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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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