Volume 26, Issue 20, Pages 2750-2761 (October 2016) Distinct Domestication Trajectories in Top-Fermenting Beer Yeasts and Wine Yeasts  Margarida Gonçalves, Ana Pontes, Pedro Almeida, Raquel Barbosa, Marta Serra, Diego Libkind, Mathias Hutzler, Paula Gonçalves, José Paulo Sampaio  Current Biology  Volume 26, Issue 20, Pages 2750-2761 (October 2016) DOI: 10.1016/j.cub.2016.08.040 Copyright © 2016 Elsevier Ltd Terms and Conditions

Current Biology 2016 26, 2750-2761DOI: (10.1016/j.cub.2016.08.040) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 1 Phylogeny of S. cerevisiae Top-Fermenting Beer Strains Based on Whole-Genome Sequences Phylogeny of 90 strains, inferred from 56 577 single nucleotide polymorphisms (SNPs), using the maximum likelihood method as implemented in RAxML with the GTRGAMMA model of sequence evolution and rooted with S. paradoxus. Branch lengths correspond to the expected number of substitutions per site. Support values from bootstrap replicates above 90% are shown. The analysis includes representatives of different types of beer starter cultures and of previously described populations (wine, Mediterranean oaks, sake, Philippines, North American and Japanese oaks, West Africa, and Malaysia). Branch colors highlight phylogenetic groups, and the ecology or industrial application of each strain is indicated in color-coded circles after strain designation. The functionality or the inactivation of PAD1, FDC1, AQY1, and AQY2 are color coded. WWA, wine-West Africa; BBSP, beer-bread-sake-Philippines; WBGaEa, wine-bread-German alt-English ale. See also Figures S1, S2, and S3 and Table S1. Current Biology 2016 26, 2750-2761DOI: (10.1016/j.cub.2016.08.040) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 2 Phylogenetic Relationships of the S. cerevisiae Sub-genomes of Lager Yeasts (A and B) Simplified phylogenies prepared following the methodologies employed in Figure 1 but including only strains of the beer, wine, and bread clades (A) and the S. cerevisiae sub-genomes of lager yeasts from the Saaz and Frohberg groups (B). The phylogeny in (A) is based on 12 303 SNPs and the phylogeny in (B) is based on 2 162 SNPs. See also Table S1. Current Biology 2016 26, 2750-2761DOI: (10.1016/j.cub.2016.08.040) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 3 Multiple Inactivations of PAD1, FDC1, AQY1, and AQY2 in Beer Strains (A–D) Median-joining networks of protein haplotypes of Pad1 (A), Fdc1 (B), Aqy1 (C), and Aqy2 (D), generated with NETWORK. The size of the circles is proportional to the number of strains they represent, and colors depict phylogenetic groups. The different protein inactivations are highlighted by colored diamonds (color codes as in Figure 1). Branches that are not affected by a given inactivation are signaled by an open diamond. Additional sequences for Pad1 and Fdc1 [22] and for Aqy1 and Aqy2 [24] were also included. See also Data S3. Current Biology 2016 26, 2750-2761DOI: (10.1016/j.cub.2016.08.040) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 4 Copy Number Variation of Genes Involved in the Metabolism of Maltose and Related Compounds (A and B) Darker color shades depict increased numbers of gene copies, and strains are highlighted according to their source (A). Copy number variation (CNV) of actin (ACT1) is indicated as reference, and the chromosome localization of each surveyed gene is indicated. Statistical significant differences of CNV between groups of strains (p < 0.05) are highlighted in red (B). See also Table S1. Current Biology 2016 26, 2750-2761DOI: (10.1016/j.cub.2016.08.040) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 5 Population Structure of S. cerevisiae STRUCTURE plot based on a subset of 10 298 parsimony informative sites for K = 9. Numbers 1–6 represent the different clusters that capture the maximum representation of population ancestry. The phylogenetic groups inferred in Figure 1 are indicated at the top of the plot (PHILI, Philippines; NA-JP, North America-Japan; WA, West Africa; M-T, Malaysia-Taiwan). See also Table S1. Current Biology 2016 26, 2750-2761DOI: (10.1016/j.cub.2016.08.040) Copyright © 2016 Elsevier Ltd Terms and Conditions