Determinants of Divergent Adaptation and Dobzhansky-Muller Interaction in Experimental Yeast Populations

Abstract

Summary Divergent adaptation can be associated with reproductive isolation in the process of speciation [1]. We recently demonstrated the link between divergent adaptation and the onset of reproductive isolation in experimental populations of the yeast Saccharomyces cerevisiae evolved from a single progenitor in either a high-salt or a low-glucose environment [2]. Here, we used whole-genome re-sequencing of representatives of three populations to identify 17 candidate mutations, six of which explained the adaptive increases in mitotic fitness in the two environments. In two populations evolved in high salt, two different mutations occurred in the proton efflux pump gene PMA1 and the global transcriptional repressor gene CYC8; the ENA genes encoding sodium efflux pumps were over-expressed once through expansion of this gene cluster and once due to mutation in the regulator CYC8. In the population from low glucose, one mutation occurred in MDS3, which modulates growth at high pH, and one in MKT1, a global regulator of mRNAs encoding mitochondrial proteins, the latter recapitulating a naturally-occurring variant. A Dobzhansky-Muller (DM) incompatibility between the evolved alleles of PMA1 and MKT1 strongly depressed fitness in the low-glucose environment. This DM interaction is the first reported between experimentally evolved alleles of known genes and shows how reproductive isolation can arise rapidly when divergent selection is strong.

Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris

“…For instance, in E. coli, mutations have been identified in the proline ABC transporter gene proV (Dragosits et al, 2013;Winkler et al, 2014), and in the osmoprotectant biosynthesis genes otsBA (Stoebel et al, 2009). In yeast, mutations were found in the proton efflux pump gene pma1, the global transcriptional repressor gene cyc8 (Anderson et al, 2010) and the mot2 gene that has an unknown role in salt tolerance (Dhar et al, 2011). Here, we employ experimental evolution coupled with whole-genome whole-population sequencing and site-directed mutagenesis to discover and verify the functional genes conferring salt tolerance in an anaerobic environmental bacterium Desulfovibrio vulgaris.…”

Genetic background affects epistatic interactions between two beneficial mutations

“…This dependence, known as epistasis, is important to many areas of developmental and evolutionary biology, including speciation [1][2][3][4], the maintenance of sex [5,6], adaptation [7][8][9], the evolution of ploidy [10] and evolutionary contingency [11 -14]. As the technology to identify and manipulate specific mutations becomes increasingly available, the influence of epistasis can be examined directly.…”

In vitro evolution goes deep

“…Recently, deep-sequencing technologies have been applied to obtain complete genome sequences for populations evolved in the laboratory, either under selection (13)(14)(15) or in its absence (16). These studies have allowed unprecedented views of the process of evolution because they allow systematic mapping of variation and direct measurements of the changes in allele frequencies in populations over time.…”