87 Works

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: 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...

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...

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: 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: 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...

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: 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...

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...

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...

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...

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...

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...

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...

Exploring the role of attitude in the acceptance of self-driving shuttles

YAN XING, Susan Handy, Giovanni Circella, Yunshi Wang & Farzad Alemi
Self-driving vehicles, as a revolution in mobility, are emerging and developing rapidly. However, public attitudes toward this new unproven technology are still uncertain. Given the significant influence of attitude toward a new technology on the intention to use it, the question arises as to why some people are in favor of this technology whereas others are not. Additionally, questions about the key attitudes influencing self-driving technology acceptance, where these attitudes come from, and how they...

Multi-scale landscape genetics of American marten at their southern range periphery

Cody Aylward, James Murdoch & C. William Kilpatrick
American marten (Martes americana) are a conservation priority in many forested regions of North America. Populations are fragmented at the southern edge of their distribution due to suboptimal habitat conditions. Facilitating gene flow may improve population resilience through genetic and demographic rescue. We used a multi-scale approach to estimate the relationship between genetic connectivity and landscape characteristics among individuals at three scales in the northeastern United States: regional, subregional, and local. We integrated multiple modeling...

Genome Synteny Has Been Conserved Among the Octoploid Progenitors of Cultivated Strawberry Over Millions of Years of Evolution

Michael Hardigan, Mitchell Feldmann, Anne Lorant, Kevin Bird, Steven Knapp, Patrick Edger, Glenn Cole, Charlotte Acharya & Randi Famula
Allo-octoploid cultivated strawberry (Fragaria × ananassa) originated through a combination of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage, and continued admixture of wild species over the last 300 years. While genes appear to flow freely between the octoploid progenitors, the genome structures and diversity of the octoploid species remain poorly understood. The complexity and absence of an octoploid genome frustrated early efforts to study chromosome evolution, resolve subgenomic structure, and develop a...

Data from: Anthropogenic Basin Closure and Groundwater Salinization (ABCSAL)

Richard Pauloo
Global food systems rely on irrigated agriculture, and most of these systems in turn depend on fresh sources of groundwater. In this study, we demonstrate that groundwater development, even without overdraft, can transform a fresh, open basin into an evaporation dominated, closed-basin system, such that most of the groundwater, rather than exiting via stream baseflow and lateral subsurface flow, exits predominantly by evapotranspiration from irrigated lands. In these newly closed hydrologic basins, just as in...

One-dimensional models of radiation transfer in heterogeneous canopies: a review, re-evaluation, and improved model

Brian Bailey, María Ponce De León & E. Scott Krayenhoff
This dataset contains the project files and data output for the publication: Bailey, Brian; Ponce de León, María; Krayenhoff, E. Scott (2019), One-dimensional models of radiation transfer in heterogeneous canopies: A review, re-evaluation, and improved model. The file main.cpp contains the main program that sets up and runs the simulations. Output files are stored in the 'output' directory. The current version of the Helios source code can be downloaded at https://www.github.com/PlantSimulationLab/Helios

Data from: A Bayesian approach for inferring the impact of a discrete character on rates of continuous-character evolution in the presence of background-rate variation

Michael R May & Brian R Moore
Understanding how and why rates of character evolution vary across the Tree of Life is central to many evolutionary questions; e.g., does the trophic apparatus (a set of continuous characters) evolve at a higher rate in fish lineages that dwell in reef versus non-reef habitats (a discrete character)? Existing approaches for inferring the relationship between a discrete character and rates of continuous-character evolution rely on comparing a null model (in which rates of continuous-character evolution...

Data from: Evolution of sexually dimorphic pheromone profiles coincides with increased number of male-specific chemosensory organs in Drosophila prolongata

Yige Luo, Yuewei Zhang, Jean-Pierre Farine, Jean-François Ferveur, Santiago Ramírez & Artyom Kopp
Binary communication systems that involve sex-specific signaling and sex-specific signal perception play a key role in sexual selection and in the evolution of sexually dimorphic traits. The driving forces and genetic changes underlying such traits can be investigated in systems where sex-specific signaling and perception have emerged recently and show evidence of potential coevolution. A promising model is found in Drosophila prolongata, which exhibits a species-specific increase in the number of male chemosensory bristles. We...

Adaptive specialization and constraint in morphological defenses of planktonic larvae

Samuel Bashevkin, John Christy & Steven Morgan
Morphological defenses of plankton can include armor, spines, and coloration. Spines defend from gape-limited fish predators while pigmentation increases visibility to fishes but defends from ultraviolet radiation (UVR). Planktonic crab larvae (zoeae) exhibit inter- and intra-specific variability in the lengths of defensive spines, extent of pigmentation, and body size. The determinants of this variability and the relationships among these traits are largely unknown. Larvae may employ generalized defenses against the dual threats of UVR and...

Registration Year

  • 2019
    87

Resource Types

  • Dataset
    87

Affiliations

  • University of California, Davis
    87
  • University of Montana
    3
  • University of Nevada Reno
    3
  • University of Washington
    2
  • Stanford University
    2
  • Lund University
    2
  • Fudan University
    2
  • University of Vermont
    2
  • University of California, Berkeley
    2
  • United States Department of Agriculture
    2