DOI: 10.5061/dryad.q83pt
title: Data from: The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae)

description: Population structure is a potential problem when testing for adaptive
 phenotypic differences among populations. The observed phenotypic
 differences among populations can simply be due to genetic drift, and if
 the genetic distance between them is not considered, the differentiation
 may be falsely interpreted as adaptive. Conversely, adaptive and
 demographic processes might have been tightly associated and correcting
 for the population structure may lead to false negatives. Here, we
 evaluated this problem in the cosmopolitan weed Capsella bursa-pastoris.
 We used RNA-Seq to analyse gene expression differences among 24
 accessions, which belonged to a much larger group that had been previously
 characterized for flowering time and circadian rhythm and were genotyped
 using genotyping-by-sequencing (GBS) technique. We found that clustering
 of accessions for gene expression retrieved the same three clusters that
 were obtained with GBS data previously, namely Europe, the Middle East and
 Asia. Moreover, the three groups were also differentiated for both
 flowering time and circadian rhythm variation. Correction for population
 genetic structure when analysing differential gene expression analysis
 removed all differences among the three groups. This may suggest that most
 differences are neutral and simply reflect population history. However,
 geographical variation in flowering time and circadian rhythm indicated
 that the distribution of adaptive traits might be confounded by population
 structure. To bypass this confounding effect, we compared gene expression
 differentiation between flowering ecotypes within the genetic groups.
 Among the differentially expressed genes, FLOWERING LOCUS C was the
 strongest candidate for local adaptation in regulation of flowering time.
description: Gene expression read
 counts for Capsella bursa-pastorisThis file contains
 expression values obtained using RNA-seq data for 24 accessions of
 Capsella bursa-pastoris. Read counting was performed using htseq-count
 program from HTSeq software v0.6.1 (Anders et al. 2014). Only reads mapped
 to non-overlapping feature positions were counted (htseq-count option: -m
 union).Cbp_RNA-Seq_HTseq_counts.zipR scripts: edgeR analysуs of Capsella bursa-pastorisThese scripts were used to perform differential gene expression analysis between and within the genetic groups (ASI, EUR, ME) of Capsella bursa-pastoris.Cbp_RNA-Seq_edgeR.R.zipR scripts: MCMCglmm analyses of Capsella bursa-pastorisThese scripts were used to perform correction for population structure in the analyses of gene expression and phenotypic variation in Capsella bursa-pastoris.Cbp_RNA-Seq_MCMCglmm.R.zipR script: Phenotypic and Environmental data analysesThis script was used to analyze phenotypic variation (flowering time and circadian rhythm) in Capsella bursa-pastoris and climatic characteristics of its collection sites.Cbp_RNA-Seq_Phenotype-Environment.R.zipPhylogentic relationships between accessions of Capsella bursa-pastorisThese phylogenetic trees were reconstructed using the GTRGAMMA model in RAxML v8.2.4 (Stamatakis et al. 2012)⁠ for 21 and 263 accessions that had SNPs data available (Cornille et al. 2015). A random tree was generated using the rcoal function from the ape package in R (Paradis et al. 2004)Cbp_RNA-Seq_RAxML_Trees_GBS_nwk.zip