Detecting Indo-Pacific finless porpoises (Neophocaena phocaenoides) around the Soko Islands, Hong Kong, using...

The Indo-Pacific finless porpoise (Neophocaena phocaenoides), a coastal cetacean species widely distributed from the Taiwan Strait to the Persian Gulf, is an iconic species that may represent an overall status indicator of marine ecosystems. However, growing anthropogenic pressures have led to declines in the population of this species in many regions such as Hong Kong waters, highlighting the need for complementary monitoring approaches. In this study, we applied two environmental DNA (eDNA) analysis methods, species-specific quantitative PCR (qPCR) and cetacean-targeting metabarcoding using μCeta primers, to detect Indo-Pacific finless porpoise eDNA around the Soko Islands, Hong Kong. First, we empirically validated the performance of the qPCR primers previously designed in another study. Then, in March 2025, water samples were collected from surface and bottom water layers at 20 locations in the Soko Islands area, a known habitat of Indo-Pacific finless porpoises in Hong Kong. The qPCR analysis detected finless porpoise eDNA in eight out of 40 samples, but all eDNA concentrations were below the limit of quantification. μCeta metabarcoding detected finless porpoise eDNA in seven out of 40 samples. The qPCR and μCeta metabarcoding approaches showed comparable detection rates for Indo-Pacific finless porpoises. Interestingly, the μCeta metabarcoding method detected a transient cetacean species, the false killer whale (Pseudorca crassidens), at a single location. Both methods showed consistent detection rates between surface and bottom water layers, with no statistically significant difference. Overall, the two eDNA analysis methods successfully detected finless porpoise eDNA around the Soko Islands, demonstrating the potential of these approaches for monitoring Indo-Pacific finless porpoises and other cetaceans in this region. Taken together, our findings provide a basis for an eDNA-based cetacean monitoring framework in Hong Kong waters.