Ancient genomes reveal over two thousand years of dingo population structure.

Dingoes are culturally and ecologically important free-living canids whose ancestors arrived in Australia over 3,000 B.P., likely transported by seafaring people. However, the early history of dingoes in Australia-including the number of founding populations and their routes of introduction-remains uncertain. This uncertainty arises partly from the complex and poorly understood relationship between modern dingoes and New Guinea singing dogs, and suspicions that post-Colonial hybridization has introduced recent domestic dog ancestry into the genomes of many wild dingo populations. In this study, we analyzed genome-wide data from nine ancient dingo specimens ranging in age from 400 to 2,746 y old, predating the introduction of domestic dogs to Australia by European colonists. We uncovered evidence that the continent-wide population structure observed in modern dingo populations had already emerged several thousand years ago. We also detected excess allele sharing between New Guinea singing dogs and ancient dingoes from coastal New South Wales (NSW) compared to ancient dingoes from southern Australia, irrespective of any post-Colonial hybrid ancestry in the genomes of modern individuals. Our results are consistent with several demographic scenarios, including a scenario where the ancestry of dingoes from the east coast of Australia results from at least two waves of migration from source populations with varying affinities to New Guinea singing dogs. We also contribute to the growing body of evidence that modern dingoes derive little genomic ancestry from post-Colonial hybridization with other domestic dog lineages, instead descending primarily from ancient canids introduced to Sahul thousands of years ago.

No evidence for widespread island extinctions after Pleistocene hominin arrival.

The arrival of modern humans into previously unoccupied island ecosystems is closely linked to widespread extinction, and a key reason cited for Pleistocene megafauna extinction is anthropogenic overhunting. A common assumption based on late Holocene records is that humans always negatively impact insular biotas, which requires an extrapolation of recent human behavior and technology into the archaeological past. Hominins have been on islands since at least the early Pleistocene and Homo sapiens for at least 50 thousand y (ka). Over such lengthy intervals it is scarcely surprising that significant evolutionary, behavioral, and cultural changes occurred. However, the deep-time link between human arrival and island extinctions has never been explored globally. Here, we examine archaeological and paleontological records of all Pleistocene islands with a documented hominin presence to examine whether humans have always been destructive agents. We show that extinctions at a global level cannot be associated with Pleistocene hominin arrival based on current data and are difficult to disentangle from records of environmental change. It is not until the Holocene that large-scale changes in technology, dispersal, demography, and human behavior visibly affect island ecosystems. The extinction acceleration we are currently experiencing is thus not inherent but rather part of a more recent cultural complex.

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.

Least-cost pathway models indicate northern human dispersal from Sunda to Sahul.

Archaeological records from Australia provide the earliest, indirect evidence for maritime crossings by early modern humans, as the islands to the north-west of the continent (Wallacea) have never been connected to the mainland. Suggested in 1977 by Joseph B. Birdsell, the two main routes from Sunda (mainland Southeast Asia) to Sahul (Australia-New Guinea), still in debate today, are a northern route through Sulawesi with a landing in New Guinea, or a southern route through Bali, Timor and thence landing in northern Australia. Here we construct least-cost pathway models of human dispersal from Sunda to Sahul at 65 ka and 70 ka by extending previous out-of-Africa least-cost models through the digitization of these routes. We recover overwhelming support for a northern route into Sahul, with a landing location on present-day Misool Island. Minimal support is also recovered for the southern route at 70 ka, with a possible crossing to Sahul from eastern Timor. Review of archaeological records on the Wallacean islands crossed by our northern route indicate a dearth of archaeological research in this region. Meanwhile, the comparatively better studied southern islands still lack any archaeological dates comparable to those known for initial occupation in Sunda and Sahul. Based on our model results we suggest Misool Island as the initial landing site for early modern humans on Sahul and recommend a future focus on archaeological fieldwork in the northern Wallacean islands.

42,000-year-old worked and pigment-stained Nautilus shell from Jerimalai (Timor-Leste): Evidence for an early coastal adaptation in ISEA.

