The Ancient Origins of Borneo’s Rainforest

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The first leaf fossil study of Borneo’s rainforest, led by Penn State University in partnership with Universiti Brunei Darussalam and published in the peer-reviewed journal PeerJ in March 2022, demonstrated that the current dominant tree family, the dipterocarps, has structured and shaped these forests without interruption for at least 4 to 5 million years.

This is not a minor footnote in botanical science. It is the first direct, macrofossil-level proof that the first leaf fossil study of Borneo’s rainforest could produce evidence of ecological continuity on a geological timescale, stretching back to the Pliocene Epoch.

The First Leaf Fossil Study of Borneo’s Rainforest

1. Background of the Research Project

The research team, led by Professor Peter Wilf of Penn State’s Department of Geosciences, set out to address a significant gap in the paleontological record of Southeast Asia.

While the Amazon basin and Central African rainforests have been studied paleobotanically for decades, the fossil record of Asia’s wet tropical forests had remained, in Wilf’s own words, “surprisingly scarce.” This scarcity was not random. It reflects a structural challenge unique to the region: the same conditions that sustain the lush vegetation also destroy potential fossils.

Acidic, deeply weathered tropical soils break down organic material rapidly, and the dense forest canopy limits the rock exposures where fossils could be found and studied. The research team spent considerable time conducting intensive geological reconnaissance across Brunei before identifying two productive fossil sites.

The study also had a deliberately applied purpose beyond pure paleontology. Wilf and his colleagues were motivated by the idea that demonstrating the long historical presence of a threatened ecosystem strengthens the ethical and scientific case for its conservation.

A forest that has existed for 4 million years carries a different kind of heritage value than one that regrew after recent disturbance. When paleontological evidence is tied to a living ecosystem, it supports the criteria for designation as a UNESCO World Heritage Site and creates a stronger public case for legal protection.

2. Location of the Fossil Discoveries

The fossil sites were located within the nation of Brunei Darussalam, a small sovereign state on the northern coast of the island of Borneo. Brunei is significant in the regional context because it is one of the very few countries in tropical Asia that still preserves more than half of its old-growth rainforest.

The two discovery sites, identified through intensive field reconnaissance, were chosen because they provided rock exposures in a region where such exposures are exceptionally rare due to dense vegetation and soil cover.

The Kampong Lugu site in Tutong district proved particularly productive, yielding fossilized leaf material from multiple dipterocarp genera as well as a diverse range of supporting plant groups.

The geographic positioning of Brunei within Borneo, at the intersection of lowland coastal rainforest, freshwater swamp forest, and mangrove systems, made its fossil record especially rich for reconstructing past ecosystem structure.

3. Research Methods and Fossil Analysis Techniques

The team employed a combination of leaf architecture analysis and palynology (the scientific study of pollen and spores, used here to reconstruct past plant communities) to interpret the fossil record. Leaf architecture analysis involves the detailed examination of physical features of fossilized leaves, including

• venation patterns (the network of veins visible on the leaf surface),
• margins (whether the leaf edge is smooth or toothed),
• shape, and
• size.

These features are taxonomically diagnostic, meaning they can reliably identify a plant family, genus, or even species without requiring soft tissue preservation. This approach is more informative than pollen analysis alone for the dipterocarp family, because dipterocarp pollen does not preserve reliably in sediment, creating a systematic undercount of dipterocarps in previous pollen-only studies.

• Leaf venation patterns, margin types, and surface textures were catalogued for each specimen to assign taxonomic identifications at the genus level or higher.
• Fossil pollen and spore assemblages were studied alongside the leaf fossils from the same rock layers to reconstruct the full plant community, including understory, swamp, and mangrove vegetation.
• Radiometric dating and biostratigraphic correlation (using known age ranges of index fossils to date the surrounding rock layers) were applied to establish the temporal age of the deposits as Pliocene, between 5.3 and 2.6 million years ago.
• Comparative morphological analysis matched fossil leaf specimens with modern dipterocarp species currently growing in Brunei, establishing visual and structural continuity between ancient and living plant forms.

