130 Works

Stepping into the past to conserve the future: archived skin swabs from extant and extirpated populations inform genetic management of an endangered amphibian

Andrew P. Rothstein, Roland A. Knapp, Gideon Bradburd, Daniel M. Boiano, Cheryl J. Briggs & Erica Bree Rosenblum
Moving animals on a landscape through translocations and reintroductions is an important management tool used in the recovery of endangered species, particularly for the maintenance of population genetic diversity and structure. Management of imperiled amphibian species rely heavily on translocations and reintroductions, especially for species that have been brought to the brink of extinction by the fungal pathogen, Batrachochytrium dendrobatidis. One striking example of disease-related declines and associated management efforts is in California’s Sequoia and...

Data from: Exploring density and frequency dependent interactions experimentally: an R program for generating hexagonal fan designs.

Carly Rozins, Janis Antonovics, Michael Hood & Jae Hoon Cho
Species interactions and diversity are strongly impacted by local processes, with both the density of a focal species and its frequency in the community having an impact on its growth, survival, and fecundity. Yet, studies that attempt to control for variation in both frequency and density have traditionally required a large number of replicates. Hexagonal fan designs can include a range of both densities and frequencies in a single plot, providing large economies in space...

Data from: Tracing the patterns of non-marine turtle richness from Triassic–Palaeogene: from origin through global spread

Terri Cleary, Roger Benson, Patricia Holroyd & Paul Barrett
Turtles are key components of modern vertebrate faunas and it is predicted that their diversity and distributions will be affected by anthropogenic climate change. Despite this, few studies have attempted to provide baseline data on turtle taxonomic richness through time or assess their past responses to global environmental change. We used the extensive Triassic–Palaeogene (252–23 Ma) fossil record of terrestrial and freshwater turtles to investigate diversity patterns, finding substantial variation in richness through time and...

Velocity field of Jupiter's Great Red Spot in December 2016

Michael H. Wong
Hubble Space Telescope (HST) data acquired around 2016-12-11 16:00 UT were used to measure the velocity field of Jupiter's Great Red Spot. The Hubble dataset is described in Tollefson et al. (2017) and Wong (2017), and the velocity extraction was performed with the ACCIV method described in Asay-Davis et al. (2009). A small subset of the resulting gridded velocity field is shown in a paper discussing small-scale waves observed with Juno's JunoCam imager (Orton et...

Data from: Role of multiple, adjustable toes in distributed control shown by sideways wall-running in geckos

Robert Full, Zhendong Dai, Yi Song & Zhouyi Wang
Remarkable progress has been made characterising one of nature’s most integrated, hierarchical structures – the fibrillar adhesive system of geckos. Surprisingly, we lack an understanding of how multiple, soft toes coordinate to facilitate gecko’s acrobatic locomotion. Here, we tested the control function of multiple toes of sideways wall running geckos by varying substrate orientation, friction, and available area. Geckos realigned the toes of top feet toward the upward direction to resist gravity. Top front and...

Data from: Maximum aerodynamic force production by the wandering glider dragonfly (Pantala flavescens, Libellulidae)

Guanting Su, Robert Dudley, Tianyu Pan, Mengzong Zheng, Liansong Peng & Qiushi Li
Maximum whole-body force production can influence behavioral outcomes for volant taxa, and may also be relevant to aerodynamic optimization in microair vehicles. Here, we describe a new method for measuring maximum force production in free-flying animals, and present associated data for the wandering glider dragonfly. Flight trajectories were repeatedly acquired from pull-up responses by insects dropped in mid-air with submaximal loads attached beneath the center of body mass. Forces were estimated from calculations of the...

Partial migration alters population ecology and food chain length: evidence from a salmonid fish

Suzanne Kelson, Mary Power, Jacques Finlay & Stephanie Carlson
Many migratory species, from monarch butterflies to wildebeest, express partial migration, where only a subset of a population migrates. This intraspecific variation is likely to have large ecological consequences. We studied the ecological consequences of partial migration in a salmonid fish, Oncorhynchus mykiss, in coastal streams in California, USA. One ecotype, steelhead trout, migrates to the ocean, whereas the other, rainbow trout, completes its lifecycle in freshwater. Migration has a strong genetic basis in O....

