Figures and data
Proportion of S-locus homozygous offspring having reached the reproductive stage for three different S-alleles.
The test is performed relative to the expected proportion of homozygous genotypes in the offspring (25% when both parents are heterozygous; 50% when one of the parents is homozygous and the other heterozygous).
Effect of homozygosity at the S-locus on 13 phenotypic traits compared to heterozygotes.
For each trait, the phenotypic values in homozygotes (in grey) were normalised relative to the mean phenotypic values in heterozygotes (in black). The distributions were obtained by 10,000 random permutations. SD: Standard Deviation.
Linkage to the S-locus locally distorts the phylogenetic relationships.
A. The two topologies of interest cluster haplotypes either by the S-allele to which they are linked (top) or by the populations where they came (bottom). Different S-alleles are represented by symbols of different colours, different populations of origin are represented by symbols of different shapes. B. Difference in log likelihood of the two topologies of interest. Dots correspond to the difference in log likelihood for overlapping series of 50 SNPs around the S-locus for A. halleri (top panel) and A. lyrata (bottom panel). Positive values correspond to chromosomal positions where the topology by S-alleles explains the phylogeny of haplotypes better than the topology by populations. The right panels show the difference in log likelihood in the control regions. 2.5 and 97.5 percentiles of the distribution in the control regions are indicated by dashed lines.
No overall effect of S-allele dominance on the total number of 0-fold degenerate mutations (S0f) in the linked genomic regions within 25kb.
Each dot represents the mean number of mutations observed among haplotypes linked to one S-allele in one population. The correlations evaluated by a GLM are represented by lines, with confidence intervals represented in grey. A: A. halleri. Black dots correspond to the Nivelle population, grey dots to the Mortagne population. The red arrow points to the copy of Ah15, corresponding to the S-allele whose sheltered load was phenotypically characterised by Llaurens et al. 13 in Nivelle. B: A. lyrata. Red dots correspond to the IND population, black dots to the PIN population and blue dots to the TSS population.
The number of 0-fold degenerate mutations fixed in the 25kb regions flanking the S-locus increases with dominance of the S-allele associated.
Each dot represents the value obtained for haplotypes linked to one S-allele in one population. The correlations evaluated by a GLM are represented by lines, with confidence intervals represented in grey. A: A. halleri. Black dots correspond to the Nivelle population, grey dots to the Mortagne population. B: A. lyrata. Red dots correspond to the IND population, black dots to the PIN population, blue dots to the TSS population.
Stochastic simulations confirm the contrasted architecture of the load of deleterious mutations linked to dominant vs. recessive S-alleles.
Number of fixed (A), segregating (B) and total (C) deleterious mutations linked to S-alleles at four different levels of dominance (I<II<III<IV). The means (bold lines) were estimated per S-allele dominance classes over 100 replicate simulations after discarding an initial burn-in of 100,000 generations. h=0. s=0.01.
Analysis of Major Components obtained for haplotypes of A. halleri of the Nivelle (black dots) and Mortagne (grey dots) populations) based on SNPs in the first 5kb, between 5 and 25kb, and between 25kb and 50kb away from the S-locus.
The S-allele to which the SNPs are linked are represented by different symbols. The right panels show the analysis on control regions, each time matching the number of SNPs with that of the corresponding linked regions (left panels).
Analysis of major components (AMC) obtained for haplotypes of A. lyrata (of the PIN: grey dots, IND: red dots and TSS: blue dots) populations based on the SNPs in the first 5kb, between 5 and 25kb, and between 25kb and 50kb away from the S-locus.
The S-allele to which the SNPs are linked are represented by different symbols. The right panels show the analysis on control regions, each time matching the number of SNPs with that of the corresponding linked regions (left panels).
Phylogenetic tree obtained by Maximum Likelihood for haplotypes of A. halleri (populations Nivelle and Mortagne) across the first 25kb flanking the S-locus.
The Tamura-Nei model was used and the percentage of trees in which the associated haplotypes clustered together is shown next to the branches. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The black braces indicate haplotypes clustering by populations. The overall pattern shows a structure by S-alleles, with exceptions highlighted in yellow.
Phylogenetic tree obtained by maximum likelihood for haplotypes of A. halleri (populations Nivelle and Mortagne) based on the nucleotide positions between 25kb and 50kb away from the S-locus.
