Neuronal complexity varies widely throughout the tree of life. Clustered protocadherins (PCDH) are known to play a significant role in neural diversity and synapse maturity in vertebrates and cephalopods (Noonan, Myers, et al. 2013). DSCAM (Down Syndrome Cell Adhesion Molecule) proteins play a similar role in arthropods in regard to neuronal wiring and axonal guidance (Armitage, Bravo, et al. 2012). Due to the role and conservation of PCDH and DSCAM in brain development, it is thought that they played an important role in the brain evolution of both arthropods, vertebrates, and cephalopods. In order to investigate the relationship of the gene evolution and neuronal diversity and evolution, I examined the similarities of the evolution of PCDH transcripts across twenty vertebrate and cephalopod species. Due to the large number of PCDH genes, I focused on PCDH11X and PCDH20 due to the overlapping presence in the selected species. PCDH11X is an x-linked protocadherin that has been linked to late onset Alzheimer's disease, while PCDH20's function is yet to be determined. Furthermore, I investigated the evolution of DSCAM2 in fifty arthropods in relation to sociality. These analyses were completed using Bayesian phylogenetic methods with follow up comparative phylogenetic analyses. Based on the phylogenetic trees created, we can conclude that the most recent common ancestor of vertebrates and cephalopods likely had both PCDH11X and PCDH20. I mapped neuron number and diversity to visualize patterns and estimate ancestral character state. Additionally, I investigated the correlation between DSCAM and sociality in arthropods. Further research should be done on the evolution of PCDH in cephalopods, specifically comparing mollusk PCDH to vertebrate PCDH in order to fully understand the origin and evolutionary path of PCDH.