Wilf et al. (PeerJ, 2022) identified three distinct genera of dipterocarp trees in the fossil leaf assemblage, including Dryobalanops, and found that dipterocarps represented more fossilized leaf specimens than any other single plant group at both sites combined.

The numerical dominance of dipterocarp leaf fossils confirms that the current ecosystem structure, where dipterocarps form the canopy framework, is not a recent development but an ancient and self-reinforcing ecological state.

What the Leaf Fossils Revealed About Borneo’s Ancient Plant Life

1. Types of Fossilized Leaves Identified

The fossil assemblage recovered from the Brunei sites was taxonomically rich and ecologically representative. Researchers documented leaf fossils from three different dipterocarp genera, including Dryobalanops, whose living species are nearly all classified as threatened or critically endangered. Beyond the dipterocarps, the team recovered fossilized material from understory plants such as

• Ziziphus (the jujube, a small tree or shrub found in the forest understory),
• Melastomataceae (a large family of tropical flowering plants that still forms a significant component of Borneo’s undergrowth today), and
• a climbing aroid plant of the genus Rhaphidophora, which is related to the popular houseplant Monstera.

The presence of these understory and climbing plant groups is significant because it shows that the ecosystem was not just dominated by large canopy trees but also had the same layered vertical complexity, from forest floor climbers to subcanopy shrubs to emergent dipterocarp giants, that characterizes modern Bornean rainforest.

2. Estimated Age of the Fossils and the 2025 Discovery

The original 2022 PeerJ study placed the fossil leaf flora firmly in the Pliocene Epoch, dating the deposits to between 4 and 5 million years ago based on biostratigraphic analysis.

A follow-up study published in the American Journal of Botany in May 2025, led by doctoral researcher Teng-Xiang Wang at Penn State, pushed the record further by identifying fossilized leaves of Dryobalanops rappa specifically, a single currently living and endangered dipterocarp species.

Those fossils, recovered from the Kampong Lugu site, were dated at a minimum of 2 million years old, representing the first time that a fossil of a specific living endangered tropical tree species had ever been identified.

This 2025 discovery is extraordinary because it collapses the conceptual distance between the fossil record and the present: the same species that researchers can photograph today in Brunei’s peatland forests was growing in the same location at least 2 million years ago.

3. Comparison Between Ancient and Modern Plant Species

The morphological comparison between fossil and modern dipterocarp leaves was striking for the degree of similarity rather than difference. Leaf venation patterns, overall shape, and margin characteristics of fossil specimens matched closely with those of living Dryobalanops species.

This level of morphological conservation across millions of years is a phenomenon known as stasis (the persistence of a species or plant type without significant structural change over geological time), and it suggests that Borneo’s environmental conditions have remained stable enough across the Pliocene and Pleistocene to sustain the same dominant plant forms without forcing significant evolutionary adaptation.

Wang et al. (American Journal of Botany, 2025) confirmed that fossilized leaves of Dryobalanops rappa from Brunei are at least 2 million years old, making this the first fossil evidence ever recorded for a living endangered tropical tree species anywhere in the world.

For conservationists and policymakers, this finding transforms the case for protecting Brunei’s peatland forests from a biodiversity argument into a paleontological heritage argument: these exact trees have been present for 2 million years.

Evidence of an Ancient and Stable Rainforest Ecosystem

1. Similarities Between Prehistoric and Present-Day Forests

One of the most striking findings from the combined leaf and pollen analysis was how accurately the ancient ecosystem mirrored the one that still exists. The fossil record showed complex coastal rainforests dominated by dipterocarps, bordered by freshwater swamp forests and mangrove systems, with a rich understory of

• ferns,
• aroids, and
• melastomes.

