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. / Doctor of Philosophy / Genes can be seen as tiny instructions inside human bodies that tell individuals how to grow and what they will look like. They are very important to understand how the human body works and to keep every person healthy.
Each individual inherits genes from their parents, who carry on the genes from their parents (the individual's ancestors). Similarly, the entire human species collectively has inherited genes from our evolutionary ancestors. Each individual may also have genes that are unique to them due to reasons such as mutations. For a group of species or related species, this may also happen, resulting in genes called de novo genes. In this dissertation human de novo genes, which are unique to humans (Homo sapiens), and primate de novo genes, which are more broadly unique to the primates, are examined. Here, primates include several evolutionarily related species, including apes, monkeys, and humans.
This dissertation first explored the emergence of primate and human de novo genes, as well as cancer genes that play certain roles in human cancer, in relation to global surface temperatures estimated at the time. The results suggested that these genes emerged more often during local warmer periods within the general trend of declining temperature in the recent 13 million years. Secondly, this series of studies looked at cancer genes compared to random human genes and found that many human cancer genes were inherited from primate ancestors. For those human cancer genes that were not inherited from such early ancestors, most have emerged within the last 20 million years. Lastly, genes highly expressed in the human brain were examined, and it was found that many such genes were also inherited from primate ancestors, more than those highly expressed in the immune system and random human genes. Genes that are highly expressed in the mouse brain, on the other hand, are often either inherited from common ancestors of mouse and primate or mouse de novo genes.
| Identifer | oai:union.ndltd.org:VTETD/oai:vtechworks.lib.vt.edu:10919/119337 |
| Date | 06 June 2024 |
| Creators | Liang, Xiao |
| Contributors | Computer Science and Applications, Heath, Lenwood S., Zhang, Liqing, Pruden-Bagchi, Amy Jill, Meng, Na, Yeung, Ka Yee |
| Publisher | Virginia Tech |
| Source Sets | Virginia Tech Theses and Dissertation |
| Language | English |
| Detected Language | English |
| Type | Dissertation |
| Format | ETD, application/pdf |
| Rights | In Copyright, http://rightsstatements.org/vocab/InC/1.0/ |
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