Improving gene annotation and understanding of mammalian evolution by identifying retrocopies of mRNA transcripts

Understanding gene creation is essential to the study of human evolution. Duplication followed by specialization has been suggested as an important mechanism for evolving new functions in multi-cellular organisms. In this work, I present a new method for recognizing non-viral retrotransposition of mRNAs as well as analysis of how this mechanism has influenced mammalian and specifically primate evolution.;My work has centered on two areas: (1) developing an automated method to annotate retroposed pseudogenes and retrogenes; (2) analyzing the resulting sets of data in human and mouse to increase our understanding of this mechanism in two mammalian lineages. This work has resulted in a number of papers in collaborations with external groups in the areas of: improved gene annotation via screening pseudogenes, pseudogene annotation and retrogene annotation.;In the analysis of the dataset, I found a set of human and mouse retrogenes that arose after their divergence. Surpisingly, these were not just simple duplication events rather a extremely diverse set of cases where "anything goes". I classify these events into broad groupings: (1) duplication events; (2) exon shuffling events, and (3) novel genes.;In the set of putative human retrogenes that showed evidence of expression, eight were determined to by specific to humans. We performed a series experiments to determine if they were fixed in the population and also to verify RNA expression in selected cases.;Finally, I show that the previously reported burst in retrotransposition in mammals, which was suppressed in primates, has not decreased the rate of gene duplication via retrotransposition in primates. Perhaps this evolutionary mechanism can help explain the rapid change in pheotypes during primate evolution.