In this paper, we describe worked and pigment-stained Nautilus shell artefacts recovered from Jerimalai, Timor-Leste. Two of these artefacts come from contexts dating to between 38,000 and 42,000 cal. BP (calibrated years before present), and exhibit manufacturing traces (drilling, pressure flaking, grinding), as well as red colourant staining. Through describing more complete Nautilus shell ornaments from younger levels from this same site (>15,900, 9500, and 5000 cal. BP), we demonstrate that those dating to the initial occupation period of Jerimalai are of anthropogenic origin. The identification of such early shell working examples of pelagic shell in Island Southeast Asia not only adds to our growing understanding of the importance of marine resources to the earliest modern human communities in this region, but also indicates that a remarkably enduring shell working tradition was enacted in this area of the globe. Additionally, these artefacts provide the first material culture evidence that the inhabitants of Jerimalai were not only exploiting coastal resources for their nutritional requirements, but also incorporating these materials into their social technologies, and by extension, their social systems. In other words, we argue that the people of Jerimalai were already practicing a developed coastal adaptation by at least 42,000 cal. BP.

Early modern human lithic technology from Jerimalai, East Timor.

Jerimalai is a rock shelter in East Timor with cultural remains dated to 42,000 years ago, making it one of the oldest known sites of modern human activity in island Southeast Asia. It has special global significance for its record of early pelagic fishing and ancient shell fish hooks. It is also of regional significance for its early occupation and comparatively large assemblage of Pleistocene stone artefacts. Three major findings arise from our study of the stone artefacts. First, there is little change in lithic technology over the 42,000 year sequence, with the most noticeable change being the addition of new artefact types and raw materials in the mid-Holocene. Second, the assemblage is dominated by small chert cores and implements rather than pebble tools and choppers, a pattern we argue pattern, we argue, that is common in island SE Asian sites as opposed to mainland SE Asian sites. Third, the Jerimalai assemblage bears a striking resemblance to the assemblage from Liang Bua, argued by the Liang Bua excavation team to be associated with Homo floresiensis. We argue that the near proximity of these two islands along the Indonesian island chain (c.100 km apart), the long antiquity of modern human occupation in the region (as documented at Jerimalai), and the strong resemblance of distinctive flake stone technologies seen at both sites, raises the intriguing possibility that both the Liang Bua and Jerimalai assemblages were created by modern humans.

Abrupt onset of intensive human occupation 44,000 years ago on the threshold of Sahul.

Archaeological evidence attests multiple early dispersals of Homo sapiens out of Africa, but genetic evidence points to the primacy of a single dispersal 70-40 ka. Laili in Timor-Leste is on the southern dispersal route between Eurasia and Australasia and has the earliest record of human occupation in the eastern Wallacean archipelago. New evidence from the site shows that, unusually in the region, sediment accumulated in the shelter without human occupation, in the window 59-54 ka. This was followed by an abrupt onset of intensive human habitation beginning ~44 ka. The initial occupation is distinctive from overlying layers in the aquatic focus of faunal exploitation, while it has similarities in material culture to other early Homo sapiens sites in Wallacea. We suggest that the intensive early occupation at Laili represents a colonisation phase, which may have overwhelmed previous human dispersals in this part of the world.

Earliest known funerary rites in Wallacea after the last glacial maximum.

The insular region of Wallacea has become a focal point for studying Pleistocene human ecological and cultural adaptations in island environments, however, little is understood about early burial traditions during the Pleistocene. Here we investigate maritime interactions and burial practices at Ratu Mali 2, an elevated coastal cave site on the small island of Kisar in the Lesser Sunda Islands of eastern Indonesia dated to 15,500-3700 cal. BP. This multidisciplinary study demonstrates extreme marine dietary adaptations, engagement with an extensive exchange network across open seas, and early mortuary practices. A flexed male and a female, interred in a single grave with abundant shellfish and obsidian at Ratu Mali 2 by 14.7 ka are the oldest known human burials in Wallacea with established funerary rites. These findings highlight the impressive flexibility of our species in marginal environments and provide insight into the earliest known ritualised treatment of the dead in Wallacea.

Dingoes, companions in life and death: The significance of archaeological canid burial practices in Australia.

The dingo, also known as the Australian native dog, was introduced in the late Holocene. Dingoes were primarily wild animals but a number resided in Aboriginal people's camps. Traditionally, these individuals were taken from wild litters before weaning and raised by Aboriginal people. It is generally believed that these dingoes were not directly provided for, and upon sexual maturity, returned to reproduce in the wild. However, some died while in the company of people and, were buried in occupation sites. This Australian practice parallels the burial of domestic dogs in many regions of the Asia-Pacific and beyond but has attracted very little research. We explore the historical and archaeological evidence for dingo burial, examining its different forms, chronological and geographic distribution, and cultural significance. Dingoes were usually buried in the same manner as Aboriginal community members and often in areas used for human burial, sometimes alongside people. This practice probably occurred from the time of their introduction until soon after European colonisation. We present a case study of dingo burials from Curracurrang Rockshelter (NSW) which provides insights into the lives of ancient tame dingoes, and suggests that domestication and genetic continuity between successive camp-dwelling generations may have occurred prior to European contact.

