Document Type



Doctor of Philosophy (PhD)



First Advisor's Name

Jose M Eirin-Lopez

First Advisor's Committee Title

Committee Chair

Second Advisor's Name

John Berry

Second Advisor's Committee Title

Committee Member

Third Advisor's Name

Kevin Feldheim

Third Advisor's Committee Title

Committee Member

Fourth Advisor's Name

Michael Heithaus

Fourth Advisor's Committee Title

Committee Member

Fifth Advisor's Name

Yannis Papastamatiou

Fifth Advisor's Committee Title

Committee Member


epigenetics, DNA methylation, age estimation, sharks, dolphins, biomarkers

Date of Defense



Worldwide, many large marine predator populations are in decline. These populations can be difficult to study due to the extensive home ranges and migration patterns often exhibited by these species. Molecular tools are therefore necessary to measure specific parameters on these populations that would otherwise be nearly impossible to obtain. This dissertation pioneers the use of environmental epigenetic approaches for that purpose, and specifically the epigenetic modification known as DNA methylation, using sharks and small cetaceans as model organisms. This work is organized into five chapters. Chapter I is an introductory chapter that lays out the fundamentals of environmental epigenetics and the future directions of the field. Chapter II is a study that culminated in the Bottlenose epigenetic aging tool (BEAT) which allows for the estimation of age in bottlenose dolphins. Chapter III extends epigenetic aging research to a non-model organism, Lemon sharks (Negaprion brevirostris), using a global DNA methylation quantification technique (MSAP) to assess age group differences in DNA methylation. This work provides the first evidence that the role epigenetics plays in aging for mammals, birds, and fish may also exists for sharks. Chapter IV is a study that explores the DNA methylation response in juvenile Lemon sharks to a major dredging event that occurred in Bimini, Bahamas. This study paves the way for incorporating epigenetics into ecological studies for long term monitoring of environmental changes. Chapter V summarizes the dissertation, showcasing how work has continued from previous chapters, and discusses the next direction of the work into the future.




Previously Published In

Beal AP, Rodriguez-Casariego, J, Rivera-Casas, C, Suarez-Ulloa, V, and Eirin-Lopez, JM. 2018. Environmental epigenomics and its applications in marine organisms. In: Populations Genomics. Springer, Cham.

Beal AP, Kiszka JJ, Wells RS, and Eirin-Lopez, JM. 2019. The Bottlenose dolphin epigenetic aging tool (BEAT): A molecular age estimation tool for small cetaceans. Frontiers in Marine Science; doi: 10.3389/fmars.2019.00561.

Beal AP, Hackerott S, Franks B, Gruber SH, Feldheim K, and Eirin-Lopez JM. 2021. Epigenetic responses in juvenile Lemon sharks (Negaprion brevirostris) during a coastal dredging episode in Bimini, Bahamas. Ecological Indicators;

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



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