Title Page
Contents
ABSTRACT 11
요약 13
1. INTRODUCTION 15
1.1. Systematics background 15
1.2. Scientific classification 16
1.3. Ecological and economical importance 17
1.4. Molecular systematics 18
1.5. Mitogenomic perspectives 21
1.6. Research gaps 21
2. MATERIAL AND METHODS 23
2.1. Sampling and species identification 23
2.2. DNA extraction, COI amplification, and sequencing 25
2.3. Long-read PCR amplification, and sequencing 25
2.4. Sequence quality check 29
2.5. Dataset construction and analyses 29
2.6. Genomic characterization and comparative analyses 30
2.7. Phylogenetic analyses and time tree 31
3. RESULTS 32
3.1. Species identification and zoogeography 32
3.2. Genetic divergence and haplotype distribution 35
3.3. MOTU estimation and Phylogenetic relationship 37
3.4. Mitogenomic structure and organization 40
3.5. Protein-coding genes (PCGs) 44
3.6. Ribosomal RNA (rRNA) and transfer RNA (tRNA) 46
3.7. Control regions 48
3.8. Matrilineal phylogeny and divergence time 50
3.9. Divergence Time 53
4. DISCUSSION 55
5. CONCLUSION 60
6. REFERENCES 61
APPENDIX 70
LIST OF PUBLICATIONS 73
Table 1. List of designed primer pairs used for the long PCR to assemble Clarias camerunensis mitoge nome. 27
Table 2. List of annotated mitochondrial genes of Clarias camerunensis. 43
Table 3. Nucleotide composition of the mitochondrial genome in different Clarias species. 45
Appendix Table S 1. List of mtCOI sequences generated and acquired from GenBank database for haplotype estimation and phylogeny. 70
Appendix Table S 2. List of sequences data generated and acquired from GenBank database for mitogenome based phylogeny. 72
Figure 1. Dorso-lateral view of Clarias catfish showing the major morphological features for species level identification. 16
Figure 2. Pictorial representation of circular view of vertebrate complete mitogenome and most useful COI gene for species identification. 20
Figure 3. Sample collection sites of Clarias camerunensis and C. gariepinus from Nyong River, Akonolinga, Cameroon. Red pins indicate the collection locality of fish... 24
Figure 4. Results of 1% agarose gel electrophoresis of the amplified PCR products targeting contigs for complete mitogenome of Clarias camerunensis. (A) COI-COIII,... 28
Figure 5. Distribution patterns of Clarias camerunensis in different drainage systems in the Africa 33
Figure 6. Distribution patterns of Clarias gariepinus in different drainage systems within and outside the Africa 34
Figure 7. Relationship among all the haplotypes from different drainage systems according to TCS haplotypic network. (A) Clarias camerunensis (B) Clarias gariepinus 36
Figure 8. Distinct clustering of Clariascamerunensis and C. gariepinus mtCOI sequences from other congeners based on Bayesian phylogeny. The MOTUs... 39
Figure 9. Circular view of the mitochondrial genome of Clarias camerunensis, drawn by the MitoAnnotator online server. 42
Figure 10. Secondary structures of different tRNA genes of Clarias camerunensis and structural variations in base pairing 47
Figure 11. Structural variations in the different conserved domains (marked by red boxes) of the Clarias camerunensis control region and comparison with other Clarias species. 49
Figure 12. The Bayesian matrilineal phylogeny based on the concatenated 13 PCG sequences displays the evolutionary relationship of Clarias camerunensis and other Clarias species 51
Figure 13. Topology recovered by maximum likelihood estimation for Clarias species 52
Figure 14. The TimeTree diagram of approximate divergence time of the Clarias species. The red dots represent the known calibration points of the targeted species acquired from the TimeTree of Life 54
Figure 15. Map showing the possible diversification pattern of Clarias species during Cenozoic era. 59