Millennial-scale reef assemblage shifts in the Spermonde Archipelago, Makassar Strait, Indonesia

The Coral Triangle is the region in the Indo-Pacific with the highest diversity of reef organisms. Coral reefs here have experienced increased anthropogenic stressors since the late 1970s due to destructive fishing, land reclamation, industrialization, and agriculture. Biological observations in the Spermonde Archipelago (SW Sulawesi, Indonesia) started only after large-scale disturbances had begun limiting insights into long-term reef assemblage dynamics. To address this knowledge gap and mitigate shifting baseline bias, we documented assemblage shifts over centennial/millennial timescales using 16 reef sediment cores from two islands in this area. These cores, previously dated using radiocarbon methods, documented the geomorphic history of these islands. We expand upon this by investigating coral, sponge, and foraminifera assemblage shifts over the past 7200 years. Our findings reveal transitions from more mixed growth forms (foliose, massive, and free-living) to predominantly branching Acroporidae over the last 6000 years, likely driven by changing sea-level regimes. The scleractinian species Palauastrea ramosa (Yabe and Sugiyama 1941) was represented in several core samples but has never been observed in modern surveys, suggesting a historical shift in coral assemblages. Foraminiferal assemblages on the reef flat transitioned from dominance of coral/rubble-associated taxa to more algal-associated substrates in recent times. Sponge spicule assemblages indicate a persistence of cryptic/excavating sponges over the past 2000 years. Since these sponges are associated with coral rubble, their presence suggests that declining coral cover has created more rubble habitat in recent millennia. These findings demonstrate that assemblage shifts began centuries to millennia before modern anthropogenic stressors accelerated these changes.