This is essentially a description of what a researcher or farmer living in rural Brunei today can observe by walking into the remaining old-growth forest. The pollen data added the swamp and mangrove communities to the picture that the leaf fossils alone could not fully represent, creating what Wilf described as “a fairly complete representation” of the ancient landscape.

This reconstruction matters for agricultural scientists because it confirms that Borneo’s forest ecosystems are not adaptive generalists that can quickly reassemble after disturbance.

They are ancient, finely tuned communities where the same keystone species have co-evolved with the same pollinators, seed dispersers, and soil organisms for millions of years. Replacing a cleared dipterocarp forest with oil palm monocultures does not simply reduce biodiversity in the present; it erases a biological relationship network that took millions of years to build.

2. Long-Term Ecological Stability

The evidence of ecological stability across the Pliocene and into the Pleistocene (2.6 million to 11,700 years ago) is particularly important given the dramatic climate fluctuations that occurred during those periods.

The Pliocene was generally warmer and wetter than today, while the Pleistocene brought repeated ice ages that dramatically altered vegetation across temperate and even many subtropical regions.

The fact that Borneo’s dipterocarp forests survived the ice ages of the Pleistocene intact tells us these are not fragile ecosystems that collapse under climatic pressure. What they cannot withstand is direct human destruction at the rate currently being applied.

Borneo, however, remained within a climatic refuge (a geographic area that retains stable environmental conditions while surrounding regions experience dramatic change), allowing its dipterocarp forests to persist continuously while other regions lost and regained forest cover repeatedly.

3. Persistence of Tropical Rainforest Characteristics Over Millions of Years

The continuity documented in the Brunei fossil record points to a deeper principle in tropical ecology: everwet equatorial climates create conditions of biological stability that are fundamentally different from the boom-and-bust cycles of temperate environments.

Borneo sits within what ecologists call the Malesian bioregion, a chain of islands stretching from Sumatra to New Guinea, positioned close enough to the equator that seasonal temperature variation is minimal and rainfall is distributed relatively evenly across the year.

This climatic constancy has allowed plant communities to accumulate diversity slowly over geological time rather than being periodically reset by glaciation or extended drought. The fossil record from Brunei is the first direct leaf-level confirmation that this process of slow, stable accumulation has been operating continuously for at least 4 to 5 million years.

Borneo’s Rainforest Through Geological Time

1. Historical Climate and Environmental Conditions

During the Pliocene Epoch, when the Brunei fossils were deposited, global average temperatures were approximately 2 to 3 degrees Celsius higher than pre-industrial levels. Sea levels were correspondingly higher, and the coastline configuration of Borneo differed from today.

Despite these differences, the fundamental climatic driver of Borneo’s ecology, which is the year-round high rainfall and stable temperature characteristic of equatorial position, remained in place.

This is why the fossil flora looks so familiar: the plants that thrived in the Pliocene climate were the same ones best suited to the current climate, and they have simply continued to dominate without being displaced.

2. Evolution of the Island’s Vegetation

Borneo’s plant diversity did not arise solely through in-situ evolution on the island. The Malesian region’s history is tied to tectonic events, particularly the collision of the Australian and Asian tectonic plates that brought new land areas and plant lineages into proximity.

Dipterocarp trees are thought to have originated in Africa and dispersed eastward across Asia over tens of millions of years, arriving in the Malesian region and subsequently diversifying into the extraordinary radiation of species seen today.

With nearly 270 dipterocarp species currently present, Borneo holds more than half of the world’s total dipterocarp diversity. The Pliocene fossil record now confirms that this diversification was largely complete and ecologically consolidated by at least 4 to 5 million years ago.

3. Major Geological Events That Shaped the Ecosystem

The most significant geological influence on Borneo’s forest history during and after the Pliocene was the cyclic lowering of sea levels during Pleistocene glaciations.

During periods of peak glaciation, sea levels dropped by as much as 120 meters, transforming the shallow Sunda Shelf into dry land and connecting Borneo to Sumatra, the Malay Peninsula, and Java into a single large landmass known as Sundaland.

