The microstratigraphy and depositional environments of Lida Ajer and Ngalau Gupin, two fossil-bearing tropical limestone caves of west Sumatra.

Lida Ajer and Ngalau Gupin are karstic caves situated in the Padang Highlands, western Sumatra, Indonesia. Lida Ajer is best known for yielding fossil evidence that places the arrival of Homo sapiens in Southeast Asia during Marine Isotope Stage 4, one of the earliest records for the region. Ngalau Gupin recently produced the first record of hippopotamid Hexaprotodon on the island, representing the only globally extinct taxon in Pleistocene deposits from Sumatra. Microstratigraphic (micromorphological) analyses were applied to unconsolidated fossil-bearing cave sediments from these two sites. We use micromorphology as part of a micro-contextualised taphonomic approach to identify the diagenetic processes affecting fossils and sediments within these caves, through phases of their depositional history. The fossil-bearing sediments in Lida Ajer have been subjected to a suite of natural sedimentation processes ranging from water action to carnivore occupation, which would indicate the fossils underwent significant reworking prior to lithification of the deposit. The results demonstrate that the base of the unconsolidated fossil-bearing sediments in Ngalau Gupin were derived from the interior of the cave, where the matrix was partially phosphatized as a result of guano-driven diagenesis. These observations can be used to test hypotheses about the integrity of incorporated vertebrate remains and to aid in local palaeoenvironmental reconstructions. The methods employed in this research have not previously been applied to cave sediments from sites in the Padang Highlands and provide key new insights into the palaeontological and natural history of the western region of Sumatra.

Cranial anatomy of the mekosuchine crocodylian Trilophosuchus rackhami Willis, 1993.

One of the best-preserved crocodylian fossil specimens from the Cenozoic of Australia is the holotype of the mekosuchine Trilophosuchus rackhami, from the middle Miocene (13.56 ± 0.67 Ma) Ringtail Site at Riversleigh, northwestern Queensland. Although lacking most of the snout, the holotype skull of T. rackhami (QMF16856) has an exceptionally well-preserved cranium. Micro-CT scanning of the holotype has allowed for all the preserved cranial bones to be digitally disarticulated, facilitating an unprecedented insight into the cranial anatomy of not just T. rackhami, but any mekosuchine. Trilophosuchus rackhami was a small-bodied crocodylian and one of the most morphologically distinct mekosuchines, characterized by a unique combination of cranial characteristics several of which are exclusive to the species. Fossil material that is definitively referrable to the species T. rackhami is currently known solely from the middle Miocene Ringtail Site. However, an isolated parietal from Hiatus Site at Riversleigh demonstrates that Trilophosuchus also occurred during the late Oligocene (~25 Ma), extending the range of the genus by more than 10 million years. The new description of T. rackhami also allowed for a reevaluation of its phylogenetic relationships. Our results reaffirm the placement of T. rackhami as a member of Mekosuchinae within the subclade Mekosuchini. In all analyses, Mekosuchinae was consistently found to be monophyletic and part of the larger crocodylian clade Longirostres. However, the assignment of Mekosuchinae as a subset of Crocodylidae is brought into question, suggesting that the status of Mekosuchinae as a subfamily should be reconsidered.

Speleological and environmental history of Lida Ajer cave, western Sumatra.

Some of the earliest evidence for the presence of modern humans in rainforests has come from the fossil deposits of Lida Ajer in Sumatra. Two human teeth from this cave were estimated to be 73-63 thousand years old, which is significantly older than some estimates of modern human migration out of Africa based on genetic data. The deposits were interpreted as being associated with a rainforest environment based largely on the presence of abundant orangutan fossils. As well as the main fossil-bearing chamber, fossil-bearing passages are present below a sinkhole, although the relationship between the different fossil deposits has only been tenuously established. Here, we provide significant new sedimentological, geochronological and palaeoecological data aimed at reconstructing the speleological and environmental history of the cave and the clastic and fossil deposits therein. Our data suggest that the Lida Ajer fossils were deposited during Marine Isotope Stage 4, with fossils from the lower passages older than the main fossil chamber. Our use of stable carbon and oxygen isotope analyses of mammalian tooth enamel demonstrates that early humans probably occupied a closed-canopy forest very similar to those present in the region today, although the fossil orangutans may have occupied a slightly different niche. This article is part of the theme issue 'Tropical forests in the deep human past'.

