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We employ high-throughput thermal-neutron tomographic imaging to visualise internal diagnostic features of dense fossiliferous breccia from three Pleistocene cave localities in Sumatra, Indonesia. We demonstrate that these seemingly homogeneous breccias are an excellent source of data to aid in determining taphonomic and depositional histories of complex depositional sites such as tropical caves. X-ray Computed Tomographic (CT) imaging is gaining importance amongst palaeontologists as a non-destructive approach to studying fossil remains. Traditional methods of fossil preparation risk damage to the specimen and may destroy contextual evidence in the surrounding matrix. CT imaging can reveal the internal composition and structure of fossils contained within consolidated sediment/rock matrices prior to any destructive mechanical or chemical preparation. Neutron computed tomography (NCT) provides an alternative contrast to X-rays, and in some circumstances, is capable of discerning denser matrices impenetrable to or yielding no contrast with CT imaging. High-throughput neutron imaging reduces neutron fluence during scanning which means there is less residual neutron-induced radioactivation in geological samples; allowing for earlier subsequent analyses. However, this approach remains unutilised in palaeontology, archaeology or geological surveys. Results suggest that the primary agents in the formation of the breccias and concentration of incorporated vertebrate remains are several rapid depositional phases of water and sediment gravity flow. This study highlights the potential for future analyses of breccia deposits in palaeontological studies in caves around the world.

Analyses of Pleistocene fossil proboscideans have long been used as indirect evidence for climactic and environmental shifts in the Sunda shelf of Southeast Asia. Reconstructing the biological effects of rainforest expansion at the Last Glacial Maximum on elephants can be enhanced by a better understanding of fossil proboscidean palaeobiology. We studied fragmented post-cranial fossil remains of an Asian elephant (Elephas maximus) from Pulau Bangka, an island to the east of Sumatra, hypothesised to be within the Late Pleistocene Sundaland savannah corridor. Bone histology of the humerus, rib, and vertebrae from the Bangka fossil were examined and compared with modern conspecifics to reconstruct remodelling. We measured secondary osteon population density, osteon area, diameter, and infill ratios in Haversian bone. Intra-skeletally, we found that the histology of the largely weight-bearing humerus indicated slower remodelling than that of the ribs and vertebrae, which are less biomechanically constrained. Inter-skeletally, the fossil rib histology showed relatively smaller osteons and Haversian canals when compared to the modern samples. Differences in lifestyles, including range-expansion, may have influenced micro-morphometric differences in elephant rib histology. Our results contribute indirect evidence of the effects of climactic variability in the Sunda palaeoenvironment on Pleistocene fauna.

Ngalau Gupin is a broad karstic cave system in the Padang Highlands of western Sumatra, Indonesia. Abundant fossils, consisting of mostly isolated teeth from small-to large-sized animals, were recovered from breccias cemented on the cave walls and unconsolidated sediments on the cave floor. Two loci on the walls and floors of Ngalau Gupin, named NG-A and NG-B respectively, are studied. We determine that NG-B most likely formed as a result of the erosion and redeposition of material from NG-A. The collection reveals a rich, diverse Pleistocene faunal assemblage (Proboscidea, Primates, Rodentia, Artiodactyla, Perissodactyla, Carnivora) largely analogous to extant fauna in the modern rainforests of Sumatra. The hippopotamid Hexaprotodon represents the only globally extinct taxon in deposits from Sumatra and the first record of this animal from the island. This deposit is dated using combined U-series/ESR dating analyses of several teeth that yield a finite age of between ~160 and ~115 ka, depending on the modalities of the dose rate evaluation. These ages constrain the fossil assemblage, not the breccia deposits. Since the direct U-series estimate obtained on the Hexaprotodon specimen is a minimum age, it is therefore not incompatible with the U-series/ESR results. Thus, the true age of the Hexaprotodon can possibly be between 160 and 115 ka, like the other fossil remains at Ngalau Gupin. These results suggest that the faunal assemblage at Ngalau Gupin correlates with late MIS 6 or early MIS 5. Ngalau Gupin likely reflects the formation of a fossil assemblage with two primary taphonomic pathways: a prime-aged dominated macrofauna component initially produced by carnivores but subsequently accumulated by porcupines and transported to the cave, and a microfauna component likely accumulated by small carnivores. Decalcification of the cemented deposit has further resulted in loss of fossil and other sedimentary material. This site adds important new chronologically constrained fossil mammal data for the Pleistocene record of Sumatra, an island relatively poorly investigated for Southeast Asia.