These land connections allowed species to disperse between the islands, while Borneo’s interior mountain ranges acted as barriers that promoted local speciation. When sea levels rose again at the end of each glaciation, Borneo was re-isolated, trapping and preserving its accumulated diversity.

This repeated cycle of connection and isolation is one of the key mechanisms behind Borneo’s extraordinary species richness, and the fossil record from Brunei places that richness in its proper deep-time context.

Wilf et al. (PeerJ, 2022) documented that the ancient fossil flora included plant groups from at least four distinct habitat types, specifically lowland dipterocarp rainforest, freshwater swamp forest, mangrove, and climbing plant communities, all co-occurring within a single stratigraphic horizon dating to the Pliocene.

The multi-habitat structure of the ancient ecosystem matches the interlocked mosaic of habitats still present in Brunei today, confirming that conservation of one habitat type in isolation is insufficient; the whole mosaic must be preserved to protect the evolutionary legacy.

Biodiversity Implications of an Ancient Ecosystem Identity

1. How Ancient Origins Contribute to Modern Biodiversity

Ancient ecosystems accumulate biodiversity through a process ecologists call time-integrated niche filling: over millions of years, species evolve to exploit progressively finer ecological distinctions within the environment, producing communities of extraordinary species richness.

Borneo’s current plant diversity reflects exactly this process. Brunei, an area roughly equivalent to the state of Delaware in the United States, contains more than seven times the plant diversity of the entire state of Pennsylvania.

That staggering ratio is not coincidental. It is the direct product of millions of years of uninterrupted ecological accumulation, now confirmed by the leaf fossil record to extend at least to the Pliocene.

2. Relationship Between Fossil Evidence and Current Plant Diversity

The practical relationship between the fossil evidence and current plant diversity operates through what conservation scientists call deep-time baseline establishment.

When researchers can prove that a specific plant community has occupied a specific location continuously for millions of years, they can establish that the current diversity patterns are not the result of recent recolonization or ecological recovery but of long-term in-place evolution.

This matters for understanding which species depend on which others, how mutualistic relationships between plants and their animal partners have co-evolved, and why the removal of a single keystone species, such as a canopy dipterocarp, can trigger cascading losses through layers of species that evolved in its presence.

3. Importance for Understanding Tropical Ecosystem Evolution

The Brunei leaf fossil study directly addresses a theoretical problem in tropical ecology known as the species-richness paradox: tropical forests are so diverse that standard ecological models cannot fully explain their richness through current-day processes alone.

The fossil evidence supports the hypothesis that much of the richness is historically accumulated over geological time rather than generated by present-day processes. This has implications for how ecologists design tropical forest models, how agronomists approach agroforestry systems in Southeast Asia, and how policymakers justify expenditure on conservation over agricultural conversion.

Scientific Importance of Leaf Fossils in Tropical Paleobotany

1. Why Leaf Fossils Are Valuable to Paleobotany

Paleobotany (the scientific study of fossilized plant material to reconstruct the history of plant life on Earth) has traditionally relied on three main types of evidence: pollen, wood, and leaves. Each type preserves different information and has different biases.

Pollen is microscopic and highly resistant to decay, making it the most commonly recovered plant fossil in most environments. However, pollen often cannot distinguish between closely related species, and as the Brunei study dramatically demonstrated, some plant families such as the dipterocarps produce pollen that decays quickly even in normally favorable preservation conditions.

Fossilized wood provides information about tree size and internal structure but cannot identify the species responsible for the understory and ground-level vegetation that give a forest much of its ecological character.

Leaf fossils, by contrast, are taxonomically informative at the genus level and sometimes species level, they preserve information about the entire plant community including understory plants, and they can directly link ancient flora to living species as the 2025 Dryobalanops rappa discovery demonstrated.

