MINIREVIEW Experimental evolution with yeast Clifford Zeyl Department of Biology, Wake Forest University, Winston-Salem, NC, USA Correspondence: Clifford Zeyl, Department Abstract of Biology, Wake Forest University, Winston- Downloaded from https://academic.oup.com/femsyr/article/6/5/685/563971 by guest on 27 September 2021 Salem NC 27109, USA. Tel.: 11 336 758-4292; Many of the difficulties of studying evolution in action can be surmounted using fax: 11 336 758-6008; populations of microorganisms, such as yeast. A readily manipulated sexual system e-mail: [email protected] and an increasingly sophisticated array of molecular and genomic tools uniquely qualify Saccharomyces cerevisiae as an experimental subject. This minireview Received 9 September 2005; revised 11 briefly describes some recent contributions of yeast experiments to current November 2005; accepted 9 December 2005. understanding of the evolution of ploidy, sex, mutation, and speciation. First published online 21 March 2006. doi:10.1111/j.1567-1364.2006.00061.x Editor: Teun Boekhout Keywords experimental evolution; adaptation; recombination; ploidy; speciation. recurrent emphasis in yeast experiments has been the Introduction evolution of the eukaryotic genetic system itself. Sex and Evolution is often thought of as being imperceptibly slow. A recombination, ploidy, and speciation are topics of espe- great deal of what we understand about evolution has cially broad evolutionary interest that have been the focus of therefore come from comparisons among existing species yeast experimental tests of theory. and from theoretical studies using modeling and simulation. A typical evolution experiment starts with microbiology But there are also increasingly frequent experimental tests of at its most basic: maintain axenic cultures for hundreds or evolutionary theory, performed on laboratory populations thousands of generations, periodically freezing samples of of organisms with generation times short enough that each population for analysis. Cultures are propagated either evolution can be observed directly, as it occurs. A pioneering by serial transfer (batch culture), in which a sample of each experiment that illustrates the potential scope of experi- population is transferred to a tube or plate of fresh medium mental microbial evolution is an ongoing study of 12 at regular intervals, or by chemostats, which balance inflow Escherichia coli populations through over 30 000 generations of fresh medium with outflow of used medium at constant in Richard Lenski’s laboratory (Table 1). From these popu- rates (Fig. 1). Chemostats are most often used to impose a lations have come rigorous tests of a great deal of evolu- constant selective environment, although periodic changes tionary theory. of medium can also be imposed, for example to induce In addition to short generation times, microbial evolu- meiosis and sporulation (Goddard et al., 2005). tion experiments have exploited the ease with which very The culture conditions define the type of selection to large populations can be maintained (allowing faster adap- which experimental populations will respond. They may tation), and the fact that samples of evolving populations include a specified type of stress, such as high osmolarity or can be frozen for later analysis and compared with their temperature (Goddard et al., 2005), or may simply place ancestor and with each other. Other experiments in evolu- populations in competition for a limiting nutrient such as tionary ecology and genetics have used Pseudomonas fluor- glucose. Whatever the selective pressure, rare mutations that escens (Rainey & Travisano, 1998) and the unicellular alga increase reproductive success will appear and increase in Chlamydomonas (Colegrave et al., 2002; Colegrave, 2002). frequency. Adaptation can then be measured either as a The current array of genetic and genomic technology makes simple growth rate or as competitive ability relative to a budding yeast ideally suited to experimental evolution. A reference genotype such as the ancestor of the experimental FEMS Yeast Res 6 (2006) 685–691 c 2006 Federation of European Microbiological Societies Published by Blackwell Publishing Ltd. All rights reserved 686 C. Zeyl Table 1. Some contributions of a long-term Escherichia coli evolution experiment Hypotheses and questions Main results Ref. The dynamics of fitness Rapid evolution for 2000 generations, then much slower change Lenski & Travisano (1994); Elena increase Replicate populations diverge in fitness et al. (1996) ‘‘Punctuated equilibrium:’’short periods of rapid change separated by periods of stasis, caused by the dynamics of selection of new mutations The roles of chance and history History and chance strongly affected cell size, which is correlated