87 Works

Archival data and code in support of uncertainty quantification of climate system properties using the MIT Earth System Model (MESM)

Chris Forest, Alex Libardoni, Andrei P. Sokolov & Erwan Monier
This archive provides the climate model outputs, observational data, and analysis codes that were used to quantify uncertainty in the climate system response properties of the MIT Earth System Model (MESM). Three papers (Libardoni et al. 2018a, 2018b, 2019) include results using these data and codes to provide conditional probability distributions of equilibrium climate sensitivity (ECS), the transient climate response (TCR), and the net radiative forcing by aerosols. The analysis codes are either written in...

Impacts of caudal autotomy on personality

Marcus Michelangeli, Brooke Melki-Wegner, Kate Laskowski, Bob Wong & David Chapple
Caudal autotomy, the voluntary shedding of a tail, is a last-ditch strategy used by many lizard species to escape from predators. There are several costs associated with caudal autotomy that may cause lizards to make behavioral adjustments during tail regeneration. These behavioral changes may be dependent upon individual differences in response to autotomy (e.g. trait or state-dependent differences) and/or the degree of tail loss, as many lizards have the capacity to only partially shed their...

Identifying conservation priorities in a defaunated tropical biodiversity hotspot

Andrew Tilker, Jesse F Abrams, An Nguyen, Lisa Hörig, Jan Axtner, Julie Louvrier, Benjamin M Rawson, Hoa Anh Nguyen Quang, Francois Guegan, Thanh Van Nguyen, Minh Le, Rahel Sollmann & Andreas Wilting
Aim: Unsustainable hunting is leading to widespread defaunation across the tropics. To mitigate against this threat with limited conservation resources, stakeholders must make decisions on where to focus anti-poaching activities. Identifying priority areas in a robust way allows decision-makers to target areas of conservation importance, therefore maximizing the impact of conservation interventions. Location: Annamite mountains, Vietnam and Laos. Methods: We conducted systematic landscape-scale surveys across five study sites (four protected areas, one unprotected area) using...

Data from: Using an arbitrary moment predictor to investigate the optimal choice of prognostic moments in bulk cloud microphysics schemes

Adele A. Igel
Most bulk cloud microphysics schemes predict up to three standard properties of hydrometeor size distributions, namely, the mass mixing ratio, number concentration, and reflectivity factor in order of increasing scheme complexity. However, it is unclear whether this combination of properties is optimal for obtaining the best simulation of clouds and precipitation in models. In this study, a bin microphysics scheme has been modified to act like a bulk microphysics scheme. The new scheme can predict...

Data from: Individual differences in behaviour explain variation in survival: a meta-analysis

Maria Moiron, Kate Laskowski & Petri Niemelä
Research focusing on among-individual differences in behaviour (“animal personality”) has been blooming for over a decade. One of the central theories explaining the maintenance of such behavioural variation posits that individuals expressing greater “risky” behaviours should suffer higher mortality. Here, for the first time, we synthesize the existing empirical evidence for this key prediction. Our results did not support this prediction as there was no directional relationship between riskier behaviour and greater mortality; however there...

Functional variants of DOG1 control seed chilling responses and variation in seasonal life history strategies in Arabidopsis thaliana

Alejandra Martinez-Berdeja, Michelle Stitzer, Mark A. Taylor, Miki Okada, Exequiel Ezcurra, Daniel E. Runcie & Johanna Schmitt
The seasonal timing of seed germination determines a plant's realized environmental niche, and is important for adaptation to climate. The timing of seasonal germination depends on patterns of seed dormancy release or induction by cold and interacts with flowering time variation to construct different seasonal life histories. To characterize the genetic basis and climatic associations of natural variation in seed chilling responses and associated life history syndromes, we selected 559 fully-sequenced accessions of the model...