The Exploitation of Toxic Fish from the Terminal Pleistocene in Maritime Southeast Asia: A Case Study from the Mindoro Archaeological Sites, Philippines.

Representatives of the Diodontidae family (porcupinefish) are known to have been fished by prehistoric Indo-Pacific populations; however, the antiquity of the use of this family is thus far unknown. We report here on the presence of Diodontidae in the archaeological sites of Bubog I, II, and Bilat in Mindoro, Philippines, dating back to c. 13,000 BP (Before Present). This evidence demonstrates the early exploitation by islanders of poisonous fish. Every part of porcupinefish can be toxic, but the toxicity is mostly concentrated in some organs, while other parts are edible. The continuous presence of Diodontidae remains throughout the stratigraphic record of these Philippines shell middens suggests that porcupinefish were prepared by human inhabitants of the sites to render them safe for consumption, indicating an advanced cultural knowledge of the preparation needed to separate the toxic principle from the edible parts. This constitutes one of the rare examples of poison processing by humans, aside from the contentious wooden stick poison applicator from Border Cave (South Africa).

Talking Dead. New burials from Tron Bon Lei (Alor Island, Indonesia) inform on the evolution of mortuary practices from the terminal Pleistocene to the Holocene in Southeast Asia.

Burial elaborations are a human behaviour that, in recent contexts can inform on social diversification, belief systems, and the introduction of new practices resulting from migration or cultural transmission. The study of mortuary practices in Mainland and Island Southeast Asia has revealed complex and diverse treatments of the deceased. This paper contributes to this topic with the description of three new burials excavated in Tron Bon Lei (Alor Island, Indonesia) dated to 7.5, 10, and 12 kya cal BP. In addition to the bioskeletal profiles and palaeohealth observations, we propose the adoption of archaeothanatological methods to characterise burial types in the region. Through the analysis of skeletal element representation, body position, articulation, and grave associations, we provide an example of a holistic approach to mortuary treatments in the Lesser Sunda Islands. Our results provide significant new data for understanding the evolution and diversification of burial practices in Southeast Asia, contributing to a growing body of literature describing prehistoric socio-cultural behaviour in this region.

Ancient genomes from the last three millennia support multiple human dispersals into Wallacea.

Previous research indicates that human genetic diversity in Wallacea-islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves-has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter-gatherer communities. Yet, inferences based on present-day groups proved insufficient to disentangle this region's demographic movements and admixture timings. Here, we investigate the spatio-temporal patterns of variation in Wallacea based on genome-wide data from 16 ancient individuals (2600-250 years BP) from the North Moluccas, Sulawesi and East Nusa Tenggara. While ancestry in the northern islands primarily reflects contact between Austronesian- and Papuan-related groups, ancestry in the southern islands reveals additional contributions from Mainland Southeast Asia that seem to predate the arrival of Austronesians. Admixture time estimates further support multiple and/or continuous admixture involving Papuan- and Asian-related groups throughout Wallacea. Our results clarify previously debated times of admixture and suggest that the Neolithic dispersals into Island Southeast Asia are associated with the spread of multiple genetic ancestries.

Mitogenomes Reveal Two Major Influxes of Papuan Ancestry across Wallacea Following the Last Glacial Maximum and Austronesian Contact.

The tropical archipelago of Wallacea contains thousands of individual islands interspersed between mainland Asia and Near Oceania, and marks the location of a series of ancient oceanic voyages leading to the peopling of Sahul-i.e., the former continent that joined Australia and New Guinea at a time of lowered sea level-by 50,000 years ago. Despite the apparent deep antiquity of human presence in Wallacea, prior population history research in this region has been hampered by patchy archaeological and genetic records and is largely concentrated upon more recent history that follows the arrival of Austronesian seafarers ~3000-4000 years ago (3-4 ka). To shed light on the deeper history of Wallacea and its connections with New Guinea and Australia, we performed phylogeographic analyses on 656 whole mitogenomes from these three regions, including 186 new samples from eight Wallacean islands and three West Papuan populations. Our results point to a surprisingly dynamic population history in Wallacea, marked by two periods of extensive demographic change concentrated around the Last Glacial Maximum ~15 ka and post-Austronesian contact ~3 ka. These changes appear to have greatly diminished genetic signals informative about the original peopling of Sahul, and have important implications for our current understanding of the population history of the region.

Stochastic models support rapid peopling of Late Pleistocene Sahul.