weakly with Travisano et al. (1995) in adaptation fitness, but not fitness itself The evolution and maintenance Two distinct, monophyletic ecotypes persisted for at least 14 000 generations, Rozen & Lenski (2000); Rozen of diversity fluctuating in frequencies, while both continued to adapt et al. (2005) The decay of metabolic functions Unused catabolic functions decayed due to antagonistic pleiotropy of Cooper & Lenski (2000) that are released from selection adaptive mutations Downloaded from https://academic.oup.com/femsyr/article/6/5/685/563971 by guest on 27 September 2021 Mutation rates and effects Elevated mutation rates evolved in three adapting populations Elena & Lenski (1997); Harmful mutations do not generally interact synergistically, as required by Sniegowski et al. (1997) one hypothesis for the evolution of sex Molecular mechanisms of Changes in the expression of 59 genes evolved in parallel in two populations, Cooper et al. (2003) adaptation many of them regulated by cAMP populations. Competitive fitness is calculated from the per- produce homozygotes for that allele. In asexuals this can generation increase in frequency of the fitter genotype. In only occur in the unlikely event of the same mutation nature, it is rarely if ever possible to know the selective occurring again in the other allele (Kirkpatrick & Jenkins, environment in which a trait evolved, so the meaning of 1989). However, most hypotheses try to explain sex through fitness measurements may be uncertain. By contrast, experi- some advantage of randomizing allele combinations at mental evolution allows fitness estimates to be performed in separate loci. Recombining harmful mutations can increase exactly the same environment as that to which the experi- the variation in mutation load of the progeny. If mutation mental population adapted. Another tremendous advantage rates are high enough, and if mutations interact with each is the availability of genetic markers that do not affect other so as to aggravate their harmful effects, then sexual competitive fitness (Goldstein & McCusker, 1999). Cassettes progeny can have more than double the fitness of clones encoding resistance to G418, hygromycin, or nurseothricin (Kondrashov, 1988). Alternative hypotheses focus on adap- can be inserted at the HO locus of an ancestral genotype, tive mutations. Recombination can pair adaptive mutations where they are typically neutral, after that ancestor has been that have arisen in separate lineages. In an asexual popula- used to establish experimental populations. This allows the tion, no more than one adaptive mutation can be selected at competitive fitness of descendents to be quantified relative a time, and any other adaptive mutations present during to that of the ancestor. that interval are lost, a phenomenon known as clonal A simple yeast experiment will serve as an introduction to interference. Recombination can relieve clonal interference the basics of experimental evolution, and to one of the by allowing successive mutations to accumulate in one high- biggest puzzles remaining in evolutionary biology, the origin fitness genotype. Genetic and ecologic variations on this and maintenance of eukaryotic sex. idea are that recombination can separate an adaptive muta- tion from linked harmful mutations, or that the greater genetic diversity of a sexual brood of offspring reduces com- The evolution of sex petition among offspring compared to clones. Finally, accor- The puzzle is most clearly seen in organisms with distinct ding to the popular Red Queen hypothesis, it is antagonistic male and female gamete types, in which females provide co-evolution, such as that between parasites and their hosts, most or all of the resources needed by zygotes, but only half that constantly selects for rare or new allele combinations, as of the alleles they carry. Alleles encoding this behavior are each species adapts to counter the most successful and transmitted half as efficiently as female alleles for cloning. In abundant genotype of the other (Hamilton, 1980). the case of isogamous organisms such as yeast there is no A simple test for an advantage to recombining mutations such cost of sex because MATa and MATa gametes make used two environments: the rich medium YPD, which equal contributions in both alleles and resources, but mating contains abundant glucose and to which laboratory yeast consumes time that could otherwise be allocated to mitotic strains have already adapted, and the same medium with reproduction. Sex also imposes the risk of breaking up galactose substituted for glucose. Otherwise initially identi- successful combinations of alleles during recombination. It cal sexual and asexual populations were maintained on YPD has been suggested that the advantage of sex