21 Works

Data from: Comparing methods for SNP calling from Genotyping-By-Sequencing (GBS) data for a large-genome conifer without a published genome sequence

Mengjun Shu & Emily Moran
Reduced-representation restriction-enzyme-based sequencing methods have been demonstrated to be robust and cost-effective genotyping methods to identify Single Nucleotide Polymorphisms (SNPs). While alignment of the short-read fragments to a genome sequence of the same species results in better SNP calling than de novo approaches, only a few tree species - and few conifers in particular - have an annotated sequence. Many conifer genomes are huge (>19 GB) and include a large proportion of repeat sequences, making...

Electronic properties of oligothiophenes

Chee-Kong Lee, Chengqiang Lu, Yue Yu, Qiming Sun, Chang-Yu Hsieh, Shengyu Zhang, Qi Liu & Liang Shi
Despite the remarkable progress of machine learning (ML) techniques in chemistry, modeling the optoelectronic properties of long conjugated oligomers and polymers with ML remains challenging due to the difficulty in obtaining sufficient training data. Here we use transfer learning to address the data scarcity issue by pre-training graph neural networks using data from short oligomers. With only a few hundred training data, we are able to achieve an average error of about 0.1 eV for...

Data from: Probing the ecology and climate of the Eocene Southern Ocean with sand tiger sharks Striatolamia macrota

Sora Kim, Sarah Zeichner, Albert Colman, Howie Scher, Jürgen Kriwet & Thomas Mörs
During the Eocene, the Earth climate system transitioned from greenhouse to icehouse conditions. Central to many explanations is the Southern Ocean—where tectonic configurations influenced oceanic gateways, ocean circulation reduced heat transport, and/or greenhouse gas declines prompted glaciation. To date, few studies have explored the implications of this climate transition on high latitude, marine vertebrates. Seymour Island near the Antarctic Peninsula preserves a rich, diverse fossil assemblage in the Tertiary Eocene La Meseta (TELM) Formation (Fm)....

Root uptake under mismatched distributions of water and nutrients in the root zone

Jing Yan, Nathaniel Bogie & Teamrat Ghezzehei
Most plants derive their water and nutrient needs from soils, where the resources are often scarce, patchy, and ephemeral. It is not uncommon for plant roots to encounter mismatched patches of water-rich and nutrient-rich regions in natural environments. Such an uneven distribution of resources necessitates plants to rely on strategies to explore and acquire nutrients from relatively dry patches. We conducted a laboratory study that elucidates the biophysical mechanisms that enable this adaptation. The roots...

Data from: Evapotranspiration response to multiyear dry periods in the semiarid western United States

Joseph Rungee, Roger Bales, Michael Goulden, Gerald Flerchinger, Greg Barron-Gafford & Xiande Meng
Analysis of measured evapotranspiration shows that subsurface plant‐accessible water storage (PAWS) can sustain evapotranspiration through multiyear dry periods. Measurements at 25 flux tower sites in the semiarid western United States, distributed across five land cover types, show both resistance and vulnerability to multiyear dry periods. Average (±standard deviation) evapotranspiration ranged from 660 ± 230 mm yr−1 (October–September) in evergreen needleleaf forests to 310 ± 200 mm yr−1 in grasslands and shrublands. More than 52% of...

Multiplex networks reveal geographic constraints on illicit wildlife trafficking

Felber Arroyave, Alexander Petersen, Jeffrey Jenkins & Rafael Hurtado
Illicit wildlife trafficking poses a threat to the conservation of species and ecosystems, and represents a fundamental source of biodiversity loss, alongside climate change and large-scale land degradation. Despite the seriousness of this issue, little is known about various socio-cultural demand sources underlying trafficking networks, for example the forthright consumption of endangered species on different cultural contexts. Our study illustrates how wildlife trafficking represents a wicked problem at the intersection of criminal enforcement, cultural heritage...

Are geometric morphometric analyses replicable? Evaluating landmark measurement error and its impact on extant and fossil Microtus classification

Nathaniel Fox, Joseph Veneracion & Jessica Blois
Geometric morphometric analyses are frequently employed to quantify biological shape and shape variation. Despite the popularity of this technique, quantification of measurement error in geometric morphometric datasets and its impact on statistical results is seldom assessed in the literature. Here, we evaluate error on 2D landmark coordinate configurations of the lower first molar of five North American Microtus (vole) species. We acquired data from the same specimens several times to quantify error from four data...

