鱸形系(Percomorpha)是棘鰭魚類(Acathomorpha)中最分歧的一群，群內關係尚未有定論。而其中的鱸目(Perciformes)是魚類中最大的一個目，共計有20 亞目160 科。
亞目間之親緣關係基於選用的特徵不同而眾說紛紜，目前以日本學者用mtDNA全序列做為探索高階分類群關係的主流。此外，還有其他學者研究採用核基因序列來探討相關之問題。最近莫顯蕎教授對鱸目鰕虎魚亞目(Gobioidei)的類緣關係的研究發現，基於骨骼特徵，鰕虎魚亞目是(魚銜)亞目(Callionymoidei)、海蛾科(Pegasidae)與豹鲂鮄目(Dactylopteriformes)的姐妹群。本研究以此論說為基礎，以粒線體基因體資訊及曾被採用過的核基因28S rRNA、Histone 3、rhodopsin，建立葉鯛科(Glaucosomatidae)之種間類緣關係，並發現臺灣的灰葉鯛(Glaucosoma buergeri)與澳洲之灰葉鯛應屬於不同物種，且得到形態證據的支持。並確認葉鯛之姐妹群為擬金眼鯛科(Pempheridae)，與以耳石及魚鰾等之形態證據所推論的關係相同。在此發現(魚銜)亞目並非一單系群。其中鼠(魚銜)科之近親為海龍魚亞目(Syngnathoidei)之魚類，蜥(魚銜)科之近親為喉盤魚亞目(Gobiesocoidei)之魚類。在粒線體基因體資訊的應用上，因日本學者未做其選用之DNA 序列的變異飽和度探討，故在此檢查粒線體DNA 序列及本研究中選用之其他基因的變異情形，對其做遺傳差異與分類階層相關的統計檢測，觀察變異是否達到飽和，並討論其在不同分類類目(category)中之適用性及類緣關係研究上的應用。

Percomorpha is the most diverse group of Acanthomorpha, and the interrelationships among the members are unsettled. Perciformes, one order of Percomorpha, is the largest fish order with 160 families placed in 20 suborders. The relationships among the suborders of Perciformes remain conflicting between the hypotheses of phylogenetic relationships based on different characters. Presently, major studies on relationships of higher taxa are from Japanese based on the mitogenome, and the other studies were based on nuclear gene sequences. Mok recently suggest a hypothesis of the Gobioidei, it is the sister group to a clade which includes the Callionymoidei, Dactylopteriformes, and possibly Pegasidae, based on osteological characters. Following this, a phylogenetic hypothesis of the Callionymoidei based on mitochondrial and nuclear genes was conducted, and the Taiwanese and Australian specimens of G. buergeri might be treated as different species. Morphological differentiation in the sagitta in these two groups points to the same conclusion. The Pempheridae is the sister group of the Glaucosomatidae that is demonstrated by molecular evidences. It is the same with the relationship based on the morphological characters, such as otolith and swimbladder, etc. The monophyly of Callionymoidei is not recovered in this study. The Syngnathoidei may be the closest group of Callionymidae, and the Gobiesocoidei is suggested to be closest with Draconettidae. In the application of mitogenomic information, the sequcences selected by Japanese have not been decided to be unsaturated, so I made statistical inference of the variation for mitochondrial sequences and selected nuclear genes. I have found out the variation-saturated genes and discuss the application of these sequences to phylogenetic studies derived from these datasets in this study.

Contents
Acknowledgments …... i
Abstract (in Chinese) .. ii
Abstract ... iii
Contents .. v
Table contents ... vi
Figure contents . vi
1. General introduction .... 1
2. Saturation analysis .. 6
2.1 Introduction .... 6
2.2 Materials and methods ... 6
2.2.1 Selection of the molecular markers .... 6
2.2.2 Plotting the mean of mutations between pairs of taxa against their taxonomic category ...8
2.3 Results and discussion ... 8
3. Phylogeny of Glaucosomatidae inferred from molecular evidence ..10
3.1 Introduction .... 10
3.2 Materials and methods ... 11
3.2.1 Materials examined ... 11
3.2.2 Amplification and sequencing .. 12
3.2.3 DNA alignment 13
3.2.4 Phylogenetic analyses 14
3.3 Results .. 15
3.3.1 Sagitta of Glaucosoma species . 15
3.3.2 Molecular phylogeny . 16
3.4 Discussion .. 17
4. Immediate relatives of Glaucosomatidae .. 20
4.1 Introduction .... 20
4.2 Materials and methods ... 20
4.2.1 Taxonomic sampling .. 20
4.2.2 Amplication and sequencing 21
4.2.3 DNA alignment 21
4.2.4 Phylogenetic analyses 21
4.3 Results .. 22
4.3.1 16S ribosomal RNA ... 22
4.3.2 Cytochrome c oxidase subunit I .... 22
4.3.3 28S ribosomal RNA ... 23
4.3.4 Histone 3 23
4.3.5 Rhodopsin ... 23
4.4 Discussion .. 23
5. Immediate relatives of Callionymoidei 25
5.1 Introduction .... 25
5.2 Materials and methods ... 26
5.2.1 Taxonomic sampling .. 26
5.2.2 Amplification and sequencing .. 27
5.2.3 DNA alignment 27
5.2.4 Phylogenetic analysis 27
5.3 Results .. 28
5.3.1 16S ribosomal RNA ... 29
5.3.2 Cytochrome c oxidase subunit I .... 29
5.3.3 Mitochondrial tRNAs 30
5.3.4 28S ribosomal RNA ... 30
5.3.5 Histone 3 30
5.3.6 Rhodopsin ... 30
5.4 Discussion .. 31
6. Conclusion .... 34
References ... 36
Table .. 45
Figure . 53
Appendix 74
Curriculum vitae .... 151

