Comparative single-cell diatom population genomics across the world's largest lakes and across the world

A single-cell method was developed for the comparative population genomics study of five Aulacoseira species from the Laurentian Great Lakes, North America and Lake Baikal, Siberia. This new methodology was necessary to investigate difficult-to-culture diatoms and overcome challenges associated with culture bias and geographically remote sampling locations. Chapter one presents this method, and documents the method's ability to detect strong genetic differentiation in instances where spatial genetic structure is expected (here, between two populations of the same species from across the globe). Additionally, the sensitivity of this method to resolving population genetic signal consistent with known demographics of the organism (here, clonality) is demonstrated. In chapter two, this method is used to explore the population genomics of three Aulacoseira species from the Great Lakes. Findings indicate that genetic differentiation and diversity vary across species, and -within species- across localities. In Chapter three, findings from previous chapters provide a benchmark to contextualize population genomic findings from A. baicalensis, an endemic diatom, which is foundational to Lake Baikal's simple but endemic pelagic food web. Specific temporal and geographic hypotheses were tested under the expectation that geographic population structure may be detected, given heterogeneous warming and nutrient conditions between basins within Lake Baikal. The null hypothesis of panmixia could not be rejected for A. baicalensis and effective population sizes were estimated to be finite, favoring drift rather than natural selection as the force driving evolution in this species. Observed and expected heterozygosity estimates for A. baicalensis were three times lower than for any other Aulacoseira species investigated, including a congener from Lake Baikal. Reduced genetic diversity in A. biacalensis could have grave consequences for the adaptability of this important endemic phytoplankter when faced with the rapid warming predicted for the Lake. This study contributes needed population genetic data on freshwater planktonic diatoms, and is the first in the diatom field to take a comparative population genomics approach. These findings, alongside those from other recent studies, challenge long-standing paradigms about natural microbial eukaryotic populations, including unlimited gene flow and infinite population sizes, emphasizing the need for more population-level, quantitative data in microbial molecular ecology.