Data from: Plant-type dominates fine-root C:N:P stoichiometry across China: a meta-analysis

Zhiqiang Wang, Shiqi Lv, Hui Song, Mingcheng Wang, Qi Zhao, Heng Huang & Karl Niklas
Aim: Fine roots play an important role in biogeochemical cycling in terrestrial ecosystems. However, our understanding of large scale biogeographic patterns and drivers of fine-root C:N:P stoichiometry is extremely limited. Location: China. Methods: We compiled data for fine-root carbon (C), nitrogen (N) and phosphorus (P) concentrations at 165 sites across China to explore large-scale biogeographic patterns and drivers of fine-root C:N:P stoichiometry. Results: The geometric means of fine-root C, N, and P concentrations were 448.81...

Data from: Comparisons of Late Ordovician ecosystem dynamics before and after the Richmondian Invasion reveal consequences of invasive species in benthic marine paleocommunities

Hannah Kempf, Ian Castro, Ashley Dineen, Carrie Tyler & Peter Roopnarine
A thorough understanding of how communities respond to extreme changes, such as biotic invasions, is essential to manage ecosystems today. Here we constructed fossil food webs to identify changes in Late Ordovician (Katian) shallow marine paleocommunity structure and functioning before and after the Richmondian Invasion, a well-documented ancient invasion. Food webs were compared using descriptive metrics and Cascading Extinction on Graphs models. Richness at intermediate trophic levels was underrepresented when using only data from the...

Data from: Desiccation resistance and micro-climate adaptation: cuticular hydrocarbon signatures of different Argentine ant supercolonies across California

Jan Buellesbach, Brian A. Whyte, Elizabeth Cash, Joshua D. Gibson, Kelsey J. Scheckel, Rebecca Sandidge & Neil D. Tsutsui
Cuticular hydrocarbons (CHCs), the dominant fraction of the insects’ epicuticle and the primary barrier to desiccation, form the basis for a wide range of chemical signaling systems. In eusocial insects, CHCs are key mediators of nestmate recognition, and colony identity appears to be maintained through a uniform CHC profile. In the unicolonial Argentine ant Linepithema humile, an unparalleled invasive expansion has led to vast supercolonies whose nestmates can still recognize each other across thousands of...

Targeted occupant surveys: A novel method to effectively relate occupant feedback with environmental conditions

Carlos Duarte Roa, Stefano Schiavon & Thomas Parkinson
Occupant satisfaction surveys are widely used in laboratory and field research studies of indoor environmental quality. Field studies pose several challenges because researchers usually have no control over the indoor environments experienced by building occupants, it is difficult to recruit and retain participants, and data collection methods can be cumbersome. With this in mind, we developed a survey platform that uses real-time feedback to send targeted occupant surveys (TOS) at specific indoor environmental conditions and...

The origin of the parrotfish species Scarus compressus in the Tropical Eastern Pacific: region-wide hybridization between ancient species pairs

David Carlon, D. R. Robertson, Robert Barron, David Anderson, Sonja Schwartz, Carlos Sanchez-Ortiz & John Choat
Background: An increasing number of hybrid zones with varying evolutionary outcomes have been documented from different reef fish families. In the Tropical Eastern Pacific (TEP), four species of parrotfishes occur in sympatry on rocky reefs from Baja California to Ecuador: Scarus. compressus,S. ghobban, S. perrico, and S. rubroviolaceus; and have complex phylogeographic histories. The most divergent,S. perrico, belongs to a Tropical American clade that diverged from a Central Indo-Pacific ancestor in the late Miocene (6.6...

Data from: Natural language processing systems for pathology parsing in limited data environments with uncertainty estimation

Anobel Odisho, Briton Park, Nicholas Altieri, John DeNero, Matthew Cooperberg, Peter Carroll & Bin Yu
Objective: Cancer is a leading cause of death, but much of the diagnostic information is stored as unstructured data in pathology reports. We aim to improve uncertainty estimates of machine-learning based pathology parsers and evaluate performance in low data settings. Materials and Methods: Our data comes from the Urologic Outcomes Database at UCSF which includes 3,232 annotated prostate cancer pathology reports from 2001-2018. We approach 17 separate information extraction tasks, involving a wide range of...

