Detection of environmental DNA of the Indo-Pacific humpback dolphins in Hong Kong waters using quantitative PCR

Environmental DNA (eDNA) analysis is a promising method to enhance the sensitivity and efficiency of biodiversity monitoring. In Hong Kong, the Indo-Pacific humpback dolphin (Sousa chinensis) is an iconic marine mammal inhabiting shallow coastal regions, playing a vital role in the local biodiversity. However, their population is declining, highlighting the need for effective monitoring methods for S. chinensis. In this study, we developed a species-specific qPCR assay for detecting S. chinensis eDNA. We designed primers and a probe targeting the Cytb region of mitochondrial DNA. Specificity tests and evaluations of the limit of detection and quantification demonstrated that the primers and probe possess sufficient specificity and sensitivity to detect S. chinensis eDNA. Our qPCR method was further validated by detecting S. chinensis eDNA in water samples collected from areas where S. chinensis individuals were sighted. Analysis of 56 coastal water samples collected over two seasons revealed that S. chinensis utilizes the western and southern Lantau regions of Hong Kong waters. With further enhancements to the eDNA-based survey method, including larger water volumes, broader spatial coverage, and targeting other cetaceans and fish, our framework will aid in the conservation of S. chinensis in Hong Kong waters.