390 Works

Data from: Female-limited colour polymorphism in the crab spider Synema globosum (Araneae: Thomisidae)

Helena Ajuria Ibarra & Tom Reader
Conspicuous colour variation, caused by the influence of the environment on phenotype or by genetic differences among individuals, is frequently observed in nature. If genetic in origin, colour variation can facilitate the study of mechanisms that contribute to the maintenance of true polymorphisms. Here we describe, for the first time, the female-limited colour polymorphism in the crab spider, Synema globosum. We looked for associations between life-history traits and female colour morph, and identified potential agents...

Data from: Natural selection for the Duffy-null allele in the recently admixed people of Madagascar

Jason A. Hodgson, Joseph K. Pickrell, Laurel N. Pearson, Ellen E. Quillen, Antonio Prista, Jorge Rocha, Himla Soodyall, Mark D. Shriver & George H. Perry
While gene flow between distantly related populations is increasingly recognized as a potentially important source of adaptive genetic variation for humans, fully characterized examples are rare. In addition, the role that natural selection for resistance to vivax malaria may have played in the extreme distribution of the protective Duffy-null allele, which is nearly completely fixed in mainland sub-Saharan Africa and absent elsewhere, is controversial. We address both these issues by investigating the evolution of the...

Data from: Environmental and biological controls on the diversity and ecology of Late Cretaceous through early Paleogene marine ecosystems in the U.S. Gulf Coastal Plain

Jocelyn A. Sessa, Timothy J. Bralower, Mark E. Patzkowsky, John C. Handley & Linda C. Ivany
The late Mesozoic through early Cenozoic is an interval of significant biologic turnover and ecologic reorganization within marine assemblages, but the timing and causes of these changes remain poorly understood. Here, we quantify the pattern and timing of changes in the diversity (richness and evenness) and ecology of local (i.e., sample level) mollusk-dominated assemblages during this critical interval using field-collected and published datasets from the US Gulf Coastal Plain. We test whether the biologic and...

Data from: Aggressive chemotherapy and the selection of drug resistant pathogens

Silvie Huijben, Andrew S. Bell, Derek G. Sim, Danielle Tomasello, Nicole Mideo, Troy Day & Andrew F. Read
Drug resistant pathogens are one of the key public health challenges of the 21st century. There is a widespread belief that resistance is best managed by using drugs to rapidly eliminate target pathogens from patients so as to minimize the probability that pathogens acquire resistance de novo. Yet strong drug pressure imposes intense selection in favor of resistance through alleviation of competition with wild-type populations. Aggressive chemotherapy thus generates opposing evolutionary forces which together determine...

Supplementary data, code, and information for ‘Atlantic Hurricane Trends linked to Climate Change’ (Mann et al. 2006)

M.E. Mann & K. Emanuel
Increases in key measures of Atlantic hurricane activity over recent decades are believed to reflect, in large part, contemporaneous increases in tropical Atlantic warmth [e.g., Emanuel, 2005]. Some recent studies [e.g., Goldenberg et al., 2001] have attributed these increases to a natural climate cycle termed the Atlantic Multidecadal Oscillation (AMO), while other studies suggest that climate change may instead be playing the dominant role [Emanuel, 2005; Webster et al., 2005]. Using a formal statistical analysis...

Supplementary data and code for ‘Oscillatory Spatiotemporal Signal Detection in Climate Studies: A Multiple-Taper Spectral Domain Approach’ (Mann and Park 1999)

M.E. Mann & J. Park
This chapter introduces a methodology for signal detection and reconstruction of irregular spatiotemporal oscillatory signals—the multiple-taper spectrum estimation method (MTM)–singular-value decomposition (SVD) methodology. This methodology is offered as an alternative technique which avoids most of the problems encountered in traditional techniques and provides an efficient exploratory method for climate signal detection. The associated signal-detection parameter—the local fractional variance spectrum (LFV) spectrum—yields the correct null distribution for a very general class of spatiotemporal climate noise processes...

The geography of parasite local adaptation to host communities

Emily Bellis, Chloee McLaughlin, Claude DePamphilis & Jesse Lasky
Fitness responses to environment can shape species distributions, though opposing eco-evolutionary processes can obscure environmental effects. For example, host specificity influences parasite dynamics, but is unclear how adaptation of parasites to local host communities may scale up to continental distributions. Here, we develop a macroecological framework to determine how host community structure affects the distribution of specialist and generalist populations of Striga hermonthica, an African parasitic plant of cereal crops. Combining data from global crop...

Patterns of recent natural selection on genetic loci associated with sexually differentiated human body size and shape phenotypes

Audrey M. Arner, Kathleen E. Grogan, Mark Grabowski, Hugo Reyes-Centeno & George H. Perry
Levels of sex differences for human body size and shape phenotypes are hypothesized to have adaptively reduced following the agricultural transition as part of an evolutionary response to relatively more equal divisions of labor and new technology adoption. In this study, we tested this hypothesis by studying genetic variants associated with five sexually differentiated human phenotypes: height, body mass, hip circumference, body fat percentage, and waist circumference. We first analyzed genome-wide association (GWAS) results for...

Analyses of vertical wind profile data from the VORTEX-Southeast 2017 field campaign

P. Markowski
This dataset contains observations from the Collaborative Lower Atmospheric Mobile Profiling System (CLAMPS) and NOAA Air Resources Laboratory, Atmospheric Turbulence and Diffusion Division) micrometeorological towers that were analyzed in the Markowski et al. (2019) study. That study used CLAMPS Doppler lidar observations of near-surface vertical wind profiles, and NOAA tower observations of near-surface shear and vertical momentum fluxes, both of which were obtained during the spring 2017 Verification of the Origins of Rotation in Tornadoes...

Electrodynamic Levitation Diffusion Chamber Measurements of the Mass Growth of Heterogeneously-Nucleated Ice Crystals Grown from the Vapor

A. Harrison, A. Moyle, M. Hanson & J.Y. Harrington
This data set comprises individual time-series for ice crystals grown in an electrodynamic levitation diffusion chamber. Descriptions of the chamber and experiments can be found in Harrison et al. (2016). Experiments were conducted by freezing small (approximately 10 micrometer radius) droplets heterogeneously using the bionucleant Snomax. Frozen droplets were levitated in the diffusion chamber and grown in a constant temperature, pressure, and supersaturation environment. The voltage ratio needed to levitate the particle was recorded as...

Observational and modeled dataset for determination of urban emissions of CO2 using an atmospheric inversion technique, Davos, Switzerland, 2011-2012.

N.L. Miles, T. Lauvaux, S.J. Richardson, A. Deng & D. Stauffer
Anthropogenic emissions from urban areas represent 70% of the fossil fuel carbon emitted globally according to carbon emission inventories. The observational and model data archived here were used in the first operational system able to monitor, in near–real time, daily emission estimates, using a mesoscale atmospheric inversion framework over the city of Davos, Switzerland, before, during, and after the World Economic Forum 2012 Meeting (WEF-2012). Two instruments that continuously measured atmospheric mixing ratios of greenhouse...

Ensemble model output of North American atmospheric CO2 simulation (full WRF-chem output)

S. Feng, T. Lauvaux, K.J. Davis, K. Keller, R. Rayner, T. Oda, K. Gurney, Y. Zhou, C. Williams, A.E. Schuh, J. Liu & I. Baker
The uncertainty in biospheric carbon dioxide (CO2) flux estimates drives divergent projections of future climate and uncertainty in prescriptions for climate mitigation. The terrestrial carbon sink can be inferred from atmospheric CO2 observations with transport models via inversion methods. Regional CO2 flux estimates remain uncertain due to the mixture of uncertainties caused by transport models, prior estimates of biospheric fluxes, large-scale CO2 boundary inflow, the assumptions in the inversion process, and the limited density of...

Impacts of the Opioid Epidemic

Sterner Glenn
This is a place and name redacted dataset of 60 qualitative interviews of those who have been affected by the opioid crisis. Individuals fit into one of four categories: (1) individuals in recovery from an opioid use disorder; (2) individuals who have lost a loved one due to an opioid overdose; (3) individuals who have supported a loved one through their opioid use; and (4) individuals who are pain management patients who have faced obstacles...

Modeled dataset for the estimation of atmospheric transport errors using a Multi-Physics and Analysis Ensemble on the Midwest US

L.I. Diaz-Isaac, T. Lauvaux & K.J. Davis
Atmospheric inversions are used to assess biosphere-atmosphere CO2 surface exchanges. However, large uncertainties exist among inverse flux estimates independent of the spatial scales. Atmospheric transport model errors are one of the main contributors to the uncertainty affecting CO2 inverse flux estimates but have not been quantified thoroughly. The model dataset archived here were used to evaluate atmospheric transport errors over the US upper Midwest with an ensemble of simulations created with the Weather Research and...

One-way nested (27km, 9km and 3km) model output of North American atmospheric CO2 simulation (full WRF-chem output)

A. Samaddar, S. Feng, T. Lauvaux, Z.R. Barkley, S. Pal & K.J. Davis
Synoptic weather systems are a major driver of spatial gradients in atmospheric CO2 mole fractions. During frontal passages air masses from different regions meet at the frontal boundary creating significant gradients in CO2 mole fractions. This study quantitatively describes the atmospheric transport of CO2 mole fractions during a mid-latitude cold front passage and explores the impact of various sources of CO2. We focus here on a cold front passage over Lincoln, Nebraska on August 4th,...

Implications of electron detachment in associative collisions of atomic oxygen anion with molecular nitrogen for modeling of transient luminous events

R. Janalizadeh & V.P. Pasko
Electron detachment from negative ion of atomic oxygen, O-, is important for understanding of lightning-induced upper atmospheric discharges. Contrary to previous studies, Rayment and Moruzzi [1978] argue that the associative detachment reaction of O- with molecular nitrogen, N2, proceeds with N2 in its ground state, and calculate the reaction rate coefficient as a function of the reduced electric field. In this work we analyze the experimental setup in [Rayment and Moruzzi, 1978] and demonstrate that...

Compact Spherical Loudspeaker Array Instrument Directivity Database

M.C. Vigeant & M. Neal
This data set contains full three-dimensional turntable measurements of a compact spherical loudspeaker array used to reconstruct the frequency-dependent radiation patterns of musical instruments. Included in this data set are array radiation control filters, driver equalization filters, measured turntable data, and simulations of the compact spherical loudspeaker array's performance using both a spherical-cap and a point-source model. For more information on the details of this data set, please refer to the paper: M. Neal, "A...

Dataset of Constraining fossil fuel CO2 emissions from urban area using OCO-2 observations of total column CO2

X. Ye, T. Lauvaux, E.A. Kort, T. Oda, S. Feng, J.C. Lin, E.G. Yang & D. Wu
Satellite observations of the total column dry-air CO2 (XCO2) are expected to support the quantification and monitoring of fossil fuel CO2 (ffCO2) emissions from urban areas. We evaluate the utility of the Orbiting Carbon Observatory 2 (OCO-2) XCO2 retrievals to optimize whole-city emissions, using a Bayesian inversion system and high-resolution transport modeling. The uncertainties of constrained emissions related to transport model, satellite measurements, and local biospheric fluxes are quantified. For the first two uncertainty sources,...

Output and Data from Semi-Analytic Functions to Calculate the Deposition Coefficients for Ice Crystal Vapor Growth in Bin and Bulk Microphysical Models.

Harrington J., G. Sokolowski & H. Morrison
This data set comprises fitting coefficients needed to calculate supersaturation-dependent deposition coefficients, along with output from model simulations. The coefficients are used in semi-analytic functions that allows fast and accurate calculations of the surface supersaturations needed for the deposition coefficients. Output are provided for test simulations that reveal the accuracy of the approximate calculations for individual crystals. Model output are also provided from test simulations using Eulerian bin and bulk cloud microphysical schemes.

Simulations and Analysis Code for the Automated Issuance of Tornado Warnings in Simulated Convective Storms

D. Steinkruger, P. Markowski & G.S. Young
These data and Python scripts were used to develop an artificially intelligent system capable of issuing tornado warnings in simulated convective storms. Contained in the dataset are 128 CM1 simulations for which the output of the simulations have been saved in netCDF format. Additionally, the Python code used to visualize the simulations, extract data from the simulations, train machine learning models, and set the AI system warning thresholds is included.

Data and analysis code for the 26 May 2010 supercell intercepted by VORTEX2 near Prospect Valley, Colorado

S. Murdzek , P. Markowski, Y.P. Richardson & R. Tanamachi
These data and computer codes contained in this zip file were used in an analysis of a supercell on 26 May 2010 near Prospect Valley, Colorado, that was intercepted by the Second Verification of the Origins of Rotation in Tornadoes Experiment (VORTEX2). The results from this analysis are discussed in the following journal article: Murdzek, S. S., P. M. Markowski, Y. P. Richardson, R.L. Tanamachi, 2020: Processes preventing the development of a significant tornado in...

Coral accurately bridges paired-end reads alignment

Q. Shi & M. Shao
Motivation: The established high-throughput RNA-seq technologies usually produce paired-end reads. A challenging problem is therefore to computationally infer the alignment of entire fragments given the alignment of the two mate ends. Solving this problem essentially provide longer RNA-seq reads, and hence benefits downstream RNA-seq analysis. Results: We introduce Coral, a new tool that can accurately bridge paired-end RNA-seq reads. The core of Coral is a novel optimization formulation that can capture the most reliable bridging...

Data from: Fear and lethality in snowshoe hares: the deadly effects of non-consumptive predation risk

Kirsty J. MacLeod, Charles J. Krebs, Rudy Boonstra & Michael J. Sheriff
Predators play a critical, top-down role in shaping ecosystems, driving prey population and community dynamics. Traditionally, studies of predator-prey interactions have focused on direct effects of predators, namely the killing of prey. More recently, the non-consumptive effects of predation risk are being appreciated; e.g., the Ecology of Fear. Prey responses to predation risk can be morphological, behavioural, and physiological, and are assumed to come at a cost to prey fitness. However, few studies have examined...

Data from: Fruit traits of pioneer trees structure seed dispersal across distances on tropical deforested landscapes: implications for restoration

Paulo H. S. A. Camargo, Marco A. Pizo, Pedro H. S. Brancalion & Tomás A. Carlo
Pioneer trees with fleshy fruits are typically planted in restoration projects to attract frugivores as a mean to increase dispersal and accelerate forest regeneration. However, differences in fruit traits of pioneer trees can potentially influence dispersal and their restoration outcomes. Here we investigated the effects of bird and plant traits, and distance to forest fragments, on the seed rain using a tree-planting experiment replicated in 12 deforested sites in Brazil. Factors were fruit traits of...

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