To access this work you must either be on the Smith College campus OR have valid Smith login credentials.

On Campus users: To access this work if you are on campus please Select the Download button.

Off Campus users: To access this work from off campus, please select the Off-Campus button and enter your Smith username and password when prompted.

Non-Smith users: You may request this item through Interlibrary Loan at your own library.

Publication Date

2023-01-13

First Advisor

Laura A. Katz

Document Type

Honors Project

Degree Name

Bachelor of Arts

Department

Biological Sciences

Keywords

evolution, high-throughput sequencing, confocal microscopy, protist, meiosis, Foraminifera, image analysis, phylogenomics, germline-soma distinction

Abstract

Meiosis is a process in which a cell replicates its genetic material and undergoes two reductive divisions to form haploid nuclei. Meiosis is a critical part of many eukaryotic life cycles, as it controls ploidy levels and generates genetic diversity through recombination. The distribution of meiosis in diverse lineages across the eukaryotic tree of life indicates that this process was present in the last eukaryotic common ancestor (LECA), thus, truly asexual eukaryotes are thought to be scarce and derived from sexual ancestors. With the advent of high-throughput genomic sequencing, putatively asexual genomes can now be probed for constituents from a conserved set of genes with known involvement in meiosis, together called the “meiosis toolkit.” However, this gene set is underexplored in many microbial lineages and the designation of some genes as “meiosis-specific” is controversial as some have been found to be active in other processes. Here, I extend a taxon-rich, gene-rich phylogenomic pipeline to explore the evolution of meiosis genes. I develop robust data curation methods to identify gene families of interest, which include multiple rounds of homology assessment. I create a user-friendly pipeline that combines gene tree topology and sequence composition to further curate gene families of interest by removing contaminant sequences. With robustly curated data, I build 67 trees for gene families involved in meiosis across more than 400 taxa from all major clades. I find that while many meiosis genes seem to be eukaryotic innovations, others likely predate LECA. Eukaryotic parasites from multiple major clades lack meiosis genes to the greatest extent, in concordance with the known gene loss and genome reduction in parasite evolution. Overall, the “meiosis toolkit” shows a bias towards metazoans, fungi, and plants, reflecting the intensity of study on these lineages and demonstrating the need for in-depth exploration of microbial genomes.

Rights

©2023 Caitlin Timmons. Access limited to the Smith College community and other researchers while on campus. Smith College community members also may access from off-campus using a Smith College log-in. Other off-campus researchers may request a copy through Interlibrary Loan for personal use.

Language

English

Download

Smith Only:
Off Campus Download

Share

COinS