| The neutral theory suggests that the majority of evolutionary changes at the molecular level is caused not by Darwinian selection but by genetic drift of selectively neutral or nearly neutral mutants. Because the expected effects of genetic drift can be mathematically described with some precision, evolutionary geneticists have claimed that genetic drift should be the "null hypothesis" used to explain an evolutionary observation unless there is positive evidence of natural selection. This present thesis aims to explore the patterns of molecular evolution of neutral genes as well as genes under positive selection in a group of Austro-Papuan birds---the Maluridae. Applying newly developed 29 anonymous nuclear DNA markers, Chapter 2 explored phylogeographic patterns in red-backed fairywrens. Although none of the genetic markers exhibited reciprocal monophyletic pattern, there was strong phylogeographic signal to detect two subpopulations when all genetic data were analyzed together. Chapter 3 expanded the scope of study to the family level. All genetic markers used in this study exhibited monophyletic patterns for each genus, but the lack of monophyly within each genus was frequently observed. Lastly, in Chapter 4, the molecular evolution of reproductive genes was studied. Taking advantage of a newly developed 454 pyrosequencing technique, reproductive genes expressed in male gonads of fairy wrens were newly identified. Further analysis revealed that seven out of twenty genes involved in reproduction had undergone strong positive selection. Reproductive genes under selection exhibited a higher level of monophyletic pattern than neutral genes used in previous phylogeographic and phylogenetic studies. By examining the patterns of molecular evolution both without and with positive selection, the present thesis showed that the lack of monophyly was a very common phenomenon within species as well as at the family level, and that positive (directional) selection can enhance the degree of monophyly. |
