The Malay Archipelago is one of the most biodiverse regions on Earth, but it suffers high extinction risks due to severe anthropogenic pressures. Paleobotanical knowledge provides baselines for the conservation of living analogs and improved understanding of vegetation, biogeography, and paleoenvironments through time. The Malesian bioregion is well studied palynologically, but there have been very few investigations of Cenozoic paleobotany (plant macrofossils) in a century or more. We report the first paleobotanical survey of Brunei Darussalam, a sultanate on the north coast of Borneo that still preserves the majority of its extraordinarily diverse, old-growth tropical rainforests. We discovered abundant compression floras dominated by angiosperm leaves at two sites of probable Pliocene age: Berakas Beach, in the Liang Formation, and Kampong Lugu, in an undescribed stratigraphic unit. Both sites also yielded rich palynofloral assemblages from the macrofossil-bearing beds, indicating lowland fern-dominated swamp (Berakas Beach) and mangrove swamp (Kampong Lugu) depositional environments. Fern spores from at least nine families dominate both palynological assemblages, along with abundant fungal and freshwater algal remains, rare marine microplankton, at least four mangrove genera, and a diverse rainforest tree and liana contribution (at least 19 families) with scarce pollen of Dipterocarpaceae, today’s dominant regional life form. Compressed leaves and rare reproductive material represent influx to the depocenters from the adjacent coastal rainforests. Although only about 40% of specimens preserve informative details, we can distinguish 23 leaf and two reproductive morphotypes among the two sites. Dipterocarps are by far the most abundant group in both compression assemblages, providing rare, localized evidence for dipterocarp-dominated lowland rainforests in the Malay Archipelago before the Pleistocene. The dipterocarp fossils include winged Shorea fruits, at least two species of plicate Dipterocarpus leaves, and very common Dryobalanops leaves. We attribute additional leaf taxa to Rhamnaceae (Ziziphus), Melastomataceae, and Araceae (Rhaphidophora), all rare or new fossil records for the region. The dipterocarp leaf dominance contrasts sharply with the family’s <1% representation in the palynofloras from the same strata. This result directly demonstrates that dipterocarp pollen is prone to strong taphonomic filtering and underscores the importance of macrofossils for quantifying the timing of the dipterocarps’ rise to dominance in the region. Our work shows that complex coastal rainforests dominated by dipterocarps, adjacent to swamps and mangroves and otherwise similar to modern ecosystems, have existed in Borneo for at least 4–5 million years. Our findings add historical impetus for the conservation of these gravely imperiled and extremely biodiverse ecosystems.
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