Document Type



Doctor of Philosophy (PhD)



First Advisor's Name

Heather Bracken-Grissom

First Advisor's Committee Title

Committee Chair

Second Advisor's Name

Joel Trexler

Second Advisor's Committee Title

Committee Member

Third Advisor's Name

Jose Maria Eirin-Lopez

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

Kalai Mathee

Fifth Advisor's Committee Title

Committee Member

Sixth Advisor's Name

Thomas Iliffe

Sixth Advisor's Committee Title

Committee Member


evolution, biospeleology, subterranean, opsin, phototransduction, RNA

Date of Defense



The unique characteristics of aquatic caves and of their predominantly crustacean biodiversity nominate them as ideal study subjects for evolutionary biology. The present dissertation capitalizes on a perfect natural experiment, the Molnar Janos thermal cave system in Budapest, Hungary. This intricate freshwater cave system and the immediately adjacent Malom Lake present the ideal opportunity to address questions of colonization, adaptation, and evolution. Despite marked environmental differences between the cave and surface waters, both localities are inhabited by natural populations of two emerging model cave species, the isopod Asellus aquaticus and the amphipod Niphargus hrabei. In the present dissertation, I first conduct an extensive literature review to examine and discuss the role that molecular methodologies have played in the study of cave biology. Additionally, I discuss the potential of “speleogenomic” methodologies to address long-standing questions in cave and evolutionary biology in fields such as biodiversity, phylogeography, and evolution. I then investigate the phylogeographic patterns and divergence-time estimates between surface and cave populations of the aforementioned species to elucidate mechanisms and processes driving the colonization of subterranean environments. These populations’ phylogenies then serve as robust frameworks on which to evaluate the transcriptional basis behind the divergence of traits involved in troglomorphy, namely vision. RNA sequencing approaches are used to identify and evaluate differences in the transcription of photoreception genes and pathways to in subterranean vs. surface populations. To achieve so, in a scalable manner suitable for modern sequencing technologies, here I produce a bioinformatics pipeline that allows for an accurate and efficient identification of genes present in a transcriptome that are involved in photoreception and visual pathways. I then use this bioinformatics pipeline to depict, in a phylogenetically informed context, the transcriptional basis behind photoreception and vision in A. aquaticus and N. hrabei, and the role these traits play in cave adaptation, and in the evolution of troglomorphy in the subphylum Crustacea. With the findings herein, the present dissertation aims to provide a framework for the discovery of evolutionarily significant molecular mechanisms that permit the survival and evolution of life in caves and other extreme environments.



Previously Published In


Pérez-Moreno JL, Iliffe TM, Bracken-Grissom HD. 2016. Life in the Underworld: Anchialine cave biology in the era of speleogenomics. International Journal of Speleology, 45(2): 149-170.


Pérez-Moreno JL, Balázs G, Wilkins B, Herczeg G, Bracken-Grissom HD. 2017. The role of isolation on contrasting phylogeographic patterns in two cave crustaceans. BMC Evolutionary Biology, 17:247.


Pérez-Moreno JL, DeLeo D, Palero F, Bracken-Grissom HD. 2018. Phylogenetic annotation and genomic architecture of opsin genes in Crustacea. Hydrobiologia, 825(1): 159-175.


Pérez-Moreno JL, Balázs G, Bracken-Grissom HD. 2018. Transcriptomic insights into the loss of vision in Molnár János Cave crustaceans. Integrative and Comparative Biology, 58(3):452-464.



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