Evapotranspiration data from eddy-covariance flux-tower measurements and Landsat imagery in California’s Sierra Nevada from 1985 to 2019

Qin Ma, Roger Bales, Joseph Rungee, Martha Conklin, Xiande Meng & Michael Goulden
The gridded annual evapotranspiration (ET) from 1985 to 2019 were calculated based on the correlations between eddy-covariance flux-tower measurements of annual evapotranspiration and satellite imagery derived Normalized Difference Vegetation Index (NDVI). Annual ET observations from 12 flux-towers across the Sierra Nevada and Southern California were collected from 2001 to 2016, resulting 97 site-years of ET observations in five main vegetation types (Evergreen Needleleaf Forest, Grasslands, Mixed Forest, Open Shrublands, and Woody Savannas). The NDVI was...

Merced Vernal Pools and Grassland Reserve sUAS-LiDAR High Resolution 0.25-meter DEM

Michael Kalua, Joshua Viers & Andreas Anderson
The Merced Vernal Pools and Grassland Reserve is 6,500 acres of protected habitat adjacent to the University of California Merced containing rare and endangered species and a unique seasonal wetland habitat. These data were gathered to be used for hydrological modelling on the Reserve for potential restoration projects and to be made public for other researchers who may find very high resolution topographical information useful for their work. This dataset contains a Digital Elevation Model...

Topological structure and dynamics of three-dimensional active nematics

Guillaume Duclos, Thomas Powers, Aparna Baskaran, Zvonimir Dogic, Vincenzo Vitelli, Federico Toschi, Raymond Adkins, Debarghya Banerjee, Matthew Peterson, Minu Varghese, Itamar Kolvin, Robert Pelcovits, Sebastian Streichan, Daniel Beller, Arvind Baskaran, Michael Hagan, Matthew S. E. Peterson, Robert A. Pelcovits, Thomas R. Powers, Michael F. Hagan & Sebastian J. Streichan
Topological structures are effective descriptors of the nonequilibrium dynamics of diverse many-body systems. For example, motile, point-like topological defects capture the salient features of two-dimensional active liquid crystals composed of energy-consuming anisotropic units. We dispersed force-generating microtubule bundles in a passive colloidal liquid crystal to form a three-dimensional active nematic. Light-sheet microscopy revealed the temporal evolution of the millimeter-scale structure of these active nematics with single-bundle resolution. The primary topological excitations are extended, charge-neutral disclination...

Soil microbial communities associated with giant sequoia: How does the world's largest tree affect some of the world's smallest organisms?

Stephen Hart, Chelsea J. Carey, Sydney I. Glassman, Thomas D. Bruns & Emma L. Aronson
Giant sequoia (Sequoiadendron giganteum) is an iconic conifer that lives in relic populations on the western slopes of the California Sierra Nevada. In these settings, it is unusual among the dominant trees in that it associates with arbuscular mycorrhizal fungi rather than ectomycorrhizal fungi. However, it is unclear whether differences in microbial associations extends more broadly to non-mycorrhizal components of the soil microbial community. To address this question, we characterized microbiomes associated with giant sequoia...

Snow depth, air temperature, humidity, soil moisture and temperature, and solar radiation data from the basin-scale wireless-sensor network in American River Hydrologic Observatory (ARHO)

Roger Bales, Guotao Cui, Robert Rice, Xiande Meng, Ziran Zhang, Peter Hartsough, Steven Glaser & Martha Conklin
Snow depth, air temperature, humidity, soil moisture and temperature, and solar radiation are measured by a basin-scale wireless-sensor network in the American River Hydrologic Observatory (ARHO). The wireless-sensor network is deployed across the upper, snow-covered areas of the American River basin from 1510 to 2723 m elevation on the western slope of the Sierra Nevada in California. The network comprises 13 sensor clusters (Schneiders, Echo Peak, MT Lincoln, Caples Lake, Alpha, Duncan Peak, Van Vleck,...


Tanya Golash-Boza

Ambient and nitrogen environment friction data for various materials and surface treatments for space applications

Azhar Vellore, Sergio Romero Garcia, Duval Johnson & Ashlie Martini
A multivariate tribological evaluation of candidate materials, surface treatments and dry film lubricants is necessary for design of moving mechanical components that function reliably in extreme conditions, including for long duration space missions. In this study, linear reciprocating or unidirectional sliding friction data was collected using ball-on-flat tests. The balls were hardened 440C stainless steel (either uncoated or sputtered with MoS2) and flat surfaces were 440C stainless steel, Nitronic 60 stainless steel or Ti6Al4V titanium...

Data from: Montane meadows: A soil carbon sink or source?

