Biology ETDs

Publication Date

Summer 7-27-2018


Comparative genomics has revolutionized virtually all fields of biology including the study of evolution. In this dissertation, I used next-generation sequencing to explore the evolutionary histories and adaptive evolution of a diverse set of taxa. Comparisons ranged across time scales, from population-level genetic diversity studies to questions spanning the deepest branches of the metazoan lineage. Whole genome sequencing of 50 unrelated Korean individuals revealed that Koreans have a distinct genetic history from the Chinese and Japanese populations. Our Korean-specific variome database was used to identify novel disease-causing variants in the Korean population, highlighting the value of high-quality ethnic variation databases for the accurate interpretation of individual genomes and genetic variations. Using multi-species comparative genomics of mammals, I identified signatures of high-altitude adaptation in the endangered long-tailed goral (Naemorhedus caudatus) in the mountains of Korea, and in a separate study in three species of closely-related montane guinea pigs in the Andes of South America. Phylogenomic analyses were used to confirm that the source species of the domestic guinea pig (Cavia porcellus) was the high-altitude species Cavia tschudii, not the lowland Cavia aperea. Finally, the first jellyfish (Nemopilema nomurai) and shark (Rhinocodon typus) genomes were assembled and used to identify genetic features unique to those lineages. Large scale genomic comparisons of over 80 metazoans revealed correlations between a number of physiological and genetic traits. Taken together, this dissertation shows the power of comparative genomics to address fundamental biological questions across evolutionary time and diverse non-model systems.



Document Type


Degree Name


Level of Degree


Department Name

UNM Biology Department

First Committee Member (Chair)

Joseph Cook

Second Committee Member

Jeremy Edwards

Third Committee Member

Christopher Witt

Fourth Committee Member

Jong Bhak

Fifth Committee Member

Joanna Kelley