The Tamura-Nei model was used and the percentage of trees in which the associated haplotypes clustered together is shown next to the branches. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The black braces indicate haplotypes clustering by populations. The overall pattern shows a structure by S-alleles, with exceptions highlighted in yellow.
Phylogenetic tree obtained by maximum likelihood for haplotypes of A. lyrata (populations PIN, IND, TSS) across the first 5kb flanking the S-locus.
The Tamura-Nei model was used and the percentage of trees in which the associated haplotypes clustered together is shown next to the branches. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The black braces indicate haplotypes clustering by populations. The overall pattern shows a structure by S-alleles, with exceptions highlighted in yellow.
Phylogenetic tree obtained by maximum likelihood for haplotypes of A. lyrata (populations PIN, IND, TSS) based on the nucleotide positions between 5kb and 10kb away from the S-locus.
The Tamura-Nei model was used and the percentage of trees in which the associated haplotypes clustered together is shown next to the branches. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The black braces indicate haplotypes clustering by populations. The overall pattern shows a structure by S-alleles, with exceptions highlighted in yellow.
The genetic structure of SNPs in the S-locus flanking regions in A. halleri and A. lyrata.
Left: Mean F ST (lines) and F ST by pair (point) analysed among S-alleles (grey) or among populations (black) in 5 kb windows in the S-locus flanking regions. Right: Distribution (count) of F ST in the control regions analysed among S-alleles (grey bars) or among populations (black bars). The 95% percentiles of the distributions are represented by dotted lines and the medians by solid lines.
Patterns of genetic associations between S-alleles and SNPs across the genome.
Each dot corresponds to a SNP showing statistically significant association (top 0.1%) with a given S-allele. The left panel confirms that SNPs physically linked to the S-locus (in red) are considerably more likely to show statistical associations with S-alleles. The chromosomes were signified by alternance of black and grey. The middle panel shows a zoom on the 50kb regions flanking the S-locus and shows that the statistical association extends over long distances, at least for some S-alleles. Each region of 25 kb was delimited by vertical lines. The right panel shows that the observed number of associated SNPs in the linked regions far exceeds that in regions of identical size from control regions. The histogram shows the distribution across control regions of the mean number of significantly associated SNPs per S-allele. The vertical lines correspond to the mean number of significantly associated SNPs in the first 25kb (solid lines) and the 25-50kb interval (dashed lines) away from S-locus.
Experimental protocol.
A) We randomly crossed A. lyrata individuals from the PIN, TSS and IND populations in North America (left) and A. halleri from the Nivelle (middle) and Mortagne (right) populations. Individuals were sequenced by a capture protocol. Numbers between parentheses represent the number of individuals per dataset. B) One offspring from each cross was sequenced along with its two parents for trio haplotyping. Offspring from the Nivelle population (black circle) were conserved for the study of the impact of homozygosity at the S-locus on fitness (G1 population). C)Individuals sequenced in A and B were used to reconstruct haplotypes linked to each copy of S-allele, assuming no recombination between the S-locus and its flanking regions between parents and offspring. D) We used the dominance hierarchy between S-alleles expressed in pollen22,23 to cross G1 individuals from theNivelle population and obtained six G2 families constituted of heterozygous and homozygous individuals for the alleles Ah01, Ah03 and Ah04 . E) Description of the traits measured and the methods used to estimate the impact of homozygosity at the S-locus in homozygotes. Traits 1-8 are related to biomass and traits 10-14 are related to reproductive success.
Crosses performed to obtain homozygotes for three S-alleles. For each S-allele, we obtained homozygous and heterozygous plants within two separate families (listed as separate rows).
Trait variation in S-locus homozygous individuals.
Trait variation in homozygous at the S-locus for the S-alleles Ah01 and Ah04 between families.
Effect of dominance on variation of phenotypic traits in S-locus homozygous individuals.
Number of phased haplotypes linked to S-alleles in each sample.
Effect of dominance on the accumulation of genetic load in S-flanking regions.
S-locus genotypes of individuals sequenced using the capture protocol.
S-locus genotypes of the offspring selected for haplotype phasing and the crosses for the study of phenotypic traits.
Effect of phytopathogen, phytophagous attacks and oxidative stress on the phenotypic traits.
