Data from: Ecotypes of an ecologically dominant prairie grass (Andropogon gerardii) exhibit genetic divergence across the U.S. Midwest grasslands environmental gradient

Gray MM, St. Amand P, Bello NM, Knapp M, Garrett KA, Morgan TJ, Baer SG, Maricle BR, Akhunov ED, Johnson LC, Galliart MB

Date Published: November 6, 2014

DOI: http://dx.doi.org/10.5061/dryad.tp96r

 

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Title ReadMe
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Description Data description file.
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Title Site Weather Data
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Description A compilation of daily weather data for various sites close to the eleven prairie collection sites of this study. Data was derived from NCDC Summary of the Day data set. Available for download also at: http://www.ksre.ksu.edu/wdl/Datafiles.htm
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Title AFLP Raw Genotypes
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Description This file contains the AFLP raw genotype scores (1=presence of AFLP band; 0=absence of AFLP band) for each of the 387 AFLP markers scored across 378 big bluestem (Andropogon gerardii) individual plants.
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Title Pairwise geographic distances between prairie sites
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Description This file contains an 11 x 11 matrix of pairwise geographic distances (in kilometers) among the eleven focal prairie populations.
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Title Allele Counts
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Description This file contains an 11 x 387 matrix of the number of samples where a selected allele of the AFLP loci was observed.
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Title Plant Sample Sizes Per AFLP Locus
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Description This file contains an 11 x 387 matrix of the number of individual plants available for each of the 387 AFLP loci.
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Title Bayescan 2.1 Input File
Downloaded 24 times
Description This is the input file for BayeScan 2.1 of 325 AFLP loci with frequencies ≥2% structured according to ecotype region: pop 1=Central Kansas [CKS], pop2=Southern Illinois [SIL], pop3=Eastern Kansas [EKS].
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Title STRUCTURE Input Data File by Ecotype
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Description Use this file as input into STRUCTURE. Locations labeled by ecotype region.
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Title STRUCTURE Input Data File by Prairie
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Description Use this file as input into STRUCTURE. Locations labeled by prairie.
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Title BEDASSLE Illustrative Code
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Description Illustrative code for implementation of BEDASSLE in this study.
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Title BAYENV2 Input File - All Markers
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Description Use this file as the 'control loci' input for BayEnv2. This file is analogous to the 'SNPSFILE' described in BayEnv2.
Download bayenv2_aflp_allmarkers.txt (23.42 Kb)
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Title BAYENV2 Input File - Outliers Removed
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Description Use this file as 'control loci' input into BayEnv2. This file is analogous to the 'SNPSFILE' described in BayEnv2. This file contains all AFLP loci except the top 14 most differentiated outlier loci have been removed.
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Title BAYENV2 Covariance Matrices
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Description Resulting covariance matrices after removing the 14 top-ranked outliers from the 'control loci' data set. Tabs separate each successive covariance matrix. These matrices result from independent runs of 10^6 iterations.
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Title BAYENV2 Input File - Individual AFLP Loci
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Description Allele count data for a single AFLP locus parsed into individual files. Use these 384 AFLP count data as the individual files as analogous to the 'SNPFILE' input data for BayEnv2. Data occur in the same prairie population order that they occur in the covariance matrix and 'bayenv2_aflp_outliersrem.txt' file.
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Title BAYENV Output - XTX
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Description Resulting XtX statistic output from BayEnv2 for each of the 384 polymorphic AFLP loci.
Download bayenv2_aflp_XtX.xlsx (65.49 Kb)
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When using this data, please cite the original publication:

Gray MM, St Amand P, Bello NM, Galliart MB, Knapp M, Garrett KA, Morgan TJ, Baer SG, Maricle BR, Akhunov ED, Johnson LC (2014) Ecotypes of an ecologically dominant prairie grass (Andropogon gerardii) exhibit genetic divergence across the U.S. Midwest grasslands environmental gradient. Molecular Ecology 23(24): 6011-6028. http://dx.doi.org/10.1111/mec.12993

Additionally, please cite the Dryad data package:

Gray MM, St. Amand P, Bello NM, Knapp M, Garrett KA, Morgan TJ, Baer SG, Maricle BR, Akhunov ED, Johnson LC, Galliart MB (2014) Data from: Ecotypes of an ecologically dominant prairie grass (Andropogon gerardii) exhibit genetic divergence across the U.S. Midwest grasslands environmental gradient. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.tp96r
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