Silver, L. (2023). Birth, Death and Diversity: Using genomes and genomics to investigate evolution of the marsupial MHC. The University of Sydney.

The major histocompatibility complex (MHC) is an immune gene family involved in the vertebrate immune response. Class I and class II genes have roles in resistance to disease and show high levels of diversity. MHC genes evolve through a birth and death process with class I genes evolving faster than class II genes. Marsupials are an interesting study system as they give birth to highly altricial and immunologically naïve young. The number of reference genomes available for marsupials has increased and it is now possible to bioinformatically annotate and compare the repertoire of MHC genes and investigate functional diversity in a number of species. Koalas are an iconic Australian marsupial threatened by two pathogens, Chlamydia pecorum and koala retrovirus (KoRV) and are currently listed as ‘Endangered’, making research into their immune system imperative for conservation of the species. This thesis investigates the birth, death and diversity of MHC genes in marsupials. This thesis provides a workflow for investigating evolution and diversity of any gene family in any wildlife species. I was able to achieve this by: i) tracing patterns of gene gain and loss in class II MHC genes across the marsupial lineage (29 species), ii) determine the minimum sequence depth required to accurately genotype MHC genes, iii) identify associations between variation in immune genes, and disease progression using koalas and Chlamydia and iv) investigate variation in SNPs and copy number within MHC genes of koalas. Overall, my thesis demonstrates the power of genomic technologies to investigate the birth, death, and diversity of MHC genes. By leveraging existing genomic resources and investigating sequencing and analysis methods, I was able to identify patterns of gene gain and loss, investigate the role of MHC diversity in disease resistance, and measure diversity across the entire range of koalas.

https://sydney.primo.exlibrisgroup.com/permalink/61USYD_INST/1c0ug48/alma991031727098905106