Integrating behavioral movement and environmental preferences to map critical habitat of whale sharks using long-term satellite tracking in the Indo-Pacific Ocean

Understanding the spatial ecology of wide-ranging marine megafauna is essential for identifying critical habitats and designing effective conservation strategies. Whale sharks undertake extensive movements far beyond well-studied aggregation sites, yet the spatial structure and environmental drivers of these movements remain poorly resolved. Here we integrate long-term satellite tracking data from 2015 to 2025 for 70 whale sharks tagged at four major aggregation sites in the Indonesian archipelago, including Cenderawasih Bay, Kaimana, Saleh Bay, and the Gulf of Tomini, with state-space modeling and MaxEnt habitat suitability analyses to provide a basin-scale assessment of whale shark movement ecology and critical habitats in the central Indo-Pacific. Behavioral states were classified into foraging and migratory movements and then modeled across regions, seasons, sexes, and life stages using oceanographic and seafloor geomorphic predictors. Whale shark habitat selections were strongly structured by behavior and region. Aggregation sites were dominated by foraging behavior and characterized by shallow productive habitats with predictable prey availability, whereas non-aggregation regions functioned primarily as migratory corridors shaped by mesoscale oceanography and seafloor geomorphic features such as canyons and escarpments. Across demographic groups, year-round suitable habitat was limited and largely confined to a few aggregation sites, particularly Cenderawasih Bay and Saleh Bay, highlighting their role as irreplaceable functional habitats. Seasonal non-aggregation habitats in the Flores Sea, Ceram Sea, Timor Sea, and Banda-Arafura transition zone provided important but transient opportunities for foraging and migration. Distinct sex and life-stage specific habitat preferences indicate the need for demographic-specific conservation approaches. Overall, our findings demonstrate that effective whale shark conservation requires combining site-based protection of persistent aggregation habitats with connectivity focused and transboundary management that accounts for seasonal movements across national waters and Areas Beyond National Jurisdiction.