Linkage date estimates across Microbotryum. Linkage between mating-type loci (PR and HD) and centromeres, or between PR and HD loci, was inferred from dates of divergence between alleles associated to the a1 and a2 mating types at genes linked to the mating-type loci. In gene genealogies, nodes separating alleles associated to the a1 and a2 mating types within species correspond to the date of linkage to the mating-type loci (to the HD locus in blue and to the PR locus in purple). Genealogies of alleles associated to the alternative mating types (a1 and a2) were reconstructed based on a concatenated alignment of both alleles at nine genes ancestrally located between the centromere and the HD-proximal region (8525 aligned codons) and of 10 genes ancestrally located between the centromere and the PR-proximal region (10,200 aligned codons). The genes used for this analysis, with both alleles in all species, are indicated by red arrows in Figure 4. (A) Marginal posterior densities for the most recent common ancestor date (MRCA time) estimated with BEAST v2.4.0 based on multiple sequence alignments of genes located between the HD-proximal (blue) or the PR-proximal (light purple) region and the corresponding centromeres in the ancestral gene order. (B) Time-calibrated tree of a1 and a2 alleles with nodes drawn at the mean date (in million years [MY]) for the genes on the HD chromosome. Inferred divergence dates for the genes located between the HD-proximal or the PR-proximal regions and the corresponding centromeres are shown in blue or purple fonts, respectively, to the right of the nodes. Light blue and light purple bars correspond to 95% confidence intervals. Speciation dates as inferred from each data set are shown in black font on the right side of the nodes (bottom, PR set; top, HD set).