Data from: Occupant satisfaction with the indoor environment in seven commercial buildings in Singapore

Toby Cheung, Stefano Schiavon, Lindsay Graham & Kwok Wai Tham
We surveyed seven Green Mark certified air-conditioned commercial buildings (666 responses) in Singapore about their satisfaction with the indoor environment. We used a 7-point scale to evaluate subjects' satisfaction with 18 Indoor Environmental Quality (IEQ) parameters. We also asked follow up questions on the reason(s) of dissatisfaction. We found that occupants were most satisfied with dress code (85 % satisfaction), electrical light (84 %) and cleanliness (81 %), while they were most dissatisfied with sound...

The theory and applications of measuring broad-range and chromosome-wide recombination rate from allele frequency decay around a selected locus

Kevin Wei, Aditya Mantha & Doris Bachtrog
Abstract Recombination is the exchange of genetic material between homologous chromosomes via physical crossovers. High throughput sequencing approaches detect crossovers genome-wide to produce recombination rate maps but are difficult to scale as they require large numbers of recombinants individually sequenced. We present a simple and scalable pooled-sequencing approach to experimentally infer near chromosome-wide recombination rates by taking advantage of non-Mendelian allele frequency generated from a fitness differential at a locus under selection. As more crossovers...

The effects of solar wind structure on nanodust dynamics in the inner heliosphere

Andrew Poppe & Christina Lee
Datasets supporting the manuscript, "The effects of solar wind structure on nanodust dynamics in the inner heliosphere", J. Geophys. Res.: Space Physics Datasets are output from a nanodust dynamics model that uses background MHD electromagnetic fields to trace 1-30 nm grains as they evolve from the inner solar system outwards under the influence of forces such as gravity, electromagnetism, and radiation pressure. Output variables include nanodust flux, velocity distributions, and both measured and predicted (relative)...

Stan code from: Simulation modeling reveals the evolutionary role of landscape shape and species dispersal on genetic variation within a metapopulation

Ming-Chih Chiu, Kei Nukazawa, Thaddeus Carvajal, Vincent Resh, Bin Li & Kozo Watanabe
Different shapes of landscape boundaries can affect the habitat networks within them and consequently the spatial genetic-patterns of a metapopulation. In this study, we used a mechanistic framework to evaluate the effects of landscape shape, through watershed elongation, on genetic divergence among populations at the metapopulation scale. Empirical genetic data from four, sympatric stream-macroinvertebrates having aerial adults were collected from streams in Japan to determine the roles of species-specific dispersal strategies on metapopulation genetics. Simulation...

Data for: Low predictability of energy balance traits and leaf temperature metrics in desert, montane, and alpine plant communities

Benjamin Blonder, Sabastian Escobar, Rozália Kapás & Sean Michaletz
Leaf energy balance may influence plant performance and community composition. While biophysical theory can link leaf energy balance to many traits and environment variables, predicting leaf temperature and key driver traits with incomplete parameterizations remains challenging. Predicting thermal offsets (δ, Tleaf – Tair difference) or thermal coupling strengths (β, Tleaf vs. Tair slope) is challenging. We ask: 1) whether environmental gradients predict variation in energy balance traits (absorptance, leaf angle, stomatal distribution, maximum stomatal conductance,...

The demise of a wonder: evolutionary history and conservation assessments of the Wonder Gecko Teratoscincus keyserlingii (Gekkota, Sphaerodactylidae) in Arabia

Karin Tamar, Johannes Els, Panagiotis Kornilios, Pritpal Soorae, Pedro Tarroso, Evanthia Thanou, John Pereira, Junid Sha, Esmat Elfaki Mohammed Elhassan, Jeruel Cabadonga Aguhob, Saoud Faisal Badaam, Mohamed Mustafa Eltayeb, Ricardo Pusey, Theodore J. Papenfuss, Robert Macey & Salvador Carranza
Effective biodiversity conservation planning starts with the genetic characterization within and among focal populations, in order to understand the likely impact of threats for ensuring the long-term viability of the species. The Wonder Gecko, Teratoscincus keyserlingii, is one of nine members of the genus. The species is distributed in Iran, Afghanistan and Pakistan, with a small isolated population in the United Arab Emirates (UAE), where it is classified nationally as Critically Endangered. Within its Arabian...

