Fig 1.
Admixture graph of population relationships shows admixture from the Asia/sake to multiple beer populations.
Population relationships were inferred using TreeMix, and horizontal branch lengths are proportional to genetic drift with the scale bar showing the average of 10 s.e. of the sample covariance matrix. Red arrows show admixture events with migration weights over 0.40, indicating the fraction of alleles derived from a source population. Migration from the ancestor of the Mediterranean/oak to the Clinical population is not shown for clarity. The data underlying this figure are available from http://doi.org/10.6084/m9.figshare.7550009.v1. s.e., standard errors.
Fig 2.
Diploid, triploid, and tetraploids are distinguished by read counts at heterozygous sites.
Plots show examples of a (A) diploid (YO700), (B) triploid (TUM205), and (C) tetraploid (YMD1952) strain by the number of reads with the reference allele (A) versus the alternative allele (B) for heterozygous (red) and homozygous (black) sites. The data underlying this figure are available from http://doi.org/10.6084/m9.figshare.7550009.v1.
Fig 3.
Beer populations are heterozygous for alleles shared with Europe/wine and Asia/sake populations.
Genotypes of 2,000 randomly selected SNPs are shown for 339 strains grouped by their ancestry to 13 populations shown by the colored panel on the left. Genotypes are homozygous for the major allele (black), minor allele (red), or heterozygous (yellow), and SNPs (columns) were ordered by hierarchical clustering. The panel on the right indicates triploid and tetraploid strains, grape and sake wine strains, and ale, lager, and baking strains. The data underlying this figure are available from http://doi.org/10.6084/m9.figshare.7550009.v1.
Fig 4.
Phased haplotypes show recombination between European and Asian alleles.
Panels for two ale strains (T.58 and A.2565) and the control hybrid (YJF1460) show haplotypes and allele configurations across chromosome XI. The purple panel shows haplotypes with more than 95% European or Asian alleles in red and blue, respectively, and in gray otherwise. Ticks indicate European (red) and Asian (blue) alleles. Haplotypes were assigned labels H1–H4 in order of longest to shortest, except for YJF1460 in which they were assigned based on predominance of Europe/wine (H1, red) or Asia/sake (H2, blue) alleles. The green panel shows ale-specific alleles for the four haplotypes (H1–H4) by green ticks. The first 100 kb of A.2565 shows a region exhibiting loss of heterozygosity. The data underlying this figure are available from http://doi.org/10.6084/m9.figshare.7550009.v1.