Fig 6. Syn OS-A /Syn OS-B′ divergence.

(A) The spectrum of synonymous, d_s, and non-synonymous, d_n, distances between Syn OS-A and Syn OS-B′ for their 1933 homologous genes (defined as reciprocal best BLAST hits with e-values < 1e − 100). In blue is a moving average of d_n over windows of size 0.05 in d_s. The genome-wide MLE ratio of d_n/d_s = 0.104 is shown (gray, from concatenating all loci together, see Methods), as well as the linear least squares fit of d_n = 0.104d_s − 0.007 for the 1726 well-diverged homologues with d_s ≥ 0.3 (dashed black). (B-C) Histograms of the spectrum of synonymous (B) and non-synonymous (C) distances between the well-diverged homologues of Syn OS-A and Syn OS-B′. (B) Distribution (purple) of the number of conserved four-fold degenerate amino acids (A,G,P,T,V) with at least one synonymous SNP and the maximum likelihood distribution (green) under the assumption of asexual divergence with a single coalescence time, T_c with θ_s = 2T_cμ = 0.620 the probability for each four-fold degenerate codon to have mutated since the most recent common ancestor of Syn OS-A and Syn OS-B′. (C) Distribution of the amino acid distances (purple) and the maximum likelihood distribution (green) under the asexual single coalescence time model with θ_n = 0.113. Note the large excess over the null model at small distances.