The rapid evolution of essential developmental genes and their protein products is both intriguing and problematic. The rapid evolution of gene products with simple protein folds and a lack of well-characterized functional domains typically result in a low discovery rate of orthologous genes. Additionally, in the absence of orthologs it is difficult to study the processes and mechanisms underlying rapid evolution. In this study, we have investigated the rapid evolution of centrosomin (cnn), an essential gene encoding centrosomal protein isoforms required during syncytial development in Drosophila melanogaster. Until recently the rapid divergence of cnn made identification of orthologs difficult and questionable because Cnn violates many of the assumptions underlying models for protein evolution. To overcome these limitations, we have identified a group of insect orthologs and present conserved features likely to be required for the functions attributed to cnn in D. melanogaster. We also show that the rapid divergence of Cnn isoforms is apparently due to frequent coding sequence indels and an accelerated rate of intronic additions and eliminations. These changes appear to be buffered by multi-exon and multi-reading frame maximum potential ORFs, simple protein folds, and the splicing machinery. These buffering features also occur in other genes in Drosophila and may help prevent potentially deleterious mutations due to indels in genes with large coding exons and exon-dense regions separated by small introns. This work promises to be useful for future investigations of cnn and potentially other rapidly evolving genes and proteins.A S the genomic era advances, molecular biology has shifted from single-gene studies to global analyses of genomes from a broad phylogenetic range of organisms. For single-gene and global studies, a critical first step for molecular biologists is the accurate identification of orthologous genes. The concept of orthology was introduced by Fitch to differentiate between orthologous genes, which have a oneto-one relationship between species, and paralogous genes, which result from a duplication event of the original ortholog within a species (Fitch 1970(Fitch , 2000. Because orthologs are often more closely related than paralogs, it is generally assumed that gene function is likely to be conserved. Since the functional annotation of uncharacterized genomes is generally computationally based on overall sequence identity with known genes from model organisms, it is essential for orthology assignments to be accurate (Hulsen et al. 2006). The importance of orthology is made evident both by the number of databases reporting orthologous gene sets and by the number of terms introduced to describe relational subcategories in the time since Fitch initially introduced the concept of orthologous and paralogous gene relationships.Since orthologous genes are related by descent and orthology is based on sequence homology and phylogeny, the process of identification should be relatively simple. Thi...