Sex-specific evolution of relative leg size in Drosophila prolongata results from changes in the intersegmental coordination of tissue growth

David Michael Luecke & Artyom Kopp
Evolution of relative organ size is the most prolific source of morphological diversity, yet the underlying molecular mechanisms that modify growth control are largely unknown. Models where organ proportions have undergone recent evolutionary changes hold the greatest promise for understanding this process. Uniquely among Drosophila species, D. prolongata displays a dramatic, male-specific increase in the size of its forelegs relative to other legs. By comparing leg development between males and females of D. prolongata and...

Life Cycle Modeling of Tech & Strategies for a Sustainable Freight System in California

Hanjiro Ambrose & Alissa Kendall
California’s freight transportation system is a vital part of the state’s economy, but generates a high portion of local pollution in parts of the state with poor air quality. In recognition of these challenges, Executive Order B-32-15 encourages adoption of advanced vehicle technologies and infrastructure, as well as the use of alternative energy and fuels in the freight sector. These measures are echoed in the state’s Sustainable Freight Action Plan. Most emissions reductions from freight...

Testing urban drivers of riparian woody vegetation composition in a precipitation-limited system

Joanna Solins & Mary Cadenasso
In precipitation-limited regions, where water availability is a key driver of vegetation patterns, altered hydrology in urban areas may have a particularly strong effect on riparian plant communities. Urban water inputs can create perennial flows in formerly intermittent streams, potentially providing a water subsidy to riparian plants during dry seasons. However, during rainy seasons, increased storm flow magnitudes in urban areas can cause stream channel incision and associated lowered water tables. Channel incision may reduce...

Data from: Reduced signal for polygenic adaptation of height in UK Biobank

Jeremy J. Berg, Arbel Harpak, Nasa Sinnott-Armstrong, Anja Moltke Joergensen, Hakhamanesh Mostafavi, Yair Field, Evan August Boyle, Xinjun Zhang, Fernando Racimo, Jonathan K. Pritchard & Graham Coop
Several recent papers have reported strong signals of selection on European polygenic height scores. These analyses used height effect estimates from the GIANT consortium and replication studies. Here, we describe a new analysis based on the the UK Biobank (UKB), a large, independent dataset. We find that the signals of selection using UKB effect estimates are strongly attenuated or absent. We also provide evidence that previous analyses were confounded by population stratification. Therefore, the conclusion...

Groove Loops: A Collection of Repeating Multi-Instrumental Patterns

Petr Janata
This dataset contains 456 musical stimuli used in the series of studies reported in: Janata, P., Peterson, J., Ngan, C., Keum, B., Whiteside, H., & Ran, S. (2018). Psychological and Musical Factors Underlying Engagement with Unfamiliar Music. Music Perception, 36(2), 175-200. doi:10.1525/mp.2018.36.2.175

Data from: Functional coupling in the evolution of suction feeding and gill ventilation of sculpins (Perciformes: Cottoidei)

Stacy C. Farina, Matthew L. Knope, Katherine A. Corn, Adam P. Summers & William E. Bemis
Suction feeding and gill ventilation in teleosts are functionally coupled, meaning that there is an overlap in the structures involved with both functions. Functional coupling is one type of morphological integration, a term that broadly refers to any covariation, correlation, or coordination among structures. Suction feeding and gill ventilation exhibit other types of morphological integration, including functional coordination (a tendency of structures to work together to perform a function) and evolutionary integration (a tendency of...

Data from: The interplay among intraspecific leaf trait variation, niche breadth and species abundance along light and soil nutrient gradients

Alex Fajardo & Andrew Siefert
It is assumed that widespread, generalist species have high phenotypic variation, but we know little about how intraspecific trait variation (ITV) relates to species abundance and niche breadth. In the temperate rainforest of southern Chile, we hypothesized that species with wide niche breadth would exhibit 1) high among-plot ITV, 2) a strong relationship between trait values and the environment, and 3) a close fit between traits and local environment trait optima. We measured leaf functional...

