The Origin, Diversity and Ancestry of Saccharomyces Yeasts in New Zealand

Abstract

Microorganisms are ubiquitous and essential to global ecological processes, but their distributions and diversities are still poorly understood. The relatively recent development of molecular genetics and DNA sequencing allows us to accurately quantify taxonomic diversity and infer evolutionary history within microbial groups, in a way that was not possible with traditional phenotypic characterization. Studying the patterns and processes of microbial distributions stands to expand our knowledge of the evolutionary process and provide insights into the ecological ramifications of microbial movements. The Saccharomyces genus of yeasts consists of seven species and has emerged as the premier model genus for the study of evolutionary genetics and genomics in a microbial system. This is partially due to its eukaryotic nature and relatively small genome, and partially due to its immense industrial importance for alcoholic fermentation and baking. This thesis focusses on the origin, diversity and ancestry of Saccharomyces yeasts in New Zealand. The short anthropogenic history of New Zealand lends itself to teasing apart the extent and ecological ramifications of humanassociated microbial dispersal. Past research has shown New Zealand harbors a population of S. cerevisiae distinct from a diverse set of international strains, but also provided evidence for human-mediated dispersal in association with wine barrels. The presence of a distinct population implies long-term restriction to gene flow and passive dispersal, which should be readily detectable in genomic data. To investigate this hypothesized New Zealand population, a set of 52 strains representing the known diversity in New Zealand were subjected to whole genome sequencing. Phylogenomics analyses of these genomes compared with a further 60 from a diversity of international geographic locations and niches conclusively placed the New Zealand population as part of a global clade containing winemaking strains with an origin in Europe. A minimum of 10 incursion events were inferred and broadly dated to correspond to the arrival of humans and winemaking to New Zealand. While these data show S. cerevisiae is the product of human-mediated range expansion, other species within the Saccharomyces genus have been identified from natural environments and display biogeographic patterns characteristic of extensive divergence. A concurrent sampling effort of the native forests of New Zealand for the presence of Saccharomyces species identified a widespread population of S. arboricola, a species previously not found outside Far East Asia, as well as S. eubayanus, also not previously identified in New Zealand. Whole genome sequencing of nine isolates of the former, and one of the latter, with subsequent comparison against international sequences, indicates that the widespread S. arboricola population is highly divergent from the Far East Asian population, but the S. eubayanus isolate is likely a recent migrant to New Zealand in association with humans. To aid in the population comparisons of the S. cerevisiae data, and to provide a useful resource to other population geneticists, a software tool called ObStruct was created to objectively analyze the outputs of Bayesian population genetics tools. Combined, these results represent a significant addition to our knowledge of the worldwide distribution of Saccharomyces and, more importantly, this is one of the first detailed studies on the evolutionary history and dispersal patterns within a microbial genus.