Species identification of Australian marsupials using collagen fingerprinting.

The study of faunal remains from archaeological sites is often complicated by the presence of large numbers of highly fragmented, morphologically unidentifiable bones. In Australia, this is the combined result of harsh preservation conditions and frequent scavenging by marsupial carnivores. The collagen fingerprinting method known as zooarchaeology by mass spectrometry (ZooMS) offers a means to address these challenges and improve identification rates of fragmented bones. Here, we present novel ZooMS peptide markers for 24 extant marsupial and monotreme species that allow for genus-level distinctions between these species. We demonstrate the utility of these new peptide markers by using them to taxonomically identify bone fragments from a nineteenth-century colonial-era pearlshell fishery at Bandicoot Bay, Barrow Island. The suite of peptide biomarkers presented in this study, which focus on a range of ecologically and culturally important species, have the potential to significantly amplify the zooarchaeological and paleontological record of Australia.

High-resolution high-throughput thermal neutron tomographic imaging of fossiliferous cave breccias from Sumatra.

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.

Multiple hominin dispersals into Southwest Asia over the past 400,000 years.

Pleistocene hominin dispersals out of, and back into, Africa necessarily involved traversing the diverse and often challenging environments of Southwest Asia1-4. Archaeological and palaeontological records from the Levantine woodland zone document major biological and cultural shifts, such as alternating occupations by Homo sapiens and Neanderthals. However, Late Quaternary cultural, biological and environmental records from the vast arid zone that constitutes most of Southwest Asia remain scarce, limiting regional-scale insights into changes in hominin demography and behaviour1,2,5. Here we report a series of dated palaeolake sequences, associated with stone tool assemblages and vertebrate fossils, from the Khall Amayshan 4 and Jubbah basins in the Nefud Desert. These findings, including the oldest dated hominin occupations in Arabia, reveal at least five hominin expansions into the Arabian interior, coinciding with brief 'green' windows of reduced aridity approximately 400, 300, 200, 130-75 and 55 thousand years ago. Each occupation phase is characterized by a distinct form of material culture, indicating colonization by diverse hominin groups, and a lack of long-term Southwest Asian population continuity. Within a general pattern of African and Eurasian hominin groups being separated by Pleistocene Saharo-Arabian aridity, our findings reveal the tempo and character of climatically modulated windows for dispersal and admixture.

First record of a tomistomine crocodylian from Australia.

Based on the known fossil record, the majority of crocodylians from the Cenozoic Era of Australia are referred to the extinct clade Mekosuchinae. The only extant crocodylians in Australia are two species of Crocodylus. Hence, the viewpoint that Crocodylus and mekosuchines have been the only crocodylians inhabiting Australia during the Cenozoic has remained largely undisputed. Herein we describe Australia's first tomistomine crocodylian, Gunggamarandu maunala gen. et sp. nov., thus challenging the notion of mekosuchine dominance during most of the Cenozoic. The holotype specimen of Gunggamarandu maunala derives from the Pliocene or Pleistocene of south-eastern Queensland, marking the southern-most global record for Tomistominae. Gunggamarandu maunala is known from a large, incomplete cranium that possesses a unique combination of features that distinguishes it from other crocodylians. Phylogenetic analyses place Gunggamarandu in a basal position within Tomistominae, specifically as a sister taxon to Dollosuchoides from the Eocene of Europe. These results hint at a potential ghost lineage between European and Australian tomistomines going back more than 50 million years. The cranial proportions of the Gunggamarandu maunala holotype specimen indicate it is the largest crocodyliform yet discovered from Australia.

Human footprints provide snapshot of last interglacial ecology in the Arabian interior.

The nature of human dispersals out of Africa has remained elusive because of the poor resolution of paleoecological data in direct association with remains of the earliest non-African people. Here, we report hominin and non-hominin mammalian tracks from an ancient lake deposit in the Arabian Peninsula, dated within the last interglacial. The findings, it is argued, likely represent the oldest securely dated evidence for Homo sapiens in Arabia. The paleoecological evidence indicates a well-watered semi-arid grassland setting during human movements into the Nefud Desert of Saudi Arabia. We conclude that visitation to the lake was transient, likely serving as a place to drink and to forage, and that late Pleistocene human and mammalian migrations and landscape use patterns in Arabia were inexorably linked.

