DOI: 10.5061/dryad.m1b66
title: Data from: Epigenetic variation reflects dynamic habitat conditions in a rare floodplain herb

description: Variation of DNA-methylation is thought to play an important role for
 rapid adjustments of plant populations to dynamic environmental
 conditions, thus compensating for the relatively slow response time of
 genetic adaptations. However, genetic and epigenetic variation of wild
 plant populations has not yet been directly compared in fast changing
 environments. Here we surveyed populations of Viola elatior from two
 adjacent habitat types along a successional gradient characterized by
 strong differences in light availability. Using AFLP and MSAP analyses we
 found relatively low levels of genetic (H’gen=0.19) and epigenetic
 (H’epi=0.23) diversity and high genetic (ϕST=0.72) and epigenetic
 (ϕST=0.51) population differentiation. Diversity and, respectively,
 differentiation were significantly correlated, suggesting that epigenetic
 variation partly depends on the same driving forces as genetic variation.
 Correlation based genome scans detected comparable levels of genetic
 (17.0%) and epigenetic (14.2%) outlier markers associated with site
 specific light availability. However, as revealed by separate
 differentiation based genome scans for AFLP, only few genetic markers
 seemed to be actually under positive selection (0-4.5%). Moreover, PCoA
 and Mantel tests showed that overall epigenetic variation was more closely
 related to habitat conditions, indicating that environmentally-induced
 methylation changes may lead to convergence of populations experiencing
 similar habitat conditions and may thus play a major role for the
 transient and/or heritable adjustment to changing environments.
 Additionally, using a new MSAP scoring approach, we found that mainly the
 unmethylated (ϕST=0.60) and CG-methylated states (ϕST=0.46) of epiloci
 contributed to population differentiation and putative habitat related
 adaptation, whereas CHG-hemimethylated states (ϕST=0.21) only played a
 marginal role.
description: AFLP
 dataPresence/absence matrix
 (1/0) of AFLP markers. The first column provides the sample ID (population
 ID + individual sample number) and the first row provides the marker ID
 (selective primer combination + fragment size).MSAP
 dataMSAP data at different
 levels of data processing: The spreadsheet “Raw_msap_calc” contains the
 input file for msap_calc.R, spreadsheet “MSAP Raw Data” contains the
 multistate data of combined HpaII and MspI profiles at the epilocus level,
 and spreadsheet “MSAP Subepiloci Data” contains the final binary data at
 the subepilocus level. For “Raw_msap_calc” the first three columns provide
 the population ID, the sample ID (population ID + individual sample
 number) and used methylation sensitive restriction enzymes (H=HpaII,
 M=MspI). The first row provides the marker ID (selective primer
 combination + fragment size). For “MSAP Raw Data” and “MSAP Subepiloci
 Data” the first column provides the sample ID and the first row provides
 the marker ID. In addition, for “MSAP Subepiloci” the three subepiloci
 types (n, m, h) are indicated in the second row.plant sampling &
 hemispherical photographyGrid based distribution
 maps (1 x 1m) and results of hemispherical photography based light
 measurements for the six surveyed populations of Viola elatior. Populated
 grid cells, grid cells for plant sampling and grid cells for hemispherical
 photographs are indicated by different colors,
 respectively.