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, Ages at the nodes are shown in million years (My). The exact relationship among species is poorly resolved, Supplementary Figures and Tables Supplementary Figure B.S1, 2010.

. Rautenberg, References Supplementary Figure B.S2. Normalised difference in allelic expression levels between S. latifolia and the two outgroups without sex chromosomes S. vulgaris and S. viscosa (hereafter ?), in autosomal and sex-linked contigs in the seedling tissue. Maternal and paternal allelic read numbers were summed at SNP positions and normalised for each individual separately, then averaged among individuals for each contig. ? was computed as follows: ? =(allelic expression in S. latifolia ? allelic expression in the outgroup) / allelic expression in the outgroup). If ? is lower, higher or equal to zero, then expression in S. latifolia is respectively lower, higher or equal to the outgroup. For all contig categories, ? was compared to zero using a Wilcoxon test. The median ?, confidence intervals and p-values adjusted for, some phylogenies S. viscosa is closest to S. latifolia, whereas in others S. vulgaris is closest as shown here, and in others both species are equally diverged to S. latifolia, 2010.

*. , The Y/X ratio was computed in S. latifolia males and averaged among individuals to use as a proxy for Y degeneration. X-hemizygous contigs have a Y/X ratio equal to zero. Contigs with sex-biased expression were removed, as well as contigs with Y/X expression ratios above 1.5. Sample sizes for the different contig categories are, p.160

, Results show that the maternal allele is hyper-expressed in S. latifolia when the Y chromosome is degenerated, both in males and females. Supplementary Figure B.S3. Normalised difference in allelic expression levels between S.latifolia and the two outgroups without sex chromosomes S. vulgaris and S. viscosa (?), in autosomal and sex-linked contigs in the flower bud tissue. Same legend as Supplementary Figure B.S2 except for sample sizes for the different contig categories, autosomal contigs were randomly selected in order to have similar statistical power among gene categories)

, Supplementary Figure B.S6. Normalised difference in allelic expression levels between S.latifolia and the two outgroups without sex chromosomes S. vulgaris and S. viscosa (?), in autosomal and sex-linked contigs that were validated (see Materials and Methods section 2.5), for the flower bud tissue. Same legend as Supplementary Figure B.S2 except for sample sizes for the different contig categories