Extinction of eastern Sahul megafauna coincides with sustained environmental deterioration.

Explanations for the Upper Pleistocene extinction of megafauna from Sahul (Australia and New Guinea) remain unresolved. Extinction hypotheses have advanced climate or human-driven scenarios, in spite of over three quarters of Sahul lacking reliable biogeographic or chronologic data. Here we present new megafauna from north-eastern Australia that suffered extinction sometime after 40,100 (±1700) years ago. Megafauna fossils preserved alongside leaves, seeds, pollen and insects, indicate a sclerophyllous forest with heathy understorey that was home to aquatic and terrestrial carnivorous reptiles and megaherbivores, including the world's largest kangaroo. Megafauna species diversity is greater compared to southern sites of similar age, which is contrary to expectations if extinctions followed proposed migration routes for people across Sahul. Our results do not support rapid or synchronous human-mediated continental-wide extinction, or the proposed timing of peak extinction events. Instead, megafauna extinctions coincide with regionally staggered spatio-temporal deterioration in hydroclimate coupled with sustained environmental change.

Australia's prehistoric 'swamp king': revision of the Plio-Pleistocene crocodylian genus Pallimnarchus de Vis, 1886.

The crocodylian fossil record from the Cenozoic of Australasia is notable for its rich taxonomic diversity, and is primarily represented by members of the clade Mekosuchinae. Reports of crocodylian fossils from Australia date back to the late nineteenth century. In 1886, Charles Walter de Vis proposed the name Pallimnarchus pollens for crocodylian fossils from southeast Queensland-the first binomen given to an extinct crocodylian taxon from Australia. Pallimnarchus has come to be regarded as a large, broad-snouted crocodylian from Australia's Plio-Pleistocene, and numerous specimens, few of which are sufficiently complete, have been assigned to it by several authors throughout the twentieth century. In the late 1990s, the genus was expanded to include a second species, Pallimnarchus gracilis. Unfortunately, the original syntype series described as Pallimnarchus pollens is very fragmentary and derives from more than one taxon, while a large part of the subsequently selected lectotype specimen is missing. Because descriptions and illustrations of the complete lectotype do not reveal any autapomorphic features, we propose that Pallimnarchus pollens should be regarded as a nomen dubium. Following this decision, the fossil material previously referred to Pallimnarchus is of uncertain taxonomic placement. A partial skull, formerly assigned to Pallimnarchus pollens and known as 'Geoff Vincent's specimen', possesses many features of diagnostic value and is therefore used as basis to erect a new genus and species-Paludirex vincenti gen. et sp. nov. A comprehensive description is given for the osteology of 'Geoff Vincent's specimen' as well as aspects of its palaeoneurology, the latter being a first for an extinct Australian crocodyliform. The newly named genus is characterized by a unique combination of premaxillary features such as a distinctive arching of the anterior alveolar processes of the premaxillae, a peculiar arrangement of the first two premaxillary alveoli and a large size disparity between the 3rd and 4th premaxillary alveoli. These features presently allow formal recognition of two species within the genus, Paludirex vincenti and Paludirex gracilis comb. nov., with the former having comparatively more robust rostral proportions than the latter. The Paludirex vincenti holotype comes from the Pliocene Chinchilla Sand of the Darling Downs, south-eastern Queensland, whereas the material assigned to Paludirex gracilis is from the Pleistocene of Terrace Site Local Fauna, Riversleigh, northwest Queensland. Phylogenetic analyses recover Paludirex vincenti as a mekosuchine, although further cladistic assessments are needed to better understand the relationships within the clade.

Hidden in plain sight: reassessment of the pig-footed bandicoot, Chaeropus ecaudatus (Peramelemorphia, Chaeropodidae), with a description of a new species from central australia, and use of the fossil record to trace its past distribution.

