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.
Data description file.
Site Weather Data
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
AFLP Raw Genotypes
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.
Pairwise geographic distances between prairie sites
This file contains an 11 x 11 matrix of pairwise geographic distances (in kilometers) among the eleven focal prairie populations.
This file contains an 11 x 387 matrix of the number of samples where a selected allele of the AFLP loci was observed.
Plant Sample Sizes Per AFLP Locus
This file contains an 11 x 387 matrix of the number of individual plants available for each of the 387 AFLP loci.
Bayescan 2.1 Input File
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].
STRUCTURE Input Data File by Ecotype
Use this file as input into STRUCTURE. Locations labeled by ecotype region.
STRUCTURE Input Data File by Prairie
Use this file as input into STRUCTURE. Locations labeled by prairie.
BEDASSLE Illustrative Code
Illustrative code for implementation of BEDASSLE in this study.
BAYENV2 Input File - All Markers
Use this file as the 'control loci' input for BayEnv2. This file is analogous to the 'SNPSFILE' described in BayEnv2.
BAYENV2 Input File - Outliers Removed
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.
BAYENV2 Covariance Matrices
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.
BAYENV2 Input File - Individual AFLP Loci
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.
BAYENV Output - XTX
Resulting XtX statistic output from BayEnv2 for each of the 384 polymorphic AFLP loci.