Representativeness and ecological alignment of Japan's marine protected areas: A reproducible national baseline and priority gaps for 30×30

Area-based conservation targets can conceal ecological bias. This study establishes a reproducible national baseline for the representativeness and ecological alignment of Japan's designated MPA/OECM estate. OBIS and GBIF records from 2000 to 2025 were harmonized and summarized on 20-km and 25-km equal-area grids, and label-specific Q90 hotspots were identified from positive occurrence-based biodiversity values. Designation coverage was evaluated alongside a study-specific Gini-based protection-alignment index (PAI), while ecological gaps were ranked on a common grid using transparent patch attributes. The harmonized and quality-filtered marine occurrence pool contained 360,240 records; retention analyses subsequently used grid-assigned, label-specific point sets. Designation overlap reached 30.2–45.9% for macro-indicator hotspots, but varied from 12.3% for corals and 15.8% for sea turtles to 66.9% for macroalgae and seagrass. Absolute coverage and PAI yielded different rankings, reflecting complementary dimensions: the amount of hotspot area designated and how rapidly coverage accumulated among stronger hotspot cells. The ten highest-ranked gap patches spanned 1.7–41,431.8 km 2 and clustered along the Nansei–Ryukyu arc, the Kuroshio-influenced Pacific margin, the northern transition belt, and selected enclosed seas. These patches represent ecological screening priorities rather than policy-ready MPA proposals. Overall, the framework provides a reproducible basis for assessing whether progress toward 30×30 improves ecological representation, rather than designated area alone.