This Is AuburnElectronic Theses and Dissertations

DNA Barcoding and Related Molecular Markers for Fish Species Authentication, Phylogenetic Assessment and Population Studies




Wong, Li Lian

Type of Degree



Fisheries and Allied Aquacultures


This study highlighted the usage of molecular genetic markers in fish species and population level studies to address food safety and ecological issues. Species level study was constructed based on the growing concern in the food safety arena involving seafood fraud. The first species level study focused on the validation of DNA barcoding using cytochrome oxidase I (COI) gene for catfish species discrimination. 651 bp barcodes from 9 catfish species (and an Ictalurid hybrid) represented by families of Ictaluriidae, Clariidae, and Pangasiidae were generated. Most of the catfish species consensus barcodes constructed from sequence alignments were in agreement with the recorded sequences in two major databases (GenBank and Barcode of Life Data Systems). Validation tests carried out in blinded studies also revealed the reliability of DNA barcoding in species identification. The second study involved the development of microchip-based Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) to be compared with DNA barcoding for efficiency in catfish species identification. Results found that RFLP profiles derived from a combination of all three enzymes were able to produce consistent restriction fragment patterns for all catfish species. Compared to conventional gel-based electrophoresis, this sensitive and robust endpoint detection method can increase resolution of RFLP patterns. In comparison, DNA barcoding has a lower operation cost and longer data collection time, whereas lab-on-chip PCR-RFLP is more suitable for a small scale and rapid identification of catfish species. Finally, the last study focused on the population structure of redeye bass (Micropterus coosae) populations in three main water drainages in Alabama using 10 polymorphic microsatellite loci. Substantial genetic differentiation was iii observed among three major river basins with the highest divergence observed between Coosa Basin and Cahaba Basin (Fst=0.256), indicating restricted gene flow at the micro-geographical scale. Both STRUCTURE analysis and a UPGMA phylogenetic tree revealed four genetic clusters with significant admixture events between water drainages. Overall, the pattern of genetic structuring, strongly associated with river basins rather than geographic distance, signified the occurrence of human-mediated translocations.