Pollution and anthropogenic stressors are associated with cetacean vulnerability in coastal waters: Fine-scale diagnostics from eDNA and multispecies modeling.

The Indo-Pacific humpback dolphin (Sousa chinensis) and the Indo-Pacific finless porpoise (Neophocaena phocaenoides) are increasingly threatened by anthropogenic activity, however the relative influence of multiple stressors in shaping their population dynamics remains unclear. Effective implementation of conservation strategies for S. chinensis and N. phocaenoides requires an understanding of the key factors affecting specific populations, including co-occurring influences of pollution, boating activity and potential prey availability, which are currently lacking. Here, we integrated multi-species eDNA metabarcoding with Joint Species Distribution Modeling (JSDM) to assess how environmental gradients, pollution, human activity, and trophic associations interactively influence cetacean distributions in Hong Kong waters. We show that degraded water quality and intensified human activity are negatively associated with cetacean occurrence, with clear differences in species-specific responses to different stressors. Sousa chinensis covaried most strongly with water clarity (i.e. Secchi disc depth), and vessel presence (i.e. boating activity), while N. phocaenoides was negatively associated with nitrate nitrogen and microbial pollution (sewage). JSDM variance partitioning analysis further highlighted that S. chinensis occurrence was primarily negatively associated with anthropogenic disturbances (30.04%), followed by declining physical water quality (e.g. water clarity) (26.63%). Comparatively, N. phocaenoides was more strongly negatively associated with declining physical water quality (40.9%) as well as being more sensitive to increasing anthropogenic disturbances (35.2%). By integrating eDNA and JSDM, we provide a means for simultaneous fine-scale diagnostics of multiple species-specific vulnerabilities, supporting adaptive conservation strategies and guiding the realignment of protected areas to mitigate biodiversity loss in urbanized marine ecosystems.