Fang Li:
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It is very common that gene trees disagree with the species tree in phylogenetic analysis. This incongruence poses challenges on tree of life construction and further biology character research. The reason behind such incongruence includes incomplete lineage sorting (ILS) and introgression. While Although ILS and introgression have frequently been reported in some closely related species, the investigation in a broad phylogenetic range is still rare.
This PhD thesis is an attempt to systematically explore ILS and introgression in two animal groups, the genus Drosophila and the order Primate. In the first chapter, with the complete genomes of 47 Drosophila species, I produced a well supported tree and found previous uncertainties in subgenus Sophophora can be largely attributed to ILS while controversy over subgenus Drosophila phylogeny is mainly attributed to hybridization.
In the second chapter, I reconstructed the phylogeny of 49 primate species using the full genomes, and inferred that most of this discordance is best explained by incomplete lineage sorting (ILS) rather than introgression in Primate species.
In the third chapter I further explored if ILS contribute to the functional diversification and adaptive selection across species, by taking the species from the great apes as examples. I found that ILS has a broad impact to the biological functions, and no effect on the gene expression profile on the whole genome scale. While we have identified ILS sites those are under positive selection in the ancestor lineage of two distinct related species, indicating that the inheritance of some polymorphism under positive selection in ancestors of ILS loci may provide selective advantages in descendant lineages.