ORCID Identifier(s)


Graduation Semester and Year

Spring 2024



Document Type


Degree Name

Doctor of Philosophy in Quantitative Biology



First Advisor

Sen Xu

Second Advisor

Matthew Walsh

Third Advisor

Jeffery Demuth


Daphnia has been used as a key model system for studying ecological changes, evolution, and genomics for the past few decades due to its rapid turnover time in reproduction. The organism possesses two fascinating modes of reproduction: obligate parthenogenesis and cyclical parthenogenesis. This dissertation delves into the intricate reproductive strategies of Daphnia pulex, focusing on hybrid F1s from different reproductive modes. The first aim is to investigate 31 hybrid F1s generated from obligate parthenogenesis (OP) and cyclical parthenogenesis (CP) parental lines. Transcriptomic analysis reveals misexpression patterns and regulatory divergences, highlighting meiosis-related genes like CDC6 as potential parthenogenesis regulators. The second aim is to address CRISPR-Cas gene editing challenges in Daphnia, developing an efficient microinjection method for Cas9 and Cas12a nucleases. Mutational analyses in scarlet mutants uncover complex mutation spectra and germline mosaicism, linking gene editing to pleiotropic effects. The third aim is to explore the origins of OP Daphnia pulex, tracing their lineage from CP isolates. Crossing CP isolates yields F1 hybrids displaying OP characteristics under stress, which has not been reported before. This expands our understanding of parthenogenesis factors in Daphnia. Together, these studies offer a comprehensive view of Daphnia reproduction, inheritance patterns, and regulatory divergence, as well as suggesting precautions for using CRISPR-Cas in Daphnia gene editing.


CRISPR, Daphnia, crossing, genetics, genomics, gene editing, parthenogenesis


Computational Biology | Evolution | Genetics | Genomics


Creative Commons Attribution 4.0 International License
This work is licensed under a Creative Commons Attribution 4.0 International License.

Available for download on Saturday, May 03, 2025