A) The proliferative lag (time to initiate proliferation), proliferative rate (population doubling time) and proliferative efficiency (change in population density) were extracted from high density growth curves (n = 2) of 86 Saccharomyces sensu stricto isolates over ∼200 environments. B) The fitness components proliferative lag, rate and efficiency were compared over all isolates and environments. Black line depicts linear correlation between the proliferative rate and efficiency (Pearson, r = 0.77). C) Hierarchical clustering of species trait averages. D) Comparing trait averages of the S. bayanus/S. kudriavzevii/S. arboricolus clade versus the S. cerevisiae/S. paradoxus/S. mikatae clade over all traits. Line indicates 1∶1 correlation. E) Frequency of significant (Student's t-test, Bonferroni correction, p<0.1) trait differences between the S. bayanus/S. kudriavzevii/S. arboricolus clade and the S. cerevisiae/S. paradoxus/S. mikatae clade, considering each class of environmental variation individually. F) Frequency of significant (Student's t-test, Bonferroni correction, p<0.1) trait differences for each species in comparison to S. cerevisiae.

A S. cerevisiae mean trait profile was calculated and the similarity (Pearson correlation) between the trait profile of each individual S. cerevisiae isolate and the S. cerevisiae mean trait profile was obtained. Strains were ranked according to degree of similarity. The universal reference strain S288C (arrow) was found to be a phenotypic extreme. * = Isolates with auxotrophic markers; these were excluded from calculations of the mean trait profile.

A) Potential loss-of-function polymorphisms in the galactose utilization pathway in the West African population; a premature stop codon in GAL3 and out of frame deletions in GAL2 and GAL4. B) A TGC→TGA (C→Stop) mutation in GAL3 associates (Bonferroni corrected Student's t-test p<0.015 and Kolmygorov-Smirnov p<0.15) to the proliferative lag during initiation of galactose proliferation in natural S. cerevisiae strains. Three West African derived genomes contain the variant mutation, 18 other strains contain the reference sequence. C) Linkage analysis of a cross between the West African DBVPG6044 and the North American YPS128 supports a link between GAL3 and poor galactose utilization. 96 haploid F1 offspring were genotyped at 130 chromosomal markers and the degree of galactose growth was determined. Chromosome numbers indicate centromere position and tick marks indicate marker position. D) Proliferation of hemizygote BY4741 (gal3Δ)×DBVPG6044 (n = 3), and the parentals DBVPG6044 (n = 2) and BY4741 (n = 2) using galactose as carbon source. E) Population doubling time (rate) and total change in population density (efficiency) of the hemizygote BY4741 (galxΔ)×273614N as compared to the parentals BY4741 and 273614 (n = 3) using galactose as carbon source. Error bars = standard errors. F) Average proliferative rates of strains in the Malaysian population (including the partially Malaysian UWOPS87-2421), the West African population (including the partially West African Y55) and all other S. cerevisiae strains, using melibiose as carbon source. Error bars = standard errors. G) Rooted N-J tree based on a multiple alignment of MEL1 from the S. cerevisiae Malaysian (UWOPS05_217_3) and West African (Y55) populations, a S. paradoxus Hawaiian isolate (UWOPS91-917.1), the S. cerevisiae MEL1 sequence stored in SGD, and previously reported MEL1 sequences from S. mikatae (S.m), S. bayanus (S.b) and S. paradoxus (S.p) [53].

