Date of Award

2021

Degree Type

Thesis

Degree Name

Master of Science in Biological and Environmental Sciences (MSBES)

Department

Biological Sciences

First Advisor

Christopher Lane

Abstract

Stramenopiles, Alveolates, and Rhizaria (SAR) are environmentally ubiquitous and form one of the most genetically diverse groups of eukaryotes on earth. Combined, these phyla encompass nearly half of all known eukaryotic genomic diversity. Stramenopiles comprise both non-photosynthetic taxa including important pathogens of animals and plants such as the gastric parasite Blastocystis and oomycetes like Phytophthora, the causative agent of the Irish Potato Famine. Additionally, photosynthetic members from the Phylum Ochrophyta, like the charismatic seaweeds such as giant kelp, create important ecosystems while diverse microbial phytoplankton including diatoms are fundamental to biogeochemical cycles and form the base of the food web. Despite the known diversity within the stramenopiles, the lack of obvious morphological characteristics for distinguishing taxa has led to some classes becoming a dumping ground for difficult to place taxa. The combination of largely understudied, yet genetically diverse taxa with few reliable distinguishing characteristics has complicated stramenopile systematics for centuries. The absence of a resolved phylogeny representing the diversity of the group significantly hinders the ability to make meaningful inferences about ochrophyte evolution. Here we expand the taxonomic sampling for ochrophytes by generating twenty-eight novel transcriptomes, focusing on classes lacking genome-scale data and species of uncertain taxonomic affiliation. By combining these data with other publicly available data, we constructed the most taxonomically comprehensive phylogeny of ochrophytes comprised of nineteen out of the twenty-one previously described classes. Our analyses robustly resolve relationships between stramenopiles and support four main clades of ochrophytes. We placed historically difficult to resolve taxa. A rapid radiation in the diversification of ochrophytes remains problematic for resolving the root of ochrophytes and deep internal branches. These outstanding questions will likely require identification and sequencing of additional, and even novel ochrophyte taxa or methodological advances to extract a reliable phylogenetic signal from these ancient events.

Available for download on Sunday, August 13, 2023

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