Phylogenetic and Transcriptomic Analyses of Vision in Two Cave Adapted Crustaceans, Asellus aquaticus (Isopoda: Asellidae) and Niphargus hrabei (Amphipoda: Niphargidae).

Abstract

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.