| The past two decades witnessed a rapid evolution of sequencing techniques, which enabled the fast accumulation of genomic data and the tremendous development of comparative genomics, a discipline to extract information from genome sequences. In this thesis, I present the applications of comparative genomics to study several important questions in vertebrate evolution.;Retroposition is one of the major mechanisms to create new genes, which are considered to be important in adaptive evolution. By surveying four primate genomes (human, chimpanzee, orangutan, and rhesus), we demonstrated at least two occurrences of "retroposition explosion" during primate evolution, and about 1 of 11 initially non-functional retrocopies will eventually become a functional gene (retrogene). We also found evidence for adaptive evolution for several human retrogenes, suggesting they may play an important role in adaptations.;Genomic changes restricted to individual species provide abundant material to develop lineage-specific traits. We studied the pattern of lineage-specific recruitment of novel genes and pseudogenization of existing genes, two types of genomic changes that have dramatic functional influence on organisms, in humans and chimpanzees. We found that the human genome has disproportionally more lineage-specific novel genes and fewer lineage-specific pseudogenes compared to chimpanzees. Signals of recent selective sweep for human-specific novel genes are detected, indicating that these genomic elements may contribute to human novelties.;It has been debated that whether the small intron size in avian species is related to powered flight, a metabolic demanding behavior. To shed light on this question, we conducted a species-rich survey of intron size variation in amniotes. We found that variation in intron size mirrors the evolution of genome size, and mammals have larger introns than birds and reptiles, which is probably due to the proliferation of repetitive elements along mammalian lineages. Further comparisons showed that introns in flying species are smaller compared to their flightless sister species, consistent with the argument that powered flight favors small genomes/introns. |
