Abstract: 

The Indo-Pacific finless porpoise (Neophocaena phocaenoides) is a critical apex predator and a sentinel species for coastal marine ecosystem health, but vulnerable to anthropogenic threats. In Hong Kong waters, its elusive nature has created substantial data acquisition bottlenecks for traditional visual and acoustic monitoring. This thesis addresses these gaps by improving and applying an environmental DNA (eDNA)-based framework, combining species-specific quantitative PCR (qPCR) and metabarcoding, to detect and monitor the Indo-Pacific finless porpoises. Field surveys around the Soko Islands validated sensitivity and compared the detection performance of qPCR and metabarcoding across surface and bottom water layers. Expanding to territory-wide water eDNA sampling, quantitative fish community eDNA data and physicochemical parameters were integrated to predict the finless porpoise eDNA detection. By using spatial interpolation of the quantitative fish eDNA data and calculating the aggregated fish eDNA concentrations at multiple spatial scales, we found that medium-sized and carnivorous fishes, as well as Clupeids family significantly influenced the finless porpoise eDNA detection. The results suggested that the prey fish availability at a certain spatial scale help predicting the presence/absence of the finless porpoises. Building on these findings and historical observation data, Species Distribution Model (SDM) was constructed to convert the static, discrete distribution data to a dynamic, continuous one to predict conservation hotspots. Currently, we used traditional visual survey data, but will combine eDNA data and investigate how integration of eDNA data improves the performance of SDM. Finally, the thesis outlines the development of mitochondrial D-loop markers for population genetic assessment of the Indo-Pacific finless porpoise. Together, this integrated framework, spanning eDNA-based detection of the finless porpoise and prey fish communities, spatial distribution modeling, and population genetics, provides data-driven support for the conservation and management of coastal cetaceans in Hong Kong waters.