The Pig-footed Bandicoot, Chaeropus ecaudatus, an extinct arid-adapted bandicoot, was named in 1838 based on a specimen without a tail from the Murray River in New South Wales. Two additional species were later named, C. castanotis and C. occidentalis, which have since been synonymised with C. ecaudatus. Taxonomic research on the genus is rather difficult because of the limited material available for study. Aside from the types of C. castanotis and C. occidentalis housed at the Natural History Museum in London, and the type of C. ecaudatus at the Australian Museum in Sydney, there are fewer than 30 other modern specimens in other collections scattered around the world. Examining skeletal and dental characters for several specimens, and using a combination of traditional morphology, morphometrics, palaeontology and molecular phylogenetics, we have identified two distinct species, C. ecaudatus and C. yirratji sp. nov., with C. ecaudatus having two distinct subspecies, C. e. ecaudatus and C. e. occidentalis. We use palaeontological data to reconstruct the pre-European distribution of the two species, and review the ecological information known about these extinct taxa.

Somewhere beyond the sea: Human cranial remains from the Lesser Sunda Islands (Alor Island, Indonesia) provide insights on Late Pleistocene peopling of Island Southeast Asia.

The migration of anatomically modern humans (AMH) from Africa to every inhabitable continent included their dispersal through Island Southeast Asia (ISEA) to Australia. Significantly, this involved overwater dispersal through the Lesser Sunda Islands between Sunda (continental Southeast Asia) and Sahul (Australia and New Guinea). However, the timing and direction of this movement is still debated. Here, we report on human skeletal material recovered from excavations at two rockshelters, known locally as Tron Bon Lei, on Alor Island, Indonesia. The remains, dated to the Late Pleistocene, are the first anatomically modern human remains recovered in Wallacea dated to this period and are associated with cultural material demonstrating intentional burial. The human remains from Tron Bon Lei represent a population osteometrically distinct from Late Pleistocene Sunda and Sahul AMH. Instead, morphometrically, they appear more similar to Holocene populations in the Lesser Sundas. Thus, they may represent the remains of a population originally from Sunda whose Lesser Sunda Island descendants survived into the Holocene.

Shifting faunal baselines through the Quaternary revealed by cave fossils of eastern Australia.

Fossils from caves in the Manning Karst Region, New South Wales, Australia have long been known, but until now have never been assessed for their palaeontological significance. Here, we report on late Quaternary faunal records from eight caves in the region. Extinct Pleistocene megafaunal taxa are recognised in two systems and include giant echidnas (Tachyglossidae gen. et sp. indet.), devils (Sarcophilus laniarius), koalas (Phascolarctos stirtoni), marsupial 'lions' (Thylacoleo carnifex), and kangaroos (Macropus giganteus titan). Some caves contain skeletal remains of introduced exotics such as sheep and dogs, but also provide a rich record of small-bodied native species including Eastern Bettongs (Bettongia gaimardi), Eastern Chestnut Mice (Pseudomys gracilicaudatus), and White-footed Rabbit Rats (Conilurus albipes). These endemics are either locally extirpated or have suffered total extinction in the historic period. Their skeletal and dental remains were recorded as unmineralised surface specimens in the caves, indicating that they are recent in age. Extant populations have never been recorded locally, thus, their probable loss from the region in historic times had gone unnoticed in the absence of palaeo-evidence. Our findings suggest that the supposed habitat tolerances of such species have been substantially underestimated. It is highly likely that modern populations have suffered niche contraction since the time of European colonisation of the continent. The local extirpations of several species of digging mammal has likely led to decreased functionality of the current ecosystem.

Short-tailed mice with a long fossil record: the genus Leggadina (Rodentia: Muridae) from the Quaternary of Queensland, Australia.

