Population and comparative genetics of thermotolerance divergence between yeast species

The relationship between cell density and cell count differs among Saccharomyces yeast species

There is a recent push to develop wild and non-domesticated Saccharomyces yeast strains into useful model systems for research in ecology and evolution. Yet, the variation between species and strains in important population parameters remains largely undescribed. Here, we investigated the relationship between two commonly used measures in microbiology to estimate growth rate - cell density and cell count - in 23 strains across all eight Saccharomyces species . We found that the slope of this relationship significantly differs among species and a given optical density (OD) does not translate into the same number of cells across species. We provide a cell number calculator based on our OD measurements for each strain used in this study. Surprisingly, we found a slightly positive relationship between cell size and the slope of the cell density-cell count relationship. Our results show that the strain- and species-specificity of the cell density and cell count relationship should be taken into account, for instance when running competition experiments requiring equal starting population sizes or when estimating the fitness of strains with different genetic backgrounds in experimental evolution studies.

Experimental evolution of Saccharomyces uvarum at high temperature yields elevation of maximal growth temperature and loss of the mitochondrial genome

An organism's upper thermal tolerance is a major driver of its ecology and is a complex, polygenic trait. Given the wide variance in this critical phenotype across the tree of life, it is quite striking that this trait has not proven very evolutionarily labile in experimental evolution studies of microbes. In stark contrast to recent studies, William Henry Dallinger in the 1880s reported increasing the upper thermal limit of microbes he experimentally evolved by >40°C using a very gradual temperature ramping strategy. Using a selection scheme inspired by Dallinger, we sought to increase the upper thermal limit of Saccharomyces uvarum . This species has a maximum growth temperature of 34-35°C, considerably lower than S. cerevisiae . After 136 passages on solid plates at progressively higher temperatures, we recovered a clone that can grow at 36°C, a gain of ~1.5°C. Additionally, the evolved clone lost its mitochondrial genome and cannot respire. In contrast, an induced rho 0 derivative of the ancestor shows a decrease in thermotolerance. Also, incubation of the ancestor at 34°C for 5 days increased the frequency of petite mutants drastically compared to 22°C, supporting the notion that mutation pressure rather than selection drove loss of mtDNA in the evolved clone. These results demonstrate that S. uvarum 's upper thermal limit can be elevated slightly via experimental evolution and corroborate past observations in S. cerevisiae that high temperature selection schemes can inadvertently lead to production of the potentially undesirable respiratory incompetent phenotype in yeasts.

Barcoded reciprocal hemizygosity analysis via sequencing illuminates the complex genetic basis of yeast thermotolerance

Decades of successes in statistical genetics have revealed the molecular underpinnings of traits as they vary across individuals of a given species. But standard methods in the field cannot be applied to divergences between reproductively isolated taxa. Genome-wide reciprocal hemizygosity mapping (RH-seq), a mutagenesis screen in an interspecies hybrid background, holds promise as a method to accelerate the progress of interspecies genetics research. Here, we describe an improvement to RH-seq in which mutants harbor barcodes for cheap and straightforward sequencing after selection in a condition of interest. As a proof of concept for the new tool, we carried out genetic dissection of the difference in thermotolerance between two reproductively isolated budding yeast species. Experimental screening identified dozens of candidate loci at which variation between the species contributed to the thermotolerance trait. Hits were enriched for mitosis genes and other housekeeping factors, and among them were multiple loci with robust sequence signatures of positive selection. Together, these results shed new light on the mechanisms by which evolution solved the problems of cell survival and division at high temperature in the yeast clade, and they illustrate the power of the barcoded RH-seq approach.

Temperature-dependent genetics of thermotolerance between yeast species

Many traits of industrial and basic biological interest arose long ago, and manifest now as fixed differences between a focal species and its reproductively isolated relatives. In these systems, extant individuals can hold clues to the mechanisms by which phenotypes evolved in their ancestors. We harnessed yeast thermotolerance as a test case for such molecular-genetic inferences. In viability experiments, we showed that extant Saccharomyces cerevisiae survived at temperatures where cultures of its sister species S. paradoxus died out. Then, focusing on loci that contribute to this difference, we found that the genetic mechanisms of high-temperature growth changed with temperature. We also uncovered an enrichment of low-frequency variants at thermotolerance loci in S. cerevisiae population sequences, suggestive of a history of non-neutral selective forces acting at these genes. We interpret these results in light of models of the evolutionary mechanisms by which the thermotolerance trait arose in the S. cerevisiae lineage. Together, our results and interpretation underscore the power of genetic approaches to explore how an ancient trait came to be.

Joint effects of genes underlying a temperature specialization tradeoff in yeast

A central goal of evolutionary genetics is to understand, at the molecular level, how organisms adapt to their environments. For a given trait, the answer often involves the acquisition of variants at unlinked sites across the genome. Genomic methods have achieved landmark successes in pinpointing these adaptive loci. To figure out how a suite of adaptive alleles work together, and to what extent they can reconstitute the phenotype of interest, requires their transfer into an exogenous background. We studied the joint effect of adaptive, gain-of-function thermotolerance alleles at eight unlinked genes from Saccharomyces cerevisiae, when introduced into a thermosensitive sister species, S. paradoxus. Although the loci damped each other’s beneficial impact (that is, they were subject to negative epistasis), most boosted high-temperature growth alone and in combination, and none was deleterious. The complete set of eight genes was sufficient to confer ~15% of the S. cerevisiae thermotolerance phenotype in the S. paradoxus background. The same loci also contributed to a heretofore unknown advantage in cold growth by S. paradoxus. Together, our data establish temperature resistance in yeasts as a model case of a genetically complex evolutionary tradeoff, which can be partly reconstituted from the sequential assembly of unlinked underlying loci.

Organisms adapt to threats in the environment by acquiring DNA sequence variants that tweak traits to improve fitness. Experimental studies of this process have proven to be a particular challenge when they involve manipulation of a suite of genes, all on different chromosomes. We set out to understand how so many loci could work together to confer a trait. We used as a model system eight genes that govern the ability of the unicellular yeast Saccharomyces cerevisiae to grow at high temperature. We introduced these variant loci stepwise into a non-thermotolerant sister species, and found that the more S. cerevisiae alleles we added, the better the phenotype. We saw no evidence for toxic interactions between the genes as they were combined. We also used the eight-fold transgenic to dissect the biological mechanism of thermotolerance. And we discovered a tradeoff: the same alleles that boosted growth at high temperature eroded the organism’s ability to deal with cold conditions. These results serve as a case study of modular construction of a trait from nature, by assembling the genes together in one genome.