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  1. Habitat loss and degradation together represent one of the five major factors contributing to the rapid decline of the Yangtze finless porpoise in the Yangtze River. Protecting key habitat patches and maintaining migration corridors between habitat patches are major conservation objectives to ensure the in situ viability of the Yangtze finless porpoise. Baseline information essential for addressing these two objectives includes that pertaining to distribution and habitat preference.
  2. To investigate the distribution and habitat preferences of the Yangtze finless porpoise, five transect surveys were conducted in the Anqing section of the Yangtze River, which has the highest porpoise density among all sections of the river. Porpoise abundance estimates were calculated, and preferences for different habitat types were evaluated.
  3. The calculated porpoise abundance in the Anqing section was 181 (95% CI 125–239) animals on average. The inter‐annual and inter‐seasonal differences in porpoise abundance estimates were not significant. The natural river banks and sandbar shores were the most preferred habitats, representing 46.3 and 29.8% of the porpoise observations, respectively. In contrast, 8.1% of the porpoises were observed in habitats along reinforced river banks, which account for 38.7% of the total coastline. In subsections with natural habitat patches, porpoises were observed in almost every survey, while porpoise occurrence became highly stochastic in subsections with long reinforced river banks. These results indicate a significant tendency of the Yangtze finless porpoise to prefer natural habitats with natural river bank or sandbars but to keep away from reinforced river‐bank habitats.
  4. According to porpoise density in different subsections, free migration may be impeded or only one migration corridor remains in some subsections.
  5. Although protecting finless porpoise habitats has become a primary conservation objective, this study highlights the need to protect frequently used habitat patches and migration corridors, particularly those near natural river banks and sandbars, and to restore ecological environments along reinforced river banks.
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  1. Habitat configuration is an important baseline to delineate protected area design, refine impact mitigation measures and define habitat protection plans for threatened species. For coastal delphinids, outlining their habitat configuration becomes a real challenge when faced with large distribution ranges that straddle international borders, leaving broad information gaps in uninvestigated areas.
  2. This study projected likely habitats of Indo‐Pacific humpback dolphins, Sousa chinensis, in the Beibu Gulf (Gulf of Tonkin) based on occurrence data and remotely sensed oceanographic characteristics. Net primary productivity was derived to measure the ecosystem service of humpback dolphin habitats.
  3. Bathymetry and chlorophyll‐a concentration are major variables contributing to humpback dolphin habitat configuration, which is characterized by shallow water depth and high primary productivity. Three major, likely habitats were identified in the northern Beibu Gulf from western Leizhou Peninsula to the China–Vietnam border, western Gulf of Tonkin from the Red River estuary to the central coast of Vietnam, and south‐western Hainan Island. Less than 9% of likely habitats are currently protected by marine protected areas.
  4. Affinity to high primary productivity and shallow depths implies that prey abundance and foraging efficiency influence habitat selection by Indo‐Pacific humpback dolphins. Anthropogenic activities potentially altering oceanographic characteristics may impact regional marine ecosystem functions, and hence habitat configuration.
  5. Habitat protection actions for Indo‐Pacific humpback dolphins include implementing coordinated and systematic surveys in major habitats, associating core habitat protection with protected area networks and maritime function zoning, ensuring ecosystem function integrity within major habitats, and reducing both explicit lethal impacts and implicit anthropogenic impacts from activities that change oceanographic features. The habitat protection plan should not only consider marine habitats, but also adjacent coastal landscapes and river catchments. This requires coordination, collaboration and information sharing between scientific research teams, government policy representatives, non‐governmental organizations, local communities and other interested stakeholders.
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