2. Insights They Provide Beyond Pollen and Wood Fossils

1. Leaf venation patterns and margin characteristics allow genus-level or species-level identification that pollen grains rarely permit, providing a much higher resolution picture of what specific trees were present in a past ecosystem.
2. The physical size and shape of fossil leaves encode paleoclimate data: larger leaves with smooth margins are statistically associated with warmer, wetter climates, a method called leaf physiognomy (the use of leaf physical characteristics to infer past climate) that provides independent temperature and rainfall estimates from the same samples.
3. Leaf fossils capture the full vertical structure of the forest community, from canopy trees down through understory shrubs and ground-level ferns, rather than the partial view provided by pollen assemblages dominated by wind-pollinated species.
4. When fossil leaves match living species with sufficient precision, as in the Dryobalanops rappa case, they create a direct temporal link between the living plant and the past, providing evidence of species longevity that no other fossil type currently delivers.

3. Challenges of Preserving and Studying Tropical Plant Fossils

The rarity of tropical leaf fossil sites is not a reflection of how few plants lived in ancient tropical forests. It reflects the destructive chemistry of tropical soils.

Deeply weathered, acidic, laterite soils (iron-rich soils formed by intense weathering under high heat and rainfall) dissolve organic material rapidly, leaving almost no fossil record in the most common soil types of tropical lowlands.

Every leaf fossil recovered from a tropical site is, in a very real sense, a survivor against overwhelming geological odds. The fact that Borneo’s ancient leaves survived at all makes what they tell us all the more valuable.

Fossil preservation requires very specific conditions: rapid burial by fine-grained sediment such as lake muds or river silts, followed by protection from the acidic conditions that dominate most tropical settings.

Finding sites where these conditions coincide with accessible rock exposure in a landscape covered by dense forest is exceptionally challenging, which is why intensive reconnaissance was a necessary first step in the Brunei research.

Conservation Relevance of the Ancient Ecosystem Identity

1. What the Findings Mean for Rainforest Conservation

The conservation implications of the leaf fossil research are direct and urgent. An ecosystem with a demonstrated 4 to 5 million year history is not replaceable on any policy-relevant timescale.

When a conservation argument is made purely on the basis of current biodiversity metrics, it can be countered with claims that cleared land can eventually revegetate or that species can survive in smaller habitat fragments. The fossil evidence removes that counterargument entirely.

The community structure of Borneo’s dipterocarp forests is the product of millions of years of co-evolution between canopy trees, understory plants, soil organisms, pollinators, and seed dispersers. Plantation monocultures and secondary scrub vegetation cannot reproduce this structure within any human lifetime, or indeed within the span of modern civilization.

2. Protecting Ecosystems with Deep Evolutionary History

The concept of paleoconservation (using fossil evidence to strengthen conservation decisions by demonstrating the deep evolutionary history of a living ecosystem) has gained momentum since the Brunei study’s publication.

Knowledge of fossil history provides foundational support for setting up conservation areas and has practical legal relevance for UNESCO World Heritage designation criteria.

Brunei’s decision to maintain more than half of its old-growth forest cover positions it as the anchor of conservation value in a region where most neighboring countries have cleared the majority of their forests.

3. Threats Facing Borneo’s Ancient Rainforest Today

The urgency of the conservation message from the fossil research is amplified by the scale of current forest loss. Estimates place the loss of Borneo’s original primary forest cover at around 92%, with the majority occurring since the 1970s. A 2020 study confirmed that 50% of the Bornean rainforest was lost between 1973 and 2015.

In 2025, Indonesia’s deforestation rate surged by 66% compared to previous years, with Kalimantan (Indonesian Borneo) among the most affected territories. The primary drivers are palm oil production, pulpwood plantations, and mining, all serving global demand chains.

1. Dipterocarp trees are specifically targeted by the logging industry because their large, slow-growing hardwood trunks command premium timber prices, making the forests that took the longest to develop the most economically attractive to clear.