The genus Leggadina (colloquially known as 'short-tailed mice') is a common component of Quaternary faunas of northeastern Australia. They represent a member of the Australian old endemic murid radiation that arrived on the continent sometime during the late Cenozoic. Here we describe two new species of extinct Leggadina from Quaternary cave deposits as well as additional material of the extinct Leggadina macrodonta. Leggadina irvini sp. nov. recovered from Middle-Upper (late) Pleistocene cave deposits near Chillagoe, northeastern Queensland, is the biggest member of the genus, being substantially larger than any other species so far described. Leggadina webbi sp. nov. from Middle Pleistocene cave deposits at Mount Etna, central eastern Queensland, shares features with the oldest species of the genus, the Early Pleistocene L. gregoriensis. Based on the current palaeoecological interpretation of the type locality, L. webbi, represents the only member of the genus that inhabited rainforest. The succession of Leggadina species through the late Quaternary suggests an ecological replacement of the extinct large-bodied L. irvini with the extant, small-bodied L. lakedownesis at Chillagoe. At Mt. Etna, the extinct rainforest species L. webbi is replaced with the extant xeric-adapted L. forresti during the latest Middle Pleistocene. This replacement is associated with a mid-Pleistocene shift towards progressive intensifying seasonal and arid climates. Our study adds to the growing list of small-bodied faunal extinctions during the late Quaternary of northern Australia.

Homo sapiens in Arabia by 85,000 years ago.

Understanding the timing and character of the expansion of Homo sapiens out of Africa is critical for inferring the colonization and admixture processes that underpin global population history. It has been argued that dispersal out of Africa had an early phase, particularly ~130-90 thousand years ago (ka), that reached only the East Mediterranean Levant, and a later phase, ~60-50 ka, that extended across the diverse environments of Eurasia to Sahul. However, recent findings from East Asia and Sahul challenge this model. Here we show that H. sapiens was in the Arabian Peninsula before 85 ka. We describe the Al Wusta-1 (AW-1) intermediate phalanx from the site of Al Wusta in the Nefud desert, Saudi Arabia. AW-1 is the oldest directly dated fossil of our species outside Africa and the Levant. The palaeoenvironmental context of Al Wusta demonstrates that H. sapiens using Middle Palaeolithic stone tools dispersed into Arabia during a phase of increased precipitation driven by orbital forcing, in association with a primarily African fauna. A Bayesian model incorporating independent chronometric age estimates indicates a chronology for Al Wusta of ~95-86 ka, which we correlate with a humid episode in the later part of Marine Isotope Stage 5 known from various regional records. Al Wusta shows that early dispersals were more spatially and temporally extensive than previously thought. Early H. sapiens dispersals out of Africa were not limited to winter rainfall-fed Levantine Mediterranean woodlands immediately adjacent to Africa, but extended deep into the semi-arid grasslands of Arabia, facilitated by periods of enhanced monsoonal rainfall.

Seasonal migration of marsupial megafauna in Pleistocene Sahul (Australia-New Guinea).

Seasonal two-way migration is an ecological phenomenon observed in a wide range of large-bodied placental mammals, but is conspicuously absent in all modern marsupials. Most extant marsupials are typically smaller in body size in comparison to their migratory placental cousins, possibly limiting their potential to undertake long-distance seasonal migrations. But what about earlier, now-extinct giant marsupial megafauna? Here we present new geochemical analyses which show that the largest of the extinct marsupial herbivores, the enormous wombat-like Diprotodon optatum, undertook seasonal, two-way latitudinal migration in eastern Sahul (Pleistocene Australia-New Guinea). Our data infer that this giant marsupial had the potential to perform round-trip journeys of as much as 200 km annually, which is reminiscent of modern East African mammal migrations. These findings provide, to our knowledge, the first evidence for repetitive seasonal migration in any metatherian (including marsupials), living or extinct, and point to an ecological phenomenon absent from the continent since the Late Pleistocene.

Direct dating of Pleistocene stegodon from Timor Island, East Nusa Tenggara.

Stegodons are a commonly recovered extinct proboscidean (elephants and allies) from the Pleistocene record of Southeast Asian oceanic islands. Estimates on when stegodons arrived on individual islands and the timings of their extinctions are poorly constrained due to few reported direct geochronological analyses of their remains. Here we report on uranium-series dating of a stegodon tusk recovered from the Ainaro Gravels of Timor. The six dates obtained indicate the local presence of stegodons in Timor at or before 130 ka, significantly pre-dating the earliest evidence of humans on the island. On the basis of current data, we find no evidence for significant environmental changes or the presence of modern humans in the region during that time. Thus, we do not consider either of these factors to have contributed significantly to their extinction. In the absence of these, we propose that their extinction was possibly the result of long-term demographic and genetic declines associated with an isolated island population.