Figure 1: Geographic distribution, phylogeny and population structure of S. uvarum.

(a) Maximum likelihood (ML) phylogeny of the genus Saccharomyces based on a concatenated alignment of 14 gene sequences and rooted with N. castellii. Representatives of populations of S. paradoxus (EUR, European; FE, Far Eastern; and NA, North American) and of the Australasian (AUST) and Holarctic (HOL) populations of S. uvarum are included. Support values correspond to 100 bootstrap replicates and branch lengths correspond to the mean number of nucleotide substitutions per site. (b) World map depicting the geographic origin of HOL and AUST S. uvarum strains. (c) Map of South America depicting the collecting sites. Locations are indicated by capital letters surrounded by light- or dark-orange coloured circles corresponding to populations SA-A and SA-B, respectively. The co-occurrence of strains of the two populations is depicted by light- and dark-orange semi-circles, and the occurrence of mosaic strains is depicted by white contour lines. The distribution of Nothofagus is shown in green. (d) Whole-genome Neighbor-Joining (NJ) phylogeny of 54 strains based on 129,096 SNPs and excluding introgressed regions from S. eubayanus, inferred with p-distance and rooted with S. eubayanus. The three main clades are marked by letters A, B and C. Support values from 1,000 bootstrap NJ and ML (RAxML rapid bootstrap) trees are included. Incongruent topologies between NJ and ML are denoted by grey lines. Branch lengths correspond to the mean number of base differences per site. Strains isolated from natural environments are marked by blue circles, whereas strains isolated from anthropic environments are marked by red circles. Strains having introgressions are marked with an ‘I’ in a yellow (introgressions from S. eubayanus), blue (introgressions from S. kudriavzevii) or orange (introgressions from S. cerevisiae) diamond. For the hybrid strains (marked with an ‘H’ in a white circle) or S. bayanus (‘B’ in a white circle), only introgressions in the S. uvarum sub-genome are depicted. South American mosaic strains are marked with an ‘M’ in an orange square. Clusters inferred with STRUCTURE considering all sequences (A) and all but the Australasian sequences (B) are depicted.