Illumina NovaSeq SP we sequenced RNA in nuclei isolated from control and maternal null CTCF pre-cellularization Drosophila melanogaster embryos.

Course materials and datasets for the Alivisatos group-based undergraduate research program

Jason Calvin, Justin Ondry, Jakob Dahl, Adam Sedlak, Amy McKeown-Green, Xingzhi Wang, Michelle Crook, Samuel Gleason, Matthew Hauwiller, Anne Baranger & Paul Alivisatos
A group-based undergraduate research program (GURP) have been developed by the Alivisatos research group at the University of California, Berkeley. To assist other groups who may be interested in developing their own undergraduate research program, we have deposited some materials from our courses here, including raw datasets, lessons, and assignments.

Transmission electron microscope images dataset for AutoDetect-mNP (nanorods)

Xingzhi Wang, Jie Li, Hyun Dong Ha, Jakob Dahl, Teresa Head-Gordon & Paul Alivisatos
AutoDetect-mNP is an unsupervised algorithm capable of detecting and segmenting particles from bright-field TEM images and classifying the particles based on their shapes, requiring minimum human intervention in the process. The algorithm was validated on TEM images of 4 different Au nanoparticle systems (nanorods with ~5 aspect ratio, nanorods with ~2 aspect ratio, mixture of the two nanorods, triangular nanoprisms). This dataset contains the unprocessed TEM images of the nanorods and mixture. For details regarding...

Data for: Hybrid dedicated and distributed coding in PMd/M1 provides separation and interaction of bilateral arm signals

Tanner Dixon, Christina Merrick, Joni Wallis, Richard Ivry & Jose Carmena
Pronounced activity is observed in both hemispheres of the motor cortex during preparation and execution of unimanual movements. The organizational principles of bi-hemispheric signals and the functions they serve throughout motor planning remain unclear. Using an instructed-delay reaching task in monkeys, we identified two components in population responses spanning PMd and M1. A “dedicated” component, which segregated activity at the level of individual units, emerged in PMd during preparation. It was most prominent following movement...

Phylogenomic analysis reveals dispersal-driven speciation and divergence with gene flow in Lesser Sunda Flying Lizards (Genus Draco)

Sean Reilly, Alexander Stubbs, Evy Arida, Benjamin Karin, Umilaela Arifin, Hinrich Kaiser, Ke Bi, Djoko Iskandar & Jimmy McGuire
The Lesser Sunda Archipelago offers exceptional potential as a model system for studying the dynamics of dispersal-driven diversification. The geographic proximity of the islands suggests the possibility for successful dispersal, but this is countered by the permanence of the marine barriers and extreme intervening currents that are expected to hinder gene flow. Phylogenetic and species delimitation analyses of flying lizards (genus Draco) using single mitochondrial genes, complete mitochondrial genomes, and exome-capture data sets identified 9–11...

Registration Year

  • 2021
    146

Resource Types

  • Dataset
    146

Affiliations

  • University of California, Berkeley
    145
  • Laboratory for Atmospheric and Space Physics
    30
  • University of Orléans
    25
  • Goddard Space Flight Center
    5
  • University of Washington
    3
  • Stanford University
    3
  • Utah State University
    3
  • University of California, Davis
    3
  • National Research Institute for Agriculture, Food and Environment
    2
  • University of Pretoria
    2