Datasets for MRMT

Zhilin Guo
Purpose of this study is to evaluate the capacity of a previously-developed upscaling approach to adequately describe main solute transport processes including the capture of late-time tails under changing boundary conditions. Potential factors that impact the performance of upscaling methods, including temporal variations in mass transfer rates and mass distributions were investigated. Advective-dispersive contaminant transport in a 3D heterogeneous domain was simulated and used as a reference solution. Equivalent transport under homogeneous flow conditions were...

Data from: New records of very high nitrous oxide fluxes from rice cannot be generalized for water management and climate impacts

Reiner Wassmann, Bjoern Ole Sander, Sudhir Yadav, Bas Bouman, Grant Singleton, Alexander Stuart, Jonathan Hellin, David Johnson, Jacqueline Hughes, Klaus Butterbach-Bahl, Ralf Kiese, David Kraus, Baldur Janz, Bruce Linquist, Yam Kanta Gaihre, Ngonidzashe Chirinda & Eva Wollenberg
This supplement aims to substantiate and expand our comments made in the Letter to the Editor. This format as a separate document was necessary due to the complexity of the issues raised in our comments vis-à-vis the word limit of PNAS Letters (500 words). The text elaborates on individual concerns raised in the letter and also adds new aspects on the research quality that have not yet been discussed in the letter. Moreover, the supplement...

Data from: The influence of size on body shape diversification across Indo-Pacific shore fishes

Sarah T. Friedman, Christopher M. Martinez, Samantha Ann Price & Peter C. Wainwright
Understanding the causes of body shape variability across the tree of life is one of the central issues surrounding the origins of biodiversity. One potential mechanism driving observed patterns of shape disparity is a strongly conserved relationship between size and shape. Conserved allometry has been shown to account for as much as 80% of shape variation in some vertebrate groups. Here, we quantify the amount of body shape disparity attributable to changes in body size...

Data from: Life table invasion models: spatial progression and species-specific partitioning

Zihua Zhao, Cang Hui, Richard E. Plant, Min Su, Tim Carpenter, Nikos Papadopoulos, Zhihong Li & James R. Carey
Biological invasions are increasingly being considered important spatial processes that drive global changes, threatening biodiversity, regional economies, and ecosystem functions. A unifying conceptual model of the invasion dynamics could serve as a useful tool for comparison and classification of invasion processes involving different species across large geographic ranges. By dividing these geographic ranges that are subject to invasions into discrete spatial units we here conceptualize the invasion process as the transition from pristine to invaded...

Initial application of the noise-sorted scanning clustering algorithm to the analysis of composition-dependent organic aerosol thermal desorption measurements

Christopher Cappa, Ziyue Li, Emma D'Ambro, Siegfried Schobesberger, John Shilling, Felipe Lopez-Hilfiker, Jiumeng Liu, Cassandra Gaston & Joel Thornton
The FIGAERO-CIMS (Filter Inlet for Gases and AEROsols + chemical ionization mass spectrometer) measures thermal desorption profiles for individual ions evolved from evaporation of organic aerosol components. Often, hundreds of individual thermograms are obtained, reflecting the compositional complexity of organic aerosol. We have developed a novel clustering algorithm, Noise-Sorted Scanning Clustering (NSSC), that provides a robust, reproducible analysis of the FIGAERO temperature-dependent mass spectral data. The NSSC allows for determination of thermal profiles for compositionally...

Unnatural selection of salmon life histories in a modified riverscape

Anna M. Sturrock, Stephanie M. Carlson, John D. Wikert, Tim Heyne, Sébastien Nusslé, Joseph E. Merz, Hugh J. W. Sturrock & Rachel C. Johnson
Altered river flows and fragmented habitats often simplify riverine communities and favor non‐native fishes, but their influence on life‐history expression and survival is less clear. Here, we quantify the expression and ultimate success of diverse salmon emigration behaviors in an anthropogenically altered California river system. We analyzed two decades of Chinook salmon monitoring data to explore the influence of regulated flows on juvenile emigration phenology, abundance, and recruitment. We then followed seven cohorts into adulthood...

