Computational Insights into Evolutionary Dynamics of Human and Primate Genes

Abstract

The evolutionary history of genes across different species is a subject of research interest. For human genes, there is a particular focus on investigating the possible origins of genes. However, there has been limited research on the development process from an evolutionary perspective. Additionally, most previous studies have focused on model organisms and representative organisms from various eras, with less attention given to primates, which are evolutionarily more closely-related to humans. With the advancement of whole genome sequencing of primates, investigating the genes of various primate species has become a viable possibility. This dissertation work integrates computational insights into the topics of primate and human gene emergence, conservation, and loss. Specifically, this series of studies contributes to three aspects of the topic: (1) the environmental conditions in evolution history that are associated with the emergence of primate and human de novo genes, (2) the evolutionary dynamics of human cancer genes in primates, and (3) gene conservation and loss in primates. Results reveal that primate and human de novo genes and cancer genes share similarities in the time of emergence, peaking later than random human genes and tending to occur in local warm periods in the context of an overall trend of decreasing global surface temperature. Cancer genes are more conserved in their evolutionary origins than random human genes, with two peaks of emergence, one before primates and the other within 20 million years, and have different patterns within the two time periods. Genes with high expression in the human brain exhibit more conservation in their evolutionary origins than those in the immune system or random genes. On the other hand, genes expressed highly in the mouse brain tend to be either prevalent in primates or specific to mouse. Overall, this dissertation work charts the evolutionary history of a number of distinct primate and human genes, elucidates the potential association of ancient environmental factors with primate genomes, provides insights into the origin, conservation, and emergence of cancer genes in primates, as well as examines the conservation and loss of genes in different tissues. The hope is that these results will contribute to a greater understanding of the picture of gene evolution in primate and human genomes.