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

James Fourqurean

Second Advisor's Committee Title

Committee member

Third Advisor's Name

Gary Rand

Third Advisor's Committee Title

Committee member

Fourth Advisor's Name

Mauricio Rodriguez-Lanetty

Fourth Advisor's Committee Title

Committee member

Fifth Advisor's Name

Deron Burkepile

Fifth Advisor's Committee Title

Committee member


corals, epigenetics, climate change, phenotypic plasticity

Date of Defense



The current pace of anthropogenic global change is imposing unprecedented conditions to biological systems. Coral reef ecosystems are particularly sensitive to the rapid increase in thermal anomalies and the changes in water chemistry caused by global change. However, although their decline has been documented worldwide, there are signs suggesting that stony corals harbor greater phenotypic plasticity than previously expected, sparking the interest in the study acquired non-genetic modifications (e.g., epigenome, microbiome) potentially increasing their resilience to global change, and constituting one of the main targets for intervention.

Epigenetics constitutes an exciting frontier to understand how the environment influences the regulation of the expression of genetic information and modulates phenotypic variation. This has the potential to change the way we understand short-term acclimation and adaptation to a changing environment, aiding to improve predictive models of ecosystemic persistence under current and future climatic scenarios. However, while there is evidence supporting the idea of epigenetic mechanisms participating in rapid-response acclimatization, specific details about how this process is influenced by specific environmental conditions are lacking. In non-model organisms, we often lack information about the presence and functionality of some of these mechanisms, limiting the application of epigenetics in the study of ecosystem resilience in response to global change.

This dissertation aims to elucidate how epigenetic mechanisms contribute to coral phenotypic responses to the effects of global change in the oceans. For that purpose, hypotheses about the presence and responsiveness of different epigenetic mechanisms in corals, its interaction with the genome and microbial communities, as well as its role modulating gene expression and phenotypic responses to diverse stressors were explored. Histone repertoires and/or full methylomes were characterized for the first time in the corals Acropora cervicornis and Montastraea cavernosa. The participation of these epigenetic mechanisms modulating responses to nutrient contamination, seasonal environmental change, thermal stress and acidification was demonstrated, providing evidence supporting its participation in intragenerational plasticity. A conserved seasonal methylation program was observed in A. cervicornis. This together with the strong influence of the genome over DNA methylation evidence its heritability and its potential to participate in intergenerational plasticity




Previously Published In

Rodriguez-Casariego, Javier A., Mark C. Ladd, Andrew A. Shantz, Christian Lopes, Manjinder S. Cheema, Bohyun Kim, Steven B. Roberts, et al. 2018. “Coral Epigenetic Responses to Nutrient Stress: Histone H2A.X Phosphorylation Dynamics and DNA Methylation in the Staghorn Coral Acropora Cervicornis.” Ecology and Evolution 8 (23): 12193–207.

Rodríguez-Casariego, Javier A., Alex E. Mercado-Molina, Daniel Garcia-Souto, Ivanna M. Ortiz-Rivera, Christian Lopes, Iliana B. Baums, Alberto M. Sabat, and Jose M. Eirin-Lopez. 2020. “Genome-Wide DNA Methylation Analysis Reveals a Conserved Epigenetic Response to Seasonal Environmental Variation in the Staghorn Coral Acropora Cervicornis.” Frontiers in Marine Science 7: 822.



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