Experimental set-up.

(A) Location of the 6 field sites and origin of the 200 accessions. (B) Heat-map showing kinship between the accessions, hierarchically clustered by similarity. Marginal colors indicate membership in one of four genetic groups—the same colors are used for the sampling locations in panel A. Numbers are FST estimates between groups. (C) Schematic of the experiments. In the common-garden experiments, which were replicated over two consecutive seasons, established seedlings (3 blocks of 8 replicates of 200 accessions per experiment) were transplanted into the field in fall, and overwinter survival and fecundity assessed the following spring. In the evolution experiments, seeds were sown in equal numbers in early fall 2011 and surviving descendants sequenced before flowering in 2013.

Figure 1—figure supplement 1. Population structure in the 200 Swedish accessions.

Figure 1—figure supplement 2. The correlation of allele frequencies between the genetic groups.

Figure 1—figure supplement 3. Photos of field sites: common gardens

Figure 1—figure supplement 4. Photos of field sites: selection experiments

Figure 1—source data 1. Table of accessions used.

Figure 1—source data 2. SNP matrix.

The distribution of accession survival probabilities across sites and years. Numbers in plots give total mortality in each experiment.

Figure 2—figure supplement 1. The distribution of survival probabilities across experiments by group.

Figure 2—source data 1. Overwinter survival data.

The joint distribution of accession survival probabilities between the three experiments with significant mortality.

The curves were fitted using the S1 accessions only.

Overwinter survival was affected by herbivory.

Left: Slug damage in the SR 2011-12 experiment affected groups differently (Kruskal-Wallis test: p < 0.01 for all comparisons). Right: Average slug damage for an accession decreased its probability of survival (ANOVA: p = 1.6 × 10−23).

Figure 4—figure supplement 1. Overwinter survival was also affected by underlying susceptibility to stress.

Figure 4—source data 1. Slug damage data.

Quantile-quantile plots of p-values for overwinter survival GWAS against the expected uniform distribution.

Left plot without correction for structure; right plot including a standard mixed-linear model kinship correction. Only SNPs with Minor Allele Frequency (MAF) greater than 5% were included to avoid outlier affects. Experiments with significant mortality exhibit genome-wide inflation of significance, while remaining experiments demonstrate that tails are inflated even for noise phenotypes.

Figure 5—figure supplement 1. Manhattan plots without structure correction.

Figure 5—figure supplement 2. Manhattan plots with structure correction.

Figure 5—figure supplement 3. Zoom-in on AOP region.

Figure 5—figure supplement 4. Zoom-in on SVP region.

Variance-partitioning (ANOVA) from full model of fecundity.

The loadings of the first three PCs from a PCA of the fecundity BLUPs on the eight experiments.

Figure 7—figure supplement 1. The distribution of each PC by group.

Figure 7—figure supplement 2. Positions of accessions in PC1-PC2 space.

Figure 7—figure supplement 3. Positions of accessions in PC2-PC3 space.

The distribution of fecundity BLUPs for each experiment by group.

Figure 8—figure supplement 1. Accession fecundity is correlated with overwinter survival.

Figure 8—source data 1. Fecundity BLUPs.

The distribution of fecundity BLUPs for each group by year and site (cf.

Figure 8).

GWAS of rosette purpleness in SU 2011-12 identifying Production of Anthocyanin Pigment 2, (PAP2, AT1G66390), located on chromosome 1 between 24,763,941 and 24,765,541 bp.

A. Genomen-wide Manhattan plot B. Zoom-in on the 100 kb window around PAP2, represented by the orange bar.

Quantile-quantile plots for GWAS fecundity data.

Left plot without correction for structure; right plot including a standard mixed-linear model kinship correction. The extreme confounding for SR 12 reflects the unusually large difference between S1/S2 and B/N in this experiment (Figure 8). Only SNPs with Minor Allele Frequency (MAF) greater than 5% were included to avoid outlier affects.

Figure 11—figure supplement 1. Manhattan plots for fecundity GWAS without correction for structure.

Figure 11—figure supplement 2. Manhattan plots for fecundity GWAS with correction for structure.

Scatter-plots comparing estimated accession frequencies in the four selection experiments.

Accessions that are potential natives in a site are indicated by color and the two obvious outliers (Bar1 in NB, and Vår2-6 in ST) are highlighted.

Figure 12—figure supplement 1. Same as Figure 12, but with the two obvious outliers removed to show remaining data better.

Figure 12—source data 1. Estimated fitnesses from evolution experiments.

The distribution of the estimated relative fitness by genetic group (same data as in Figure 12 but rescaled by dividing by the expected frequency in the absence of selection).

Left: The distribution of seed size (data from Clauw et al., 2022) by genetic group. Right: Mean fitness (from Figure 13) as a function of seed size.

Mean fitness as functions of various phenotypes related to seedling establishment.

A. Root length, from Slovak et al. (2020). B. Same as A, but corrected for seed size, which was positively correlated with early root growth. C. Hypocotyl elongation. D. Primary seed dormancy, from Kerdaffrec et al. (2016).

Figure 15—figure supplement 1. Fitness as a function of hypocotyl elongation in each experiment.

Figure 15—figure supplement 2. Fitness as a function of primary seed dormancy in each experiment.

Seed size distribution for 246 additional accessions sampled from 9 sites in southern Sweden in 2017 (see Methods).

The top 6 sites were located on beaches and the bottom 3 were located inland. The experimental B accessions hail from the top four sites.

Left: results of selection scan for chromosome 1. Right: scatter plot of p-values from selection scan (all chromosomes) vs. seed size GWAS.

Figure 17—figure supplement 1. Zoom-in of selection scan for chromosome 1 peak.

Figure 17—figure supplement 2. Result of selection scan for chromosomes 2–4.

Figure 17—source data 1. Results of selection scan.

The 200 accessions plotted in the simplex space generated by the K = 4 admixture proportions.

Sowing and installation date for common-garden experiments.

Blocks A–C were sown with two-day intervals.

Workflow for classifying selection experiment samples.

Figure 19—figure supplement 1. The number of samples in each category per site and plot.

Figure 19—source data 1. Accession frequencies after selection.

Isolation-by-distance in Swedish A. thaliana.

On the left, sample locations and the decay in pairwise identity as a function of distance using the data of Platt et al. (2010a); on the right, the same plots for the new samples from Skåne (Figure 16). The blue dots show the sites used in the evolution experiments.

Figure 20—source data 1. Location and genotypes of new samples.

Top: the distribution of Δ p in the four selection experiments. Middle: the variance of Δ p as a function of p0(1 − p0). Bottom: the distribution of Δ p scaled by its standard deviation. The curves are PDFs of normal distributions with the observed mean and variance 1.

Figure 21—source data 1. Allele frequencies before and after selection.