Particle-in-cell modeling of Martian magnetic cusps

Andrew Poppe
Datasets supporting the manuscript, "Particle-in-cell modeling of Martian magnetic cusps and their role in enhancing nightside ionospheric ion escape", published in Geophysical Research Letters. All datasets are output from a 1.5-dimensional, particle-in-cell model of magnetospheric-ionospheric particle interactions along an open magnetic field line in a Martian magnetic cusp region. Particles are self-consistently traced according to the combined magnetic mirror force, parallel electrostatic fields, and Martian gravity. Particle densities, velocity distributions, and domain potentials are printed...

Phylogenomics of Perityleae (Compositae) provides new insights into morphological and chromosomal evolution of the rock daisies

Isaac H. Lichter-Marck
Rock daisies (Perityleae; Compositae) are a diverse clade of seven genera and ca. 84 minimum-rank taxa that mostly occur as narrow endemics on sheer rock-cliffs throughout the southwest U.S. and northern Mexico. Taxonomy of Perityleae has traditionally been based on morphology and cytogenetics. To test taxonomic hypotheses and utility of characters emphasized in past treatments, we present the first densely sampled molecular phylogenies of Perityleae and reconstruct trait and chromosome evolution. We inferred phylogenetic trees...

Data from: Terrestrial evaporation and global climate: lessons from Northland, a planet with a hemispheric continent

Marysa M. Lague, Marianne Pietschnig, Sarah Ragen, Timothy A. Smith & David S. Battisti
Motivated by the hemispheric asymmetry of land distribution on Earth, we explore the climate of Northland, a highly idealized planet with a Northern Hemisphere continent and a Southern Hemisphere ocean. The climate of Northland can be separated into four distinct regions: the Southern Hemisphere ocean, the seasonally wet tropics, the mid-latitude desert, and the Great Northern Swamp. We evaluate how modifying land surface properties on Northland drives changes in temperatures, precipitation patterns, the global energy...

Supporting data: 3D projection electrophoresis for single-cell immunoblotting (Part 1)

Samantha Grist, Andoni Mourdoukoutas & Amy Herr
Immunoassays and mass spectrometry are powerful single-cell protein analysis tools; however, interfacing and throughput bottlenecks remain. Here, we introduce three-dimensional single-cell immunoblots to detect both cytosolic and nuclear proteins. The 3D microfluidic device is a photoactive polyacrylamide gel with a microwell array-patterned face (x-y) for cell isolation and lysis. Single-cell lysate in each microwell is ‘electrophoretically projected’ into the 3rd dimension (z-axis), separated by size, and photo-captured in the gel for immunoprobing and confocal/light-sheet imaging....

Supporting data: 3D projection electrophoresis for single-cell immunoblotting (Part 3)

Samantha Grist, Andoni Mourdoukoutas & Amy Herr
Immunoassays and mass spectrometry are powerful single-cell protein analysis tools; however, interfacing and throughput bottlenecks remain. Here, we introduce three-dimensional single-cell immunoblots to detect both cytosolic and nuclear proteins. The 3D microfluidic device is a photoactive polyacrylamide gel with a microwell array-patterned face (x-y) for cell isolation and lysis. Single-cell lysate in each microwell is ‘electrophoretically projected’ into the 3rd dimension (z-axis), separated by size, and photo-captured in the gel for immunoprobing and confocal/light-sheet imaging....

The type of leg lost affects habitat use but not survival in a non-regenerating arthropod

Ignacio Escalante & Damian Elias
Finding shelter and surviving encounters with predators are pervasive challenges for animals. These challenges may be exacerbated after individuals experience bodily damage. Certain forms of damage arise voluntarily in animals, for instance, some taxa release appendages (tails, legs, or other body parts) as a defensive strategy (‘autotomy’). This behavior, however, may pose long-term negative consequences for habitat use and survival. Additionally, these putative consequences are expected to vary according to the function of the lost...

Registration Year

  • 2020

Resource Types

  • Dataset


  • University of California, Berkeley
  • University of California, Davis
  • Cornell University
  • University of Minnesota
  • University of Georgia
  • University of Washington
  • Stanford University
  • Duke University
  • Ehime University
  • University of Pennsylvania