Table Contents
Table 1. Classification of taxa included in phylogentic analyses of Glaucoso- matidae and corresponding GenBank accession numbers ...45
Table 2. Primers used in this study 47
Table 3. Classification of taxa included in the study of relatives of Calliony- moidei and corresponding GenBank accession number ...50

Figure Contents
2. Saturation analysis
Fig. 1. Mutational saturation analysis for the genes used in the phylogenetic analysis ...53
3. Phylogeny of Glaucosomatidae inferred from molecular evidence
Fig. 2. The most-parsimonious tree with all nucleotides weighted equally 53
Fig. 3. The 50% majority rule consensus tree of the 9990 pooled trees from the two independent Bayesian analyses of 16S, COI , Cytb and rho- dopsin data set ..54
Fig. 4. Internal (or medial) view of the left saccular otoliths (sagitta), ante- rior to the left and ventral to the top ...54
4. Immediate relatives of Glaucosomatidae
Fig. 5. Phylogenetic tree based on 16S rDNA using the Neighbor-Joining method ....55
Fig. 6 The most-parsimonious tree from 16S rDNA data set with all nucleo- tides weighted equally ....56
Fig. 7. The 50% majority rule consensus tree from the Bayesian analyses of 16S data set ....56
Fig. 8. Phylogenetic tree based on COI using the Neighbor-Joining method ..57
Fig. 9. Phylogenetic tree based on COI (third codon position are excluded) using the Neighbor-Joining method ....58
Fig. 10. The most-parsimonious tree from COI data set with all nucleotides weighted equally ... 59
Fig. 11. The 50% majority rule consensus tree from the Bayesian analyses of COI data set ....59
Fig. 12. Phylogenetic tree based on 28S rDNA using the Neighbor-Joining method ....60
Fig. 13. The most-parsimonious tree from 28S data set with all nucleotides weighted equally ... 60
Fig. 14. The 50% majority rule consensus tree from the Bayesian analyses of 28S data set ....61
Fig. 15. Phylogenetic tree based on H3 using the Neighbor-Joining method ..61
Fig. 16. The most-parsimonious tree from H3 data set with all nucleotides weighted equally ....62
Fig. 17. The 50% majority rule consensus tree from the Bayesian analyses of H3 data set ...62
Fig. 18. Phylogenetic tree based on rhodopsin using the Neighbor-Joining method ....63
Fig. 19. The most-parsimonious tree from rhodopsin data set with all nucleo- tides weighted equally....63
Fig. 20. The 50% majority rule consensus tree from the Bayesian analyses of rhodopsin data set ....64
5. Immediate relatives of Callionymoidei
Fig. 21. Phylogenetic tree based on 16S rDNA using the Neighbor-Joining method ....64
Fig. 22. The most-parsimonious tree from 16S rDNA data set with all nu- cleotides weighted equally ...65
Fig. 23. The 50% majority rule consensus tree from the Bayesian analyses of 16S data set ....65
Fig. 24. Phylogenetic tree based on COI using the Neighbor-Joining method ....66
Fig. 25. Phylogenetic tree based on COI (third codon position are excluded) using the Neighbor-Joining method ....66
Fig. 26. The most-parsimonious tree from COI data set with all nucleotides weighted equally ...67
Fig. 27. The 50% majority rule consensus tree from the Bayesian analyses of COI data set ....67
Fig. 28. Phylogenetic tree based on tRNAs using the Neighbor-Joining method ....68
Fig. 29. The most-parsimonious tree from tRNAs data set with all nucleo- tides weighted equally ....68
Fig. 30. The 50% majority rule consensus tree from the Bayesian analyses of tRNAs data set...69
Fig. 31. Phylogenetic tree based on 28S using the Neighbor-Joining method ....69
Fig. 32. The most-parsimonious tree from 28S data set with all nucleotides weighted equally ...70
Fig. 33. The 50% majority rule consensus tree from the Bayesian analyses of 28S data set ...70
Fig. 34. Phylogenetic tree based on H3 using the Neighbor-Joining method ..71
Fig. 35 The most-parsimonious tree from H3 data set with all nucleotides weighted equally ...71
Fig. 36. The 50% majority rule consensus tree from the Bayesian analyses of H3 data set ...72
Fig. 37. Phylogenetic tree based on rhodopsin using the Neighbor-Joining method ....72
Fig. 38. The most-parsimonious tree from rhodopsin data set with all nucleo- tides weighted equally ....73
Fig. 39. The 50% majority rule consensus tree from the Bayesian analyses of rhodopsin ....73

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