Brooklyn Lennes

While pseudogenization has previously been under-discussed by evolutionary biologists as a process with adaptive potential, recent research has revealed that it may be important in trait evolution. Cavefishes offer a system for studying these processes, as distantly related species have independently evolved traits such as eye reduction and neuromast expansion. In this project, I examine three candidate sensory genes, tfap2d, rgrb, and rgra, for evidence of selection across cavefish lineages. I use codon-based tests (BUSTED, RELAX, aBSREL, and MEME) to evaluate patterns of gene-wide and site-specific selection. Preliminary results indicate that tfap2d is generally under relaxed selection across cavefishes, with some branches and sites experiencing episodic positive selection. This result is consistent with the evolution of neuromast expansion or eye loss via pseudogenization. Similarly, rgrb shows relaxation of constraint, and multiple lineages exhibit premature stop codons, suggesting that pseudogenization may contribute to eye loss in these cases. In contrast, rgra is under intensified selection across cavefish lineages overall, but one lineage shows episodic positive selection with a premature stop codon, pointing to possible pseudogenization. These findings suggest that both relaxed and episodic selection, including pseudogenization, play roles in shaping convergent cavefish phenotypes. While these results are preliminary, they highlight the potential role of selection and pseudogenization in the evolution of eye degeneration and neuromast expansion in cavefishes. This work establishes a foundation for understanding the molecular basis of convergent cave-adapted phenotypes and highlights the adaptive potential of pseudogenization in evolution.