Sequence diversity, reproductive isolation and species concepts in Saccharomyces

Abstract

Using the biological species definition, yeasts of the genus Saccharomyces sensu stricto comprise six species and one natural hybrid. Previous work has shown that reproductive isolation between the species is due primarily to sequence divergence acted upon by the mismatch repair system and not due to major gene differences or chromosomal rearrangements. Sequence divergence through mismatch repair has also been shown to cause partial reproductive isolation among populations within a species. We have surveyed sequence variation in populations of Saccharomyces sensu stricto yeasts and measured meiotic sterility in hybrids. This allows us to determine the divergence necessary to produce the reproductive isolation seen among species. Rather than a sharp transition from fertility to sterility, which may have been expected, we find a smooth monotonic relationship between diversity and reproductive isolation, even as far as the well-accepted designations of S. paradoxus and S. cerevisiae as distinct species. Furthermore, we show that one species of Saccharomyces--S. cariocanus--differs from a population of S. paradoxus by four translocations, but not by sequence. There is molecular evidence of recent introgression from S. cerevisiae into the European population of S. paradoxus, supporting the idea that in nature the boundary between these species is fuzzy.

Figure 1.—

Plot of K_a/K_s ratio of the genes sequenced in this study. The means and standard errors of K_a/K_s for the five coding genes are plotted. TLC1 is the RNA template of telomerase and therefore cannot be included in the analysis.

Figure 2.—

Phylogenetic trees (neighbor-joining) of the six genes sequenced in this study. Sp, S. paradoxus; Sc, S. cerevisiae; Sm, S. mikatae; Sk, S. kudriavzevii; Sb, S. bayanus.

Figure 3.—

Phylogenetic relationship among strains. Phylogenetic tree obtained from the concatenated analysis of NEJ1, EST2, yKU70, and yKU80 (total length of 7.4 kbp). TLC1 and SPT4 were excluded from the analysis because they were missing from some strains. The tree was obtained using the neighbor-joining algorithm with 1000 bootstrap iterations. The tree was rooted at the S. bayanus branch according to Rokas et al. (2003) and 100% of bootstrap value is indicated. The scale represents the number of nucleotide substitutions. An asterisk indicates strains with gross chromosomal rearrangements and colored dots indicate geographic origin (blue, North and South America; red, Europe; yellow, Far East; green, Africa; orange, Middle East).

Figure 4.—

Sequence divergence vs. fertility. Sequence divergence was plotted against gamete viability on a linear scale. In A, spore viability was not corrected for chromosomal translocations. In B, spore viability values were adjusted for the decrease in viability caused by translocations (see text). Various curves fit the data (dotted, linear; dashed, exponential; solid, exponential decay) with high correlation scores (r): linear (0.9347), exponential (0.9614), exponential decay (0.9805), and second order polynomial (0.9798; not shown). Log-transformed spore viabilities (not shown) resulted in a higher correlation (0.9518, linear curve fit) in agreement with Roberts and Cohan (1993).

Figure 5.—

Chromosome analysis in hybrid segregants. Chromosome separations using CHEF gel. Lanes: p, S. paradoxus YPS138; c, S. cariocanus UFRJ50816^T; H, cross S. paradoxus × S. cariocanus; 1–11, independent spores dissected from the hybrid. Chromosome aneuploidy, which appears as double-intensity bands, was not detected.

Figure 6.—

Molecular evidence of introgression from S. cerevisiae into the European population of S. paradoxus. (A) VISTA alignment of S. cerevisiae S288C and S. paradoxus CBS432 genomes along the left subtelomeric region of chromosome XIV. The sequence identity is plotted along the pairwise comparison of the left subtelomere. The region showing high identity between S. cerevisiae and S. paradoxus is shown along with the small region resequenced and then checked in several isolates of both species. (B) Phylogenetic tree of various S. cerevisiae and S. paradoxus strains using sequence reads from the transferred subtelomeric region. S. paradoxus strains thought to be of European descent (shaded box) in this region are much more closely related to S. cerevisiae strains than to other geographical groups of S. paradoxus. The tree was produced by DNAstar using the neighbor-joining method.