Fig 3. Genome-wide pairwise nucleotide sequence divergence to lager yeasts.

A) and C) are pairwise nucleotide divergence comparisons to a Saaz and a Frohberg representative, respectively. Comparisons are made to the Patagonia A population, the Patagonia B strains, the two North Carolina strains, and the Tibetan representative. Dots represent average values, while standard deviations from the average are represented by the colored shadow area; red for Patagonia A, dark blue for Patagonia B, blue for Tibet (T), and light blue for North Carolina (NC). B) and D) are the log₂ ratios of the minimum NC-Lager divergence (d_NC-X) and the T-Lager nucleotide divergence (d_T-X) in 50-kbp windows, where X is B) Saaz (S) or D) Frohberg (F). log₂ < 0 or >0 indicate whether that part of the genome is more closely related to T or NC, respectively. Red lines in B) and D) are significance thresholds established by permutation tests (unbiased P < 0.019). Regions lacking values are due to filters imposed based on coverage, data quality, or their absence in some strains (see S1 Text). Roman numerals represent chromosomes.