Theses and Dissertations

ORCID

https://orcid.org/0000-0001-5227-4773

Advisor

Brown, Matthew W.

Committee Member

Counterman, Brian A.

Committee Member

Dapper, Amy L.

Committee Member

Gout, Jean-Francois

Date of Degree

8-13-2024

Original embargo terms

Visible MSU Only 2 Years

Document Type

Dissertation - Campus Access Only

Major

Biological Sciences

Degree Name

Doctor of Philosophy (Ph.D.)

College

College of Arts and Sciences

Department

Department of Biological Sciences

Abstract

Protists are defined as eukaryotic organisms that are not animals, land plants, or fungi and make up the vast majority of eukaryotic diversity. Unfortunately, they are often overlooked and under sampled. Some rationales behind this are that they are often microscopic, most rarely the cause of human disease, and are often difficult to get into culture. Molecular phylogenetics has revolutionized our understanding of the evolutionary history of eukaryotes and without a clear picture of protist evolution our understanding would be severely hindered. Phylofisher is an easy-to-use phylogenomic software package, with an accompanying database and various utilities, intended for deep phylogenomic analyses. Here I present thorough documentation for the use of PhyloFisher. I also developed a PhyloFisher utility, nucl_matrix_constructor.py, to allow the software package to build nucleotide phylogenomic matrices. This will allow users to address more shallow evolutionary questions. I developed a metabarcoding pipeline based on Oxford Nanopore Technology’s long read sequencing platform to explore the diversity of eukaryotic organisms in environmental samples. I characterized a novel discosean amoeba. Lastly, I predicted the proteomes from publicly available, but non-annotated genomes for 19 Acanthamoeba spp. and two Balamuthia spp. and used the PhyloFisher tools documented and developed to gain a better understanding into the evolutionary history of the clade as well as provide key resources in the future research of the clade.

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