PMC

The phylogeny was obtained by the neighbour-joining method on pairwise proportion of nucleotide divergence after Jukes-Cantor's correction. Brackets indicate interspecific pairs of sequences assumed to represent “trans-specifically shared S-alleles”, i.e. alleles assumed to have evolved from a single S-allele in the direct ancestor of A. lyrata and A. halleri.

Note the distinct peak of highly similar sequences observed. The vertical arrow represents the chosen threshold to define “trans-specifically shared” pairs of sequences (≤12 nucleotide differences). Note also that the two pairs of sequences with intermediate nucleotide differences (45 between AlSRK03 and AhSRK28, and 50 between AlSRK28 and AhSRK03) cannot represent trans-specifically shared S-alleles because they are not monophyletic (see ).

Divergence times were taken from Koch et al. ,. θ_lyrata, θ_halleri and θ_A, refer to polymorphism (θ = 4Nμ· in A. lyrata, A. halleri and their common ancestor. As compared to unlinked genes, divergence between trans-specifically shared S-alleles is affected by two confounding factors: (1) lower effective population size than the genomic background reducing coalescence time in the ancestral species, and (2) expected higher introgression as represented by thicker dark grey arrows.

10,000 coalescent simulations were performed for each case using maximum likelihood parameter estimates obtained under the “isolation with migration” model, except for the dotted line, where the 2.5% low ancestral population size estimate was used in order to be conservative. Observed nucleotide divergence for the genomic background and S-alleles are represented by grey and black stars on the x-axis, respectively.