Life history plasticity and water use trade-offs associated with drought resistance in a clade of California jewelflowers

Sharon Strauss, Ian Pearse, Jessica Aguilar, Patrick McIntyre & N. Ivalu Cacho
Water limitation is a primary driver of plant geographic distributions and individual plant fitness. Drought resistance is the ability to survive and reproduce despite limited water, and numerous studies have explored its physiological basis in plants. However, it is unclear how drought resistance and trade-offs associated with drought resistance evolve within plant clades. We quantified the relationship between water availability and fitness for 13 short-lived plant taxa in the Streptanthus clade that vary in their...

Data from: What is in a general plan? using natural language processing to read 461 California city general plans

Carl Stahmer & Catherine Brinkley
This repository contains all data outputs related to reasearch that analyzed General Plans from cities across the state of California to understand what topics are adressed and the spacial distribution of topic rerpresentation. We assembles a database of 421 California city-level General Plans and used Natural Language Processing to read their contents. The plans contained over 60 discrete topics and wer generally optimistic in sentiment. A quarter of the topics were reagionally specific. Housing is...

Survey data for: Planning and policymaking for TOD, transit, and AT in California cities

Elisa Barbour
This in-progress two-year research project for the California Department of Transportation, through the National Center for Sustainable Transportation, is assessing planning and policymaking for transit-oriented development , transit, and active transport in California cities located in the state's four largest regions, the San Francisco Bay, Los Angeles, San Diego, and Sacramento areas. The dataset we provide here is an anonymous version of our survey results of city planning directors in these regions, conducted between April...

Data from: Estimating body mass of free-living whales using aerial photogrammetry and 3D volumetrics

Fredrik Christiansen, Mariano Sironi, Michael J. Moore, Matías Di Martino, Marcos Ricciardi, Hunter A. Warick, Duncan J. Irschick, Robert Gutierrez & Marcela M. Uhart
1. Body mass is a key life history trait in animals. Despite being the largest animals on the planet, no method currently exists to estimate body mass of free-living whales. 2. We combined aerial photographs and historical catch records to estimate the body mass of free-living right whales (Eubalaena sp.). First, aerial photogrammetry from unmanned aerial vehicles was used to measure the body length, width (lateral distance) and height (dorso-ventral distance) of free-living southern right...

Seedling response to water stress in valley oak (Quercus lobata) is shaped by different gene networks across populations

Alayna Mead, Juan Peñaloza Ramirez, Megan Bartlett, Jessica Wright, Lawren Sack & Victoria Sork
Drought is a major stress for plants, creating a strong selection pressure for traits that enable plant growth and survival in dry environments. Many drought responses are conserved species-wide responses while others vary among populations distributed across heterogeneous environments. We tested how six populations of the widely-distributed California valley oak (Quercus lobata) sampled from contrasting climates would differ in their response to soil drying relative to well-watered controls in a common environment by measuring ecophysiological...

Quantifying the effects of species traits on predation risk in nature: a comparative study of butterfly wing damage

Freerk Molleman, Juhan Javoiš, Robert Davis, Melissa Whitaker, Toomas Tammaru, Andreas Prinzing, Erki Õunap, Niklas Wahlberg, Ullasa Kodandaramaiah, Kwaku Aduse-Poku, Ants Kaasik & James Carey
1) Evading predators is a fundamental aspect of the ecology and evolution of all prey animals. In studying the influence of prey traits on predation risk, previous researchers have shown that crypsis reduces attack rates on resting prey, predation risk increases with increased prey activity, and rapid locomotion reduces attack rates and increases chances of surviving predator attacks. However, evidence for these conclusions is nearly always based on observations of selected species under artificial conditions....

Registration Year

  • 2019

Resource Types

  • Dataset


  • University of California, Davis
  • University of Montana
  • University of Nevada Reno
  • University of Washington
  • Stanford University
  • Lund University
  • Fudan University
  • University of Vermont
  • University of California, Berkeley
  • United States Department of Agriculture