Diversity of HD1/HD2 alleles and evolution of HD1 in two different clades of red yeast species. (a) Phylogeny of the HD1/HD2 alleles in two groups of red yeasts. Abbreviations of generic names are as in Figure 1. Strains belonging to the same species are indicated by boxes of the same colour after strain numbers: Clade A - S. salmonicolor (green) and S. johnsonii (light green); clade B - Rh. glutinis (red), R. babjevae (pink) and Rh. graminis (light pink). R. diobovatum formed a more divergent group external to clade B. Sexual (MAT A1/A2), asexual and self-fertile strains are indicated as "A1/A2", "As" and "Sf", respectively, after strain numbers. Circles before each strain depict the type of pheromone receptor genes (yellow, STE3.A1; blue, STE3.A2). White stars in tree branches symbolize premature stop codons detected in the corresponding HD2 alleles. Branch lengths are given in number of substitutions per site. Bootstrap values (>50%) from 1000 replicates are shown. (b) Posterior probabilities of site classes for codons along the N-terminal and HD domains of the HD1 gene, obtained under model M8 (beta&ω) for the clade B dataset. The first six categories are collapsed into one, represented as ω < 0.26 (purifying selection) as well as the categories seven to ten that are represented as 0.26 < ω < 0.92. (c) Posterior probabilities obtained for the dataset of clade A under the model M8. The first 5 categories are collapsed into one (ω <0.26) as well as the categories six to ten (0.26 < ω < 0.93). Sites for which the posterior probability for the site class of positive selection (with ω > 1) exceeds 0.80 are inferred to be under diversifying selection and are indicated by asterisks (see Supplementary Tables S1 and S2 in Additional File 4 for details).