CRUSTACEAN PHYLOGENETIC SYSTEMATICS AND OPSIN EVOLUTION by

CRUSTACEANS AND OPSIN EVOLUTION Megan L. Porter Department of Microbiology and Molecular Biology Doctor of Philosophy Composed of a chromophore bound to an integral membrane protein (opsin), visual pigments are phenotypically characterized by the wavelength of maximal absorption (λmax). The underlying molecular mechanism controlling λmax is the interaction between the opsin amino acid sequence and the chromophore. While a plethora of studies have looked at structure/function relationships in vertebrate opsins, fewer studies have investigated similar issues in invertebrates. Furthermore, those few studies undertaken in invertebrate systems suggest different mechanisms of spectral tuning and photoactivation compared to vertebrate systems. This dissertation research is focused on expanding our knowledge of opsin evolution in invertebrate systems, particularly from non-insect taxa. First, issues related to opsin evolution and the maintenance of supposedly ‘nonfunctional’ genes were explored in a review of regressive and reverse evolution. Second, in order to place studies of crustacean opsin evolution in context, phylogenetic studies of two crustacean groups (Mysidae and Decapoda) were completed. Studies of Mysidae utilized 16S mtDNA, and 18S and 28S rDNA to reconstruct phylogenetic relationships and assess newly developed Bayesian methods of assessing pattern heterogeneity. Using this suite of genetic markers, there are incongruencies between current taxonomy and inferred phylogenetic relationships. Studies of Decapoda assessed phylogenetic relationships and estimated divergence times using 16S mtDNA, H3 nDNA, and 18S and 28S rDNA sequence data in conjunction with a set of eight fossil calibrations. Reconstructed phylogenies show support for two well supported nodes corresponding to the Pleocyemata and the informal ‘Reptantia’ and place the emergence of the Decapod lineage in the early Devonian (407 MYA). Finally, opsin sequences and spectral sensitivity data from species within the Mysidae and Decapoda were combined with previously characterized invertebrate sequences to investigate opsin evolution. Standard dN/dS methods did not detect any evidence of selection. Methods investigating selection on amino acid properties, however, identified four properties (coil tendencies, compressibility, power to be at the middle of the alpha helix, and refractive index) to be under positive destabilizing selection. These properties occurred mostly at sites in transmembrane helices and included residues previously identified to affect spectral tuning as well as identifying