A) A copy number variation in ENA gene locus associates to Na⁺ and Li⁺ tolerance in natural S. cerevisiae isolates. Strains were divided into equally sized bins on the basis of an estimate of ENA copy numbers, log[(1+observed reads)/(1+expected reads)], and the average proliferative efficiency in presence of Na⁺ and Li⁺ was determined in each bin. Error bars = standard errors. B) Linkage analysis of crosses between representatives of natural yeast populations supports co-segregation of the marker closest to the ENA locus and proliferation during Li⁺ (left panel) and Na⁺ (right panel) exposure. Left panel: a cross between the West African DBVPG6044 and the European DBVPG6765, right panel: a cross between the Sake Y12 and the European DBVPG6765. For each cross, 96 haploid F1 offspring were obtained, genotyped for parental genotype at 130 chromosomal markers loci and the proliferative ability in presence of 1 M NaCl and 0.225 mM LiCl was determined. Chromosome numbers indicate centromere position and tick marks indicate marker position. C) Unrooted N-J tree based on a multiple alignment of ENA1, 2 and 5 from the S. cerevisiae reference genome, ENA6 obtained from the mosaic CEN.PK2 strain [37], and all ENA genes detected in S. paradoxus, S. bayanus and S. mikatae. D) ENA6 from the West African derived SK1 was transferred to an ENA triple deletion (ena1Δ2Δ5Δ) in the mostly European BY4741. The proliferative rate (doubling time, h) and efficiency (density change, OD units) of the WT (ENA1,2,5), ena1Δ2Δ5Δ, and ena1Δ2Δ5Δ+ENA6 strains (n = 4–8, error bars = standard errors) in 0.5 M NaCl, 1.4 M NaCl and 0.3 M LiCl were measured. E) The proliferative rate (doubling time, h) and lag (adaptation time, h) of the WT (ENA1,2,5), ena1Δ2Δ5Δ, and ena1Δ2Δ5Δ+ENA6 strains (n = 4–8, error bars = standard errors) in pH 7, 1 mM CuCl₂, 2 M KCl, 10 mM methylglyoxal and 80 mM dihydoxyacetone (DHA).

Hierarchical clustering of Saccharomyces sensu stricto isolates based on trait profiles over 600 traits (all proliferation variables) performed using a centered Pearson correlation metric and average linkage mapping. Species are indicated by line color. For S. cerevisiae isolates, source habitats (shape) and populations (color) are indicated with symbols. Heat map depicts the relative proliferation rate (Log₂ [BY4741/strain]); relative proliferation lag and efficiency are given in Figure S7. Green = inferior proliferation, red = superior proliferation, black = BY4741 proliferation, grey = missing data.

The frequency of population specific traits for each S. cerevisiae population mapped onto a recently established population genomics tree based on low coverage genome sequence data [16]. Population specific traits were defined as traits for which the performance of one population deviated significantly from the performance of isolates in all other populations (FDR = 2%), Percentages indicate frequency of population specific traits. Total number of population specific traits: West African = 190, European = 30, North American = 13, Malaysian = 13 and Sake = 3.

A) A gene amplification of CUP1 associates strongly to copper tolerance in S. cerevisiae. The proliferative efficiency of each S. cerevisiae isolate in presence of 0.75 mM CuCl₂ versus the CUP1 gene number estimate for each strain is displayed. The gene number estimate was defined as log[(1+observed reads)/(1+expected reads)]. Linear correlation is displayed. B) To verify a causative link between the CUP1 CNV and copper tolerance, the European DBVPG6765 was crossed to the North American YPS128, 96 haploid offspring were obtained after meiotic recombination and co-inheritance of the proliferation performance during 0.75 mM CuCl2 exposure and 130 chromosomal markers was investigated using linkage analysis [26]. Chromosome numbers indicate centromere position on each chromosome and tick marks marker position. C) The CUP1 region in the West African DBVPG6044, the Sake Y12 and the European derived mosaic W303, was determined by high coverage (25–31×) sequencing. The gene arrangement in DBVPG6044 agreed with the S. paradoxus reference assembly and no amplifications were detected. For Y12 and W303, amplified segments, but not gene arrangements, could be unambiguously determined. Two independent segment amplifications were detected in Y12, encompassing only CUP1 and CUP1 plus 1624 bp of the neighboring RSC30 respectively. One amplified segment, encompassing CUP1 plus 1069 bp of RSC30, was detected in W303. Breakpoints were completely strain specific: no Y12 reads matched the W303 breakpoint and no W303 reads matched the Y12 breakpoints. The W303 amplification matched the known amplification in the S288C reference genome.