Cody C. Reed, Amy G. Merrill, W. Mark Drew, Beth Christman, Rachel A. Hutchinson, Levi Keszey, Melissa Odell, Sherman Swanson, Paul S. J. Verburg, Jim Wilcox, Stephen C. Hart & Benjamin W. Sullivan
As the largest biogeochemically active terrestrial reserve of carbon (C), soils have the potential to either mitigate or amplify rates of climate change. Ecosystems with large C stocks and high rates of soil C sequestration, in particular, may have outsized impacts on regional and global C cycles. Montane meadows have large soil C stocks relative to surrounding ecosystems. However, anthropogenic disturbances in many meadows may have altered the balance of C inputs and outputs, potentially...

Data from: An initial comparative genomic autopsy of wasting disease in sea stars

Dannise V. Ruiz‐Ramos, Lauren M. Schiebelhut, Katharina J. Hoff, John P. Wares & Michael N. Dawson
Beginning in 2013, sea stars throughout the Eastern North Pacific were decimated by wasting disease, also known as ‘asteroid idiopathic wasting syndrome’ (AIWS) due to its elusive etiology. The geographic extent and taxonomic scale of AIWS meant events leading up to the outbreak were heterogeneous, multifaceted, and oftentimes unobserved; progression from morbidity to death was rapid, leaving few tell-tale symptoms. Here we take a forensic genomic approach to discover candidate genes that may help explain...

Identifying hidden biocomplexity and genomic diversity in Chinook salmon, an imperiled species with a history of anthropogenic influence

Mariah Meek, Molly R. Stephens, Alisha Goodbla, Bernie P May & Melinda R. Baerwald
Biocomplexity is an important mechanism for population resilience in changing environments. However, we are just beginning to understand how to identify biocomplexity so that species management efforts promote resilience and stability. Genomic techniques are emerging as an important method for identifying biocomplexity. Central Valley (CV) Chinook salmon are an example of a species at risk of extinction if better methods for identifying and protecting biocomplexity are not employed. To address this knowledge gap, we employed...

Foraging shifts and visual preadaptation in ecologically diverse bats

Kalina T. J. Davies, Laurel R. Yohe, Jesus Almonte, Miluska K. R. Sánchez, Edgardo M. Rengifo, Elizabeth R. Dumont, Karen E. Sears, Liliana M. Dávalos & Stephen J. Rossiter
Changes in behaviour may initiate shifts to new adaptive zones, with physical adaptations for novel environments evolving later. While new mutations are commonly considered engines of adaptive change, sensory evolution enabling access to new resources might also arise from standing genetic diversity, and even gene loss. We examine the relative contribution of molecular adaptations, measured by positive and relaxed selection, acting on eye expressed genes associated with shifts to new adaptive zones in ecologically diverse...

California grid electrical energy storage requirements for select renewables integration and fleet electrification scenarios

Arun S.K. Raju & Alexander Vu
Significant electrification of the transportation sector is necessary for the State to achieve several important greenhouse gas (GHG) reduction and renewable energy targets. The State’s electricity generation and transmission capabilities must increase in order to meet the demand generated by increasing levels of fleet electrification. The increased demand, combined with the Renewables Portfolio Standard (RPS) targets will require significantly increased energy storage capabilities that can accommodate demand while integrating renewable power sources into the grid....

Multi-scale drivers of soil resistance predict vulnerability of seasonally wet meadows to trampling by pack stock animals in the Sierra Nevada, USA

Joy S. Baccei, Mitchel P. McClaran, Tim J. Kuhn & Stephen C. Hart
Background Meadow ecosystems have important ecological functions and support socioeconomic services, yet are subject to multiple stressors that can lead to rapid degradation. In the Sierra Nevada of the western USA, recreational pack stock (horses and mules) use in seasonally wet mountain meadows may lead to soil trampling and meadow degradation, especially when soil water content is high and vegetation is developing. Methods In order to improve the ability to predict meadow vulnerability to soil...

Data from: Measuring attitude towards chemistry, biology, and math at a Hispanic-serving institution

Erik Menke & Jordan Chang
This work describes the evaluation of the Attitude toward the Subject of Chemistry Inventory (ASCI), as well as two modifications (one for attitude toward math and one for attitude toward biology), for college students at a Hispanic Serving Institution. Confirmatory factor analysis supported a two-factor structure, similar to an existing model of a revised version of the ASCI, for all three instruments. These instruments show little change in student attitude with respect to biology, chemistry,...

Registration Year

  • 2020

Resource Types

  • Dataset
  • Output Management Plan


  • University of California, Merced
  • University of California, Davis
  • University of Arizona
  • University of California, Riverside
  • University of California, Irvine
  • Max Planck Institute for Dynamics and Self Organization
  • Rice University
  • Tencent (China)
  • West Virginia Division of Natural Resources
  • University of Greifswald