The peopling of Sahul (the combined continent of Australia and New Guinea) represents the earliest continental migration and settlement event of solely anatomically modern humans, but its patterns and ecological drivers remain largely conceptual in the current literature. We present an advanced stochastic-ecological model to test the relative support for scenarios describing where and when the first humans entered Sahul, and their most probable routes of early settlement. The model supports a dominant entry via the northwest Sahul Shelf first, potentially followed by a second entry through New Guinea, with initial entry most consistent with 50,000 or 75,000 years ago based on comparison with bias-corrected archaeological map layers. The model's emergent properties predict that peopling of the entire continent occurred rapidly across all ecological environments within 156-208 human generations (4368-5599 years) and at a plausible rate of 0.71-0.92 km year-1. More broadly, our methods and approaches can readily inform other global migration debates, with results supporting an exit of anatomically modern humans from Africa 63,000-90,000 years ago, and the peopling of Eurasia in as little as 12,000-15,000 years via inland routes.

Early ground axe technology in Wallacea: The first excavations on Obi Island.

The first excavations on Obi Island, north-east Wallacea, reveal three phases of occupation beginning in the terminal Pleistocene. Ground shell artefacts appear at the end of the terminal Pleistocene, the earliest examples in Wallacea. In the subsequent early Holocene occupation phase, ground stone axe flakes appear, which are again the earliest examples in Wallacea. Ground axes were likely instrumental to subsistence in Obi's dense tropical forest. From ~8000 BP there was a hiatus lasting several millennia, perhaps because increased precipitation and forest density made the sites inhospitable. The site was reoccupied in the Metal Age, with this third phase including quadrangular ground stone artefacts, as well as pottery and pigs; reflecting Austronesian influences. Greater connectivity at this time is also indicated by an Oliva shell bead tradition that occurs in southern Wallacea and an exotic obsidian artefact. The emergence of ground axes on Obi is an independent example of a broader pattern of intensification at the Pleistocene-Holocene transition in Wallacea and New Guinea, evincing human innovation in response to rapid environmental change.

Microanatomical Record of Cortical Bone Remodeling and High Vascularity in a Fossil Giant Rat Midshaft Femur.

Rat cortical bone does not typically undergo secondary (Haversian) remodeling. Haversian organization of rat bone has been mainly observed in experimental settings following biomechanical or dietary manipulation. Here, we report an observation of cortical secondary osteons within a histological femur cross-section from an extinct (late Quaternary) form of Timorese giant rat (Murinae gen. et sp. indet). The medio-lateral midshaft diameter of its femur, used as a measure of bone size, is 6.15 mm and indicates a heavier than normal skeletal frame. We compare this sample to bone histology in a small rat's midshaft femur of 2.33 mm diameter. A complete lack of Haversian bone remodeling characteristics is noted for the smaller sample, which is dominated by radial vascular canals. The giant rat shows clear secondary osteons and diffuse vascularity mainly composed of tightly packed longitudinal canals across its cortex. It appears that rat cortical bone can undergo bone remodeling, and is organized in a highly vascularized manner, in insular giant cases. Our findings from Timor align with results reported in experimental rat model skeletal biology literature and other insular fossil rat material. Where macroanatomical examination is limited, histological observations on fossil rat limb bones have the potential to aid reconstructions of life history and skeletal growth aspects in these rodents. Anat Rec, 302:1934-1940, 2019. © 2019 American Association for Anatomy.

Early human settlement of Sahul was not an accident.

The first peopling of Sahul (Australia, New Guinea and the Aru Islands joined at lower sea levels) by anatomically modern humans required multiple maritime crossings through Wallacea, with at least one approaching 100 km. Whether these crossings were accidental or intentional is unknown. Using coastal-viewshed analysis and ocean drift modelling combined with population projections, we show that the probability of randomly reaching Sahul by any route is <5% until ≥40 adults are 'washed off' an island at least once every 20 years. We then demonstrate that choosing a time of departure and making minimal headway (0.5 knots) toward a destination greatly increases the likelihood of arrival. While drift modelling demonstrates the existence of 'bottleneck' crossings on all routes, arrival via New Guinea is more likely than via northwestern Australia. We conclude that anatomically modern humans had the capacity to plan and make open-sea voyages lasting several days by at least 50,000 years ago.

New dates on dingo bones from Madura Cave provide oldest firm evidence for arrival of the species in Australia.

The dingo is the only placental land mammal aside from murids and bats to have made the water crossings to reach Australia prior to European arrival. It is thought that they arrived as a commