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- Creator:
- Forrest, Stephen R., Panda, Anurag, Qu, Yue, Che, Xiaozhou, Coburn, Caleb, and Burlingame, Quinn
- Description:
- Mathematica Diffusion Simulation: Programmed by Coburn, Caleb. Simulation of diffusion in organic heterostructures, including least square fits and statistical goodness of fit analysis. Used to calculate fits to transient data in Fig 1, 3 and Extended Data Fig.2. Example data file included for download Matlab Montecarlo simulation: Programmed by Coburn, Caleb. Montecarlo simulation of charge diffusion on a cubic lattice to determine lateral diffusion length as a function of barrier height, assuming thermionic emission over the barrier. Matlab 2D Diffusion Simulation:Programmed by Coburn, Caleb. Modified from BYU Physics 430 Course Manual. Simulates diffusion around a film discontinuity, such a cut. Used to generate fits to Extended Data Fig. 1
- Keyword:
- Organic semiconductors and Charge diffusion
- Discipline:
- Science
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- Creator:
- Flanner, Mark
- Description:
- Greenhouse gas (GHG) additions to Earth’s atmosphere initially reduce global outgoing longwave radiation (OLR), thereby warming the planet. In select environments with temperature inversions, however, increased GHG concentrations can actually increase local OLR. Negative top-of-atmosphere and effective radiative forcing (ERF) from this situation give the impression that local surface temperatures could cool in response to GHG increases. Here we consider an extreme scenario in which GHG concentrations are increased only within the warmest layers of winter near-surface inversions of the Arctic and Antarctic. We find, using a fully coupled Earth system model, that the underlying surface warms despite the GHG addition exerting negative ERF and cooling the troposphere in the vicinity of the GHG increase. This unique radiative forcing and thermal response is facilitated by the high stability of the polar winter atmosphere, which inhibits thermal mixing and amplifies the impact of surface radiative forcing on surface temperature. These findings also suggest that strategies to exploit negative ERF via injections of short-lived GHGs into inversion layers would likely be unsuccessful in cooling the planetary surface. and Note: A revised data description file was added to this work on April 11, 2018 containing additional information about the data set than was provided in the original description. Additional keywords and a full citation to the related article were added as well.
- Keyword:
- climate, greenhouse gas, polar inversion layers, radiative forcing (and/or effective radiative forcing), and MODTRAN simulation
- Discipline:
- Science
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- Creator:
- Johnson, Jena E.
- Description:
- Note: The "Readme_Metadata" file was updated on March 15, 2018 to include a citation to the related article making use of this data and was reformatted to be presented as a pdf file rather than as a docx file. and This data set is comprised of synchrotron-based X-ray transmission and absorption spectroscopy data as well as X-ray diffraction patterns that were performed to characterize the best-preserved examples of nanoscale iron silicate mineral inclusions from 2.5 billion-year-old Banded Iron Formations (BIFs) and ferruginous cherts.
- Keyword:
- Precambrian banded iron formations and nanoparticle inclusions of iron silicates in chert
- Discipline:
- Science
-
- Creator:
- Ozturk, Dogacan
- Description:
- The global magnetosphere-ionosphere-thermosphere (M-I-T) system is intrinsically coupled and susceptible to external drivers such as solar wind dynamic pressure enhancements. In order to understand the large-scale dynamic processes in the M-I-T system due to the compression from the solar wind, the 17 March 2015 sudden commencement was studied in detail using global numerical models. This data set is comprised of the simulation data generated from these models. and NOTE: The following changes were made to this dataset on March 28, 2018. First, two mp4 files were added. Second, the symbol representing "degree" was not rendering properly in the README file. The symbols were removed and replaced with the word "degree". Third, the metadata in the "methodology" and "description" fields were revised for content and clarity. On April 16, 2018 a citation to the corresponding article was added to the metadata record.
- Keyword:
- MHD model, BATS'R'US, and GITM
- Discipline:
- Science
-
- Creator:
- Tye, Alexander R, Wolf, Aaron S, and Niemi, Nathan A
- Description:
- Detrital zircon age distributions provide robust insights into past sedimentary systems, but these age distributions are often complex and multi-peaked, with sample sizes too small to confidently resolve population distributions. This limited sampling hinders existing quantitative methods for comparing detrital zircon age distributions, which show systematic dependence on the sizes of compared samples. The proliferation of detrital zircon studies motivates the development of more robust quantitative methods. We present the first attempt, to our knowledge, to infer probability model ensembles (PMEs) for samples of detrital zircon ages using a Bayesian method. Our method infers the parent population age distribution from which a sample is drawn, using a Monte Carlo approach to aggregate a representative set of probability models that is consistent with the constraints that the sample data provide. Using the PMEs inferred from sample data, we develop a new estimate of correspondence between detrital zircon populations called Bayesian Population Correlation (BPC). Tests of BPC on synthetic and real detrital zircon age data show that it is nearly independent from sample size bias, unlike existing correspondence metrics. Robust BPC uncertainties can be readily estimated, enhancing interpretive value. When comparing two partially overlapping zircon age populations where the shared proportion of each population is independently varied, BPC results conform almost perfectly to expected values derived analytically from probability theory. This conformity of experimental and analytical results permits direct inference of the shared proportions of two detrital zircon age populations from BPC. We provide MATLAB scripts to facilitate the procedures we describe.
- Keyword:
- provenance, statistics, zircon, Bayesian, detrital, and density estimation
- Discipline:
- Science
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- Creator:
- Azari, A. R.
- Description:
- ABSTRACT: We present a statistical study of interchange injections in Saturn's inner and middle magnetosphere focusing on the dependence of occurrence rate and properties on radial distance, partial pressure, and local time distribution. Events are evaluated from over the entirety of the Cassini mission’s equatorial orbits between 2005 and 2016. We identified interchange events from CHarge Energy Mass Spectrometer (CHEMS) H+ data using a trained and tested automated algorithm, which has been compared with manual event identification for optimization. We provide estimates of interchange based on intensity, which we use to investigate current inconsistencies in local time occurrence rates. This represents the first automated detection method of interchange, estimation of injection event intensity, and comparison between interchange injection survey results. We find the peak rates of interchange occur between 7 - 9 Saturn radii and that this range coincides with the most intense events as defined by H+ partial particle pressure. We determine that nightside occurrence dominates as compared to the dayside injection rate, supporting the hypothesis of an inversely dependent instability growth rate on local Pedersen ionospheric conductivity. Additionally, we observe a slight preference for intense events on the dawn side, supporting a triggering mechanism related to large-scale injections from downtail reconnection. Our observed local time dependence paints a dynamic picture of interchange triggering due to both the large-scale injection driven process and ionospheric conductivity. Within this repository we provide a readme file (description of data file and usage) and the event list provided as a .txt file. The event list includes start and stop times, comparison to previous surveys, and the average location of events identified. Additional formats are available on request. , Further details on this method can be found in "Interchange Injections at Saturn: Statistical Survey of Energetic H+ Sudden Flux Intensifications" by Azari et al., 2018 in the Journal of Geophysical Research: Space Physics. https://doi.org/10.1029/2018JA025391. , and Curation notes: The files 'events_CORRECTED.txt' and 'readme_UPDATED.rtf' were added to this record July 31 and August 7, 2018 and supersede the previous data file 'events.txt' and readme file 'readme.rtf'. The file 'events.txt' uploaded May 9, 2018 should not be used, as this file contains a duplication error where the last column, InAllSurveys, is incorrectly presented as a duplicate of the column InAnySurvey. 'readme_UPDATED.rtf' contains additional context and updated references to the new data file.
- Keyword:
- Planetary Science, Automated Event Detection, Space Physics, Magnetospheric Physics, Interchange Injections, and Saturn
- Discipline:
- Science
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- Creator:
- Mason, Lacey A., Riseng, Catherine M., Layman, Andrew J., and Jensen, Robert
- Description:
- Wind exposure is a key physical driver of coastal systems in aquatic environments influencing circulation and wave dynamics. A measure of wind exposure is fetch, the distance over which wind can travel across open water. In large lake systems, such as the Laurentian Great Lakes, estimating fetch has proved to be difficult due to their vast size and complex topobathymetry. Here we describe the development of two spatially discrete indicators of exposure to provide a more accurate indicator of influence of wind exposure in the nearshore of the Laurentian Great Lakes. We summarized wind data from offshore buoys and leveraged existing tools to calculate effective fetch and relative exposure index (effective fetch scaled by mean wind speed) at a 30 m grid cell resolution. We validated these models by comparing our exposure maps to the U.S. Army Corps of Engineers Wave Information Studies models and found general agreement. These exposure maps are available for public download for the years 2004-2014.
- Keyword:
- GLAHF, Great Lakes, waves, fetch, REI, wind exposure, and geospatial
- Discipline:
- Science
-
- Creator:
- Cole, Shannon L
- Description:
- The nucleus accumbens (NAc) contains multiple subpopulations of medium spiny neurons (MSNs): one subpopulation expresses D1-type dopamine receptors, another expresses D2-type receptors, and a third expresses both. The relative roles in NAc of D1 neurons versus D2 neurons in appetitive motivation were assessed here. Specifically, we asked whether D1-Cre mice or D2-Cre mice would instrumentally seek optogenetic self-stimulation of those respective subpopulations in NAc, or instead avoid NAc laser stimulation. and Some statistical forms have been exported from SPSS for the purposes of accessibility to viewers. Please see the "readme" text for descriptions of each individual excel file.
- Keyword:
- Motivation Striatum Optogenetics
- Discipline:
- Science
-
- Creator:
- Gliske, Stephen V and Stacey, William C
- Description:
- This data is part of a large program to translate detection and interpretation of HFOs into clinical use. A zip file is included which contains hfo detections, metadata, and Matlab scripts. The matlab scripts analyze this input data and produce figures as in the referenced paper (note: the blind source separation method is stochastic, and so the figures may not be exactly the same). A file "README.txt" provides more detail about each individual file within the zip file.
- Keyword:
- hfo, high frequency oscillation, ripple, fast ripple, blind source separation, non-negative matrix factorization, and temporal variability
- Discipline:
- Science, Engineering, and Health Sciences
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- Creator:
- Ward, Jamie L ., Flanner, Mark G., Bergin, Mike, Dibb, Jack E., Polashenski, Chris M., Soja, Amber J., and Thomas, Jennie L.
- Description:
- Biomass burning produces smoke aerosols that are emitted into the atmosphere. Some smoke constituents, notably black carbon (BC), are highly effective light-absorbing aerosols (LAA). Emitted LAA can be transported to high albedo regions like the Greenland Ice Sheet (GrIS) and affect local snowmelt. In the summer, the effects of LAA in Greenland are uncertain. To explore how LAA affect GrIS snowmelt and surface energy flux in the summer, we conduct idealized global climate model simulations with perturbed aerosol amounts and properties in the GrIS snow and overlying atmosphere. The in-snow and atmospheric aerosol burdens we select range from background values measured on the GrIS to unrealistically high values. This helps us explore the linearity of snowmelt response and to achieve high signal-to-noise ratios. With LAA operating only in the atmosphere, we find no significant change in snowmelt due to the competing effects of surface dimming and tropospheric warming. Regardless of atmospheric LAA presence, in-snow BC-equivalent mixing ratios greater than ~60 ng/g produce statistically significant snowmelt increases over much of the GrIS. We find that net surface energy flux changes correspond well to snowmelt changes for all cases. The dominant component of surface energy flux change is solar energy flux, but sensible and longwave energy fluxes respond to temperature changes. Atmospheric LAA dampen the magnitude of solar radiation absorbed by in-snow LAA when both varieties are simulated. In general, the significant melt and surface energy flux changes we simulate occur with LAA quantities that have never been recorded in Greenland.
- Keyword:
- climate, Greenland Ice Sheet, black carbon, biomass burning, snowmelt, and surface energy balance
- Discipline:
- Science
-
- Creator:
- Bemmels, Jordan B. and Dick, Christopher W.
- Description:
- Raw SNP genotypes are provided in STRUCTURE format, with a maximum of one SNP reported per ddRAD locus. The files "caryco_SNP.str" and "caryov_SNP.str" are genotypes for Carya cordiformis and Carya ovata, respectively. The first column of each file is the individual name, the second column is the population (see original publication for information on population locations), and the remaining columns are genotypes of individual SNPs. Rows represent individuals, with the diploid genotypes contained on two lines per individual. Missing data are entered as "0" (zero). The first row is a header with a unique identifier for each SNP. and Occurrence records for each species are provided in the file "occs_carya.csv" and contain the latitude and longitude of each record.
- Keyword:
- eastern North America, glacial refugia, phylogeography, temperate trees, and single nucleotide polymorphisms
- Discipline:
- Science
-
- Creator:
- Mirshams Shahshahani, Payam
- Description:
- Investigating minimum human reaction times is often confounded by the motivation, training, and state of arousal of the subjects. We used the reaction times of athletes competing in the shorter sprint events in the Athletics competitions in recent Olympics (2004-2016) to determine minimum human reaction times because there's little question as to their motivation, training, or state of arousal. The reaction times of sprinters however are only available on the IAAF web page for each individual heat, in each event, at each Olympic. Therefore we compiled all these data into two separate excel sheets which can be used for further analyses.
- Keyword:
- minimum reaction time, sprinter, Olympics, Athletics, sex difference, starting block, and false start
- Discipline:
- Engineering, Health Sciences, Science, Other, and General Information Sources
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- Creator:
- Adam Schneider and Mark Flanner
- Description:
- This dataset contains all data used to generate the figures in The Cryosphere manuscript “Measuring Snow Specific Surface Area with 1.30 and 1.55 micro-meter Bidirectional Reflectance Factors,” by Adam Schneider, Mark Flanner, and Roger De Roo. These data support the theory, calibration, and application of the Near-Infrared Emitting and Reflectance Monitoring Dome (NERD), an instrument engineered to rapidly retrieve surface snow specific surface area in the field. Note that this deposit includes a microCT scan database for natural snowfall samples collected in New Hampshire during 2015-2017, comprised of raw tiff files as well as reconstructions, binarized reconstructions, and some 3D model reconstructions. and Running python scripts generally require that the following packages are installed: NumPy, SciPy, Matplotlib, Pandas, and ipdb (for debugging).
- Keyword:
- Snow specific surface area, Monte Carlo, X-ray micro-computed tomography, SNICAR, Near-Infrared Emitting and Reflectance-Monitoring Dome, Bidirectional reflectance factor, Cryosphere, and 3D
- Discipline:
- Science
-
- Creator:
- Alsip, Peter
- Description:
- Percent Weight Change Data: The model was run continuously on a daily time step for seasonal intervals (Spring: March thru May; Summer: June thru August; Fall: September thru November) as well as contiguously from Spring to Fall to assess total growth over the likely growing season (March thru November). CSV files represent the simulated weight change (%) of Bighead and Silver Carp for the respective time periods associated with the file name. Initial fish mass for each seasonal interval and growing season was 4350 g for Silver Carp and 5480 g for Bighead Carp. Maximum and mean total weight change (%) was determined for three depth ranges (near surface depths [NS]: 0 – 10 m; deep chlorophyll layer depths [DCL]: 10 - 50 m; and whole water column [WC]). Coordinates are in decimal degrees. File naming convention: speciesSeasonWtChange (e.g. bigheadFallWtChange = % weight change of Bighead Carp from September through November) , Monthly Habitat Quality Data: Rdata files contain matrices of Bighead or Silver carp growth rate potential as represented as a mass-proportional growth rate (gram of carp/gram of carp/day [g/g/d]) for the 15th day of each month. Habitats with growth rate potential >= 0 g/g/d were deemed suitable. Matrix attributes: Rows: Row numbers refer to the spatial node with 20 equally-spaced vertical layers. Columns: Columns 1-20 refer to the growth rate potential value for each vertical layer of each node. Vertical layers are evenly spaced based on the total depth of the water column for each node. Depth for each node can be found in the grid attributes data file. Columns 21 ("meanG") and 22 ("Gmax") represent the average and maximum growth rate potential, respectively, of the fish across the whole water column for the corresponding node. File naming convention: species_MonthNumber (e.g. silver_06 = Silver carp growth rate potential in June) Spatial coordinates for each node can be found in the grid attributes data files., Grid attributes data: This Rdata file provides the spatial reference data and other grid attributes. Coordinates are provided in UTM (x & y) and latitude and longitude (decimal degrees). Depth (meters) for each node is listed in this file. , GRP Model code: Details bioenergetics equations, foraging equation, functions for running the model on a monthly time-step and daily time step, and functions for basic analyses. Model is coded in R., and The simulated input data (prey and temperature) used to run our model is not included in this data set. Instead we provide the model code, grid attributes, and outputs of the model. The readRDS() function (R Base Package v.3.5.1) is required to read in .Rdata files in R.
- Keyword:
- Asian Carp, Laurentian Great Lakes, Habitat Suitability, Invasive Species, Lake Michigan, and Ecological Modeling
- Discipline:
- Science
-
- Creator:
- Thomaz, Andréa T. (UMICH) and Knowles, L. Lacey (UMICH)
- Description:
- The eastern coastal basins of Brazil are a series of small and isolated rivers that drain directly into the Atlantic Ocean. During the Pleistocene, sea-level retreat caused by glaciations exposed the continental shelf, resulting in enlarged paleodrainages that connected rivers that are isolated today. Using Geographic Information System (GIS), we infer the distribution of these paleodrainages, and their properties for the east Brazilian coast. Here, we publicly make available the shapefiles that demonstrate the paleodrainage structure along the Brazilian coast during the largest sea-level retreats in the Pleistocene, the riverine vectors during the same period and the coastal line for a drop of -125m in the sea.
- Keyword:
- Paleodrainages, Glaciations, Pleistocene, Brazil, Neotropical, and Sea-level retreat
- Discipline:
- Science
-
- Creator:
- Kort, EA, Gvakharia, A, Smith, ML, and Conley, S
- Description:
- Data is collected from research flights based in West Memphis, Arkansas, covering the Mississippi River Valley. The data file contains all merged flight data from each flight day.
- Keyword:
- Greenhouse gas
- Discipline:
- Science
-
- Creator:
- Liemohn, Michael W, McCollough, James P, Engel, Miles A, Jordanova, Vania K, and Morley, Steven K
- Description:
- There is a directory tree inside this zipped file. The main directory has the Adobe Illustrator plots of the figures in the paper, Space Weather journal manuscript # 2018SW002067, "Model evaluation guidelines for geomagnetic index predictions" by M. W. Liemohn and coauthors. The three subdirectories have the files for the individual models, the data to which they are compared, and the IDL code used to create the figure plots and metrics calculations. and Date coverage is specific to each model. The RAMSCB model covers January 2005, the WINDMI model all of 2014, and the UPOS model 1.5 solar cycles, from 1 October 2001 through 29 July 2013.
- Keyword:
- space weather, model assessment, time series metrics, and geomagnetic indices
- Discipline:
- Science
-
- Creator:
- R Paul Drake
- Description:
- The specific focus of the project was radiative shocks, which develop when shock waves become so fast and hot that the radiation from the shocked matter dominates the energy transport. This in turn leads to changes in the shock structure. Radiative shocks are challenging to simulate, as they include phenomena on a range of spatial and temporal scales and involve two types of nonlinear physics Ð- hydrodynamics and radiation transport. Even so, the range of physics involved is narrow enough that one can hope to model all of it with sufficient fidelity to reproduce the data. CRASH was focused on developing predictions for a sequence of experiments performed in Project Year 5, in which those experiments represented an extrapolation from all previously available data. The previous data involved driving radiative shocks within cylindrical structures, and mainly straight tubes. The Year 5 experiments drove a radiative shock down an elliptical tube. Our long-stated goal for these predictions was that the distribution of predicted values would overlap significantly with the observed distribution. We achieved this goal. Achieving our goal required the conversion of an established space-weather code to model radiative shocks at high energy density. To obtain reasonable fidelity with respect to the experimental data required implementing a laser absorption package, in addition to a hydrodynamic solver, electron physics and heat conduction, and multigroup diffusive radiation transport. The dedicated experiments provided evidence of experimental variability, validation of the calculation of initial shock wave behavior, and validation data at many observation times using cylindrical shock tubes. Following this were preparatory experiments for and finally the execution of the Year 5 experiments. The predictive science research included a wide range of sensitivity studies to determine which variables were important and a sequence of predictive studies focused on specific issues and sets of data. This led ultimately to predictions of shock location for the Year 5 experiments. A conclusion from this project is that the serious quantification of uncertainty in simulations is a dauntingly difficult and expensive prospect. Pre-existing codes are unlikely to have been built with attention to what will be needed to quantify their uncertainty. Pre-existing experimental results are even more unlikely to include a sufficiently detailed analysis of the experimental uncertainties. And this will also be true of most experiments that might be used to validate components of the simulation. The analysis of uncertainty in any one of the physical processes (and related physical constants) is a major effort. And addressing model form uncertainty is an even bigger challenge, that may in principle require development of complete, alternative simulation models. We made a start at all of this, and completed almost none of it. But by the end of a project, we finally had all the pieces in place and working that would have enabled a range of important studies and advances in relatively near-term years. But the sponsor terminated the program after only five years. For most of the participants this was a relatively minor development, although for a few of them it proved to be enormously disruptive. We believe that the cost to the nation, in work that was ready be done but now will not be, was much much larger. The sketch of the target was produced using a drawing program based on the experimental dimensions. The annotated photograph of the target was obtained using a visible-light camera. The colorized radiographs were obtained via backilit-pinhole radiography of a radiative shock propagating down an elliptical tube, at 26 ns after the lasers driving the shock tube fired. The graph showing lines and circles was produced by running many computer models, analyzing their statistical distribution, and measuring actual shock positions in the experiment.
- Keyword:
- Radiative shock
- Discipline:
- Science
-
- Creator:
- Ramasubramani, Vyas
- Description:
- The goal of the work is to elucidate the stability of a complex experimentally observed structure of proteins. We found that supercharged GFP molecules spontaneously assemble into a complex 16-mer structure that we term a protomer, and that under the right conditions an even larger assembly is observed. The protomer structure is very well defined, and we performed simulations to try and understand the mechanics underlying its behavior. In particular, we focused on understanding the role of electrostatics in this system and how varying salt concentrations would alter the stability of the structure, with the ultimate goal of predicting the effects of various mutations on the stability of the structure. There are two separate projects included in this repository, but the two are closely linked. One, the candidate_structures folder, contains the atomistic outputs used to generate coarse-grained configurations. The actual coarse-grained simulations are in the rigid_protein folder, which pulls the atomistic coordinates from the other folder. All data is managed by signac and lives in the workspace directories, which contain various folders corresponding to different parameter combinations. The parameters associated with a given folder are stored in the signac_statepoint.json files within each subdirectory. The atomistic data uses experimentally determined protein structures as a starting point; all of these are stored in the ConfigFiles folder. The primary output is the topology files generated from the PDBs by GROMACS; these topologies are then used to parametrize the Monte Carlo simulations. In some cases, atomistic simulations were actually run as well, and the outputs are stored alongside the topology files. In the rigid_protein folder, the ConfigFiles folder contains MSMS, the software used to generate polyhedral representations of proteins from the PDBs in the candidate_structures folder. All of the actual polyhedral structures are also stored in the ConfigFiles folder. The actual simulation trajectories are stored as general simulation data (GSD) files within each subdirectory of the workspace, along with a single .pos file that contains the shape definition of the (nonconvex) polyhedron used to represent a protein. The logged quantities, such as energies and MC move sizes, are stored in .log files. The logic for the simulations in the candidate_structures project is in the Python scripts project.py, operations.py, and scripts/init.py. The rigid_protein folder also includes the notebooks directory, which contains Jupyter notebooks used to perform analyses, as well as the Python scripts used to actually perform the simulations and manage the data space. In particular, the project.py, operations.py and scripts/init.py scripts contain most of the logic associated with the simulations.
- Keyword:
- Protein assembly, Cryo TEM, Hierarchical Assembly, Monte Carlo simulation, and Coarse-grained simulation
- Discipline:
- Science and Engineering
-
- Creator:
- Thomaz, Andréa T. (UMICH), Carvalho, Tiago P. (UFRGS), Malabarba, Luiz R. (UFRGS), and Knowles, L. Lacey (UMICH)
- Description:
- Estimated phylogenetic relationships based on more than 18,000 loci in 93 individuals (full data) or 21 individuals (subset data) representing 19 described species and two putative undescribed species. Nine files are part of this dataset, including all input files to infer the phylogenetic reconstructions and the outputs obtained, in addition to a pruned tree used to infer the ancestral state reconstructions.
- Keyword:
- dusky millions poeciliids, sexual selection, South America, and ddRADseq
- Discipline:
- Science