DOI: 10.5061/dryad.tp96r
title: Data from: Ecotypes of an ecologically dominant prairie grass (Andropogon gerardii) exhibit genetic divergence across the U.S. Midwest grasslands environmental gradient

description: Big bluestem (Andropogon gerardii) is an ecologically dominant grass with
 wide distribution across the environmental gradient of U.S. Midwest
 grasslands. This system offers an ideal natural laboratory to study the
 nature of population divergence and adaptation in spatially varying
 climates. Objectives were to: (i) characterize neutral genetic diversity
 and structure within and among three regional ecotypes derived from 11
 prairies across the U.S. Midwest environmental gradient, (ii) distinguish
 between the relative roles of isolation-by-distance (IBD) vs.
 isolation-by-environment (IBE) on ecotype divergence, (iii) identify
 outlier loci under selection, and (iv) assess the association between
 outlier loci and climate. Using two primer sets, we genotyped 378 plants
 at 384 polymorphic AFLP loci across regional ecotypes from central and
 eastern Kansas, and Illinois. Neighbor-joining tree and PCA revealed
 strong genetic differentiation between Kansas and Illinois ecotypes, which
 was better explained by IBE than IBD. High genetic variability within
 prairies was found (80%) and even fragmented Illinois prairies,
 surprisingly, contain high within-prairie genetic diversity (92%). Using
 Bayenv2, we identified 14 top-ranked outlier loci among ecotypes to be
 associated with temperature and precipitation variables. Six of seven
 BayeScan FST-outliers were also found in common with Bayenv2 outliers.
 High genetic diversity may enable big bluestem populations to better
 withstand changing climates; however, population divergence supports the
 use of local ecotypes in grassland restoration. Knowledge of genetic
 variation in this ecological dominant and other grassland species will be
 critical to understanding grassland response and restoration challenges in
 the face of a changing climate.
description: ReadMeData description
 file.Site Weather
 DataA
 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.htmweather.csvAFLP Raw GenotypesThis 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.aflp_raw_genotypes.csvPairwise geographic distances between prairie sitesThis file contains an 11 x 11 matrix of pairwise geographic distances (in kilometers) among the eleven focal prairie populations.pairwise_geographic_distances.csvAllele CountsThis file contains an 11 x 387 matrix of the number of samples where a selected allele of the AFLP loci was observed.allele_counts.csvPlant Sample Sizes Per AFLP LocusThis file contains an 11 x 387 matrix of the number of individual plants available for each of the 387 AFLP loci.sample_sizes.csvBayescan 2.1 Input FileThis 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].bayescan_input.txtSTRUCTURE Input Data File by EcotypeUse this file as input into STRUCTURE. Locations labeled by ecotype region.STRUCTURE_ECOTYPE.txtSTRUCTURE Input Data File by PrairieUse this file as input into STRUCTURE. Locations labeled by prairie.STRUCTURE_PRAIRIE.txtBEDASSLE Illustrative CodeIllustrative code for implementation of BEDASSLE in this study.BEDASSLE_Illustrativecode.R.txtBAYENV2 Input File - All MarkersUse this file as the 'control loci' input for BayEnv2. This file is analogous to the 'SNPSFILE' described in BayEnv2.bayenv2_aflp_allmarkers.txtBAYENV2 Input File - Outliers RemovedUse 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.bayenv2_aflp_outliersrem.txtBAYENV2 Covariance MatricesResulting 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.BAYENV2_covariance_matrices.zipBAYENV2 Input File - Individual AFLP LociAllele 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.BAYENV2_AFLPFILES.zipBAYENV Output - XTXResulting XtX statistic output from BayEnv2 for each of the 384 polymorphic AFLP loci.bayenv2_aflp_XtX.xlsx