Mutation, adaptation, and speciation in experimental populations of fungi

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The overall goal of this proposal is to observe and measure mutation, adaptation, and incipient speciation in experimental populations, each with a known ancestor and history. Mutation is the ultimate source of all genetic variation and yet inferences on mutations and their rates in natural populations have remained indirect. Objective 1 is to sample long-lived individuals of Armillaria gallica, an important opportunistic fungal pathogen of tree roots. Each individual of A. gallica arises in a single mating event and then grows to occupy a discrete spatial territory including many adjacent tree root systems. In effect, this leaves a spatial record of growth over time and allows estimation of the rate of selectively neutral and advantageous mutations in a direct manner not previously possible under natural conditions. To identify the mutations, the entire genomes of samples of individuals will be sequenced. Objective 2 is observe the mutations and measure their effects on fitness and on reproductive isolation in 12 diploid populations of the yeast Saccharomyces cerevisiae, that were propagated in two different environments, high salt and low glucose for 500 generations. Most studies of speciation, the process by which one species splits into two, are based on extant, fully fledged species. This can be problematic because the earliest events of speciation may be obscured by changes accumulated during the long evolutionary history since the split. The evolution experiments proposed here will bring focus to the earliest stages of the speciation process, with all underlying mutations identified at the DNA level and characterized for fitness effects. This will establish which modes of adaptation and reproductive isolation occur most generally. Objective 3 is to propagate all 12 yeast populations for a further 10,000 generations in their respective environments with daily transfers over the next four years, extending the time frame for observation of adaptation and speciation by more than an order of magnitude, again with full characterization of the underlying molecular determinants. This will establish which mechanisms of adaptation and isolation are modified over time and will identify any new mechanisms that emerge with confidence.