2. Palm oil conversion is largely irreversible on ecological timescales, because monoculture oil palm plantations so fundamentally alter soil chemistry, hydrology, and light conditions that spontaneous dipterocarp forest regeneration does not occur after abandonment.

3. Climate change presents an additional threat: while Borneo’s forests survived past climate cycles as a refuge species, those transitions occurred over thousands to tens of thousands of years, whereas the current rate of warming is orders of magnitude faster, potentially exceeding the adaptive capacity of long-lived tree species.

4. Infrastructure expansion, including new roads associated with mining and plantation development, fragments previously continuous forest and reduces the genetic connectivity that long-lived tree populations need to maintain resilience.

According to Global Forest Watch data cited in multiple 2024 and 2025 analyses, Indonesia cleared approximately 264,000 hectares of forest in its Kalimantan and Sumatran territories in 2024 alone, with 2024 recorded as one of the highest deforestation years globally for tropical primary forests.

At this rate of clearing, areas that the fossil record confirms have supported continuous dipterocarp forest for 4 to 5 million years could be completely converted within one or two human generations.

Future Research Directions in Borneo’s Paleobotany

1. Additional Fossil Studies Planned in Borneo

The Brunei discoveries are explicitly described by the research team as a starting point rather than a conclusion. Wilf and collaborators at Universiti Brunei Darussalam have expressed intent to expand reconnaissance into other parts of Borneo where similar Pliocene or Miocene sedimentary rock exposures might exist.

The Malaysian states of Sabah and Sarawak, which occupy the northern and western parts of the island, and the Indonesian province of Kalimantan to the south, all potentially contain unexplored fossil sites.

Expanding the geographic coverage of fossil sampling would allow researchers to determine whether the ecological patterns documented in Brunei represent a localized or island-wide feature of Borneo’s forest history.

2. Unanswered Questions About Rainforest Evolution

Several significant questions remain open from the current data. The fossil record so far confirms dipterocarp dominance from the Pliocene onward, but the timing of the initial dipterocarp radiation in Borneo, which likely occurred in the Miocene (23 to 5.3 million years ago), is still poorly understood due to the absence of Miocene-age leaf fossil sites.

Resolving this earlier history would establish whether the Pliocene landscape was itself the product of a long established community or a relatively recent ecological assembly.

Researchers also want to understand the relationship between Borneo’s fossil flora and contemporaneous fossil floras from the rest of the Malesian bioregion, including Sumatra and the Philippines, to map the historical geography of dipterocarp dominance across the entire region.

3. Potential Discoveries from Further Paleobotanical Research

Beyond leaf fossils, the research team anticipates that more intensive sampling at the Brunei sites and newly discovered sites could yield fossil fruits, seeds, and even insect herbivory traces on leaf surfaces.

Fossil herbivory traces (bite marks, mine tunnels, and gall structures preserved on fossilized leaves) provide direct evidence of plant-insect interactions in the past and can reveal whether the specific insect communities that pollinate and feed on dipterocarp trees today have similarly ancient origins.

This line of evidence would extend the fossil argument beyond plants alone and into the co-evolutionary networks that make Borneo’s forest so biologically complex and so difficult to reconstruct once destroyed.

Advances in ancient DNA extraction from exceptionally well-preserved specimens may also eventually allow molecular confirmation of the taxonomic identifications currently based on morphology alone.

Conclusion

The first leaf fossil study of Borneo’s rainforest has permanently altered the scientific understanding of what this ecosystem is and how long it has existed. By demonstrating through direct macrofossil evidence that dipterocarp-dominated forests have structured Borneo’s landscape continuously for at least 4 to 5 million years, the research led by Wilf, Wang, and their international collaborators has done something that no biodiversity survey or remote sensing study alone could accomplish: it has given Borneo’s forests a documented geological identity. The first leaf fossil study of Borneo’s rainforest reveals the current ecosystem is ancient in the most precise scientific sense of that word, not metaphorically old or ecologically mature, but measurably continuous across Pliocene and Pleistocene time.