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Caves have been an important source of vertebrate fossils for much of Southeast Asia, particularly for the Quaternary. Despite this importance, the mechanisms by which vertebrate remains accumulate and preserve in Southeast Asian caves has never been systematically reviewed or examined. Here, we present the results of three years of cave surveys in Indonesia and Timor-Leste, describing cave systems and their attendant vertebrate accumulations in diverse geological, biogeographical, and environmental settings. While each cave system is unique, we find that the accumulation and preservation of vertebrate remains are highly dependent on local geology and environment. These factors notwithstanding, we find the dominant factor responsible for faunal deposition is the presence or absence of biological accumulating agents, a factor directly dictated by biogeographical history. In small, isolated, volcanic islands, the only significant accumulation occurs in archaeological settings, thereby limiting our understanding of the palaeontology of those islands prior to human arrival. In karstic landscapes on both oceanic and continental islands, our understanding of the long-term preservation of vertebrates is still in its infancy. The formation processes of vertebrate-bearing breccias, their taphonomic histories, and the criteria used to determine whether these represent syngenetic or multiple deposits remain critically understudied. The latter in particular has important implications for arguments on how breccia deposits from the region should be analysed and interpreted when reconstructing palaeoenvironments.

Genetic evidence for anatomically modern humans (AMH) out of Africa before 75 thousand years ago (ka)1 and in island southeast Asia (ISEA) before 60 ka (93–61 ka)2 predates accepted archaeological records of occupation in the region3. Claims that AMH arrived in ISEA before 60 ka (ref. 4) have been supported only by equivocal5 or non-skeletal evidence6. AMH evidence from this period is rare and lacks robust chronologies owing to a lack of direct dating applications7, poor preservation and/or excavation strategies8 and questionable taxonomic identifications9. Lida Ajer is a Sumatran Pleistocene cave with a rich rainforest fauna associated with fossil human teeth7,10. The importance of the site is unclear owing to unsupported taxonomic identification of these fossils and uncertainties regarding the age of the deposit, therefore it is rarely considered in models of human dispersal. Here we reinvestigate Lida Ajer to identify the teeth confidently and establish a robust chronology using an integrated dating approach. Using enamel–dentine junction morphology, enamel thickness and comparative morphology, we show that the teeth are unequivocally AMH. Luminescence and uranium-series techniques applied to bone-bearing sediments and speleothems, and coupled uranium-series and electron spin resonance dating of mammalian teeth, place modern humans in Sumatra between 73 and 63 ka. This age is consistent with biostratigraphic estimations7, palaeoclimate and sea-level reconstructions, and genetic evidence for a pre-60 ka arrival of AMH into ISEA2. Lida Ajer represents, to our knowledge, the earliest evidence of rainforest occupation by AMH, and underscores the importance of reassessing the timing and environmental context of the dispersal of modern humans out of Africa.

Islands of the western part of the Indonesian archipelago were impacted by climatic and sea level changes during Pleistocene, which affected the dispersals and/or isolation of hominins in this region. This study aims to characterize the diversity of ancient human populations in the Sundaland based on dental collections from several localities in Sumatra and Java. The material consists of 111 teeth, 57 from Pleistocene hominins and 54 from Holocene Homo sapiens. The study of external morphology was done by geometric morphometric analysis on the occlusal surface of the upper (N = 47) and lower second molars (N = 64). We observe group clustering among the samples. There are at least four groups (dental types) of hominins during Pleistocene times. Result suggest that there is an overlapping among them throughout the Lower and early Middle Pleistocene; another group persists until the Late Pleistocene, and two other groups of H. sapiens are present during the Holocene. The implication of this study sheds light on the history of ancient human occupation (continuity/rupture) in Island Southeast Asia during the Quaternary period.

Java is a volcanic island arc formed by the northwards subduction of the Eurasian and Australian Plates. Due to this active subduction, Java has been frequently shocked by earthquakes, which might induce tsunami events. However, there are hardly any ancient geological records of tsunami events in the area. This study aims to determine the presence and to identify sedimentary characters of tsunami deposit in Tegal Buleud, South Sukabumi, West Java. In the study area, there were 4 tsunami layers which were found as thin intercalation within the claystone layer of the Bentang Formation. Those paleotsunami deposits characterized by the occurrence of irregular/disturbed structure such as siltstone rip up, clay clasts, and flame structure occur in normal graded bedding sandstone layer. The grain-size distributions show bimodal and multimodal patterns, with mixing of marine microfossils from inner and middle neritic. The planktonic foraminiferal assemblage indicates that the age of the sediment comparable to N19 (equivalent to Late Miocene - Early Pliocene, at about 5.33 – 3.6 Ma), suggested that these paleotsunami layers were deposited due to the Mio-Pliocene tectonic activity. All the paleotsunami deposits found in Study area are the first and oldest tsunami deposit recorded in Java even in Indonesia. With the discovery of the previously unexplored Late Miocene to Pliocene tsunami deposits found in the study area, the result of this study can be used as a reference for the identification of the Tertiary tsunami deposits present in other parts of Indonesia.