Pfeiffer et al_JOH-2010-168.R1_Mercurialis_01matrices

Primary data: 01 matrices (3 scoring routines) for the SSR fingerprinting (8 loci) in polyploid Mercurialis perennis; see sheet "Description" for further detail

SNP_data

Raw SNP data called from transcriptome accession no.: JV134525–JV157085 TSA NCBI, and inferred SNP data using the software PHAS

IBE_vs_IBD_tests

R scripts to perform the Mantel tests for detecting isolation-by-distance and isolation by-environment patterns using the ecodist packag

STRUCTURE

Shell scripts and results of the STRUCTURE analysis with K=1 to

sampling_sites

Lambert 3 coordinates and altitude of all sampled individual

environmental_data

A list of environmental variables characterizing the four studied sites from southern France (Ventoux, Lure, Issole and Vésubie

KASP_details

Sequences (raw data) on which primer design for KASP assay was based and SNPs therei

common_garden_data_and_Qst-Fst_tests

A series of files containing common garden data (budburst, survival and growth) from a nursery tests (see Sagnard et al. 2002) and R scripts to perform the Qst-Fst tests with the QstFstComp packag

Hierarchical (multi-site) outlier detection.

<p>Result of HBM (hierarchical Bayesian approach) on the complete <i>A</i>. <i>alba</i> dataset. <i>θ</i>_{<i>Elev(m)</i>} are locus-specific effects on genetic differentiation among populations belonging to different elevations. On the left, the estimated values of <i>θ</i>_{<i>Elev(m)</i>} with their 95% posterior credible intervals. The markers are sorted by decreasing values of <i>θ</i>_{<i>Elev(m)</i>} and the dotted lines represent the inter-quantile limits [Q₁-1.5(Q₃-Q₁); Q₃+1.5(Q₃-Q₁)]. On the right, the distribution of <i>θ</i>_{<i>Elev(m)</i>} and the fitted normal distribution. The arrow indicates the two loci detected below the neutral background in the complete dataset under a 1% probability threshold.</p

Idiosyncrasy between sites.

<p>Observed genotypic frequencies in the different sites at SNP 255 (genotypes CC, CT and TT). SNP 255 was detected by two within-site outlier detection methods (FDIST and SBM) in site 9 (purple line), but in no other site. In addition, significant GEAs were detected in site 9 (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158216#pone.0158216.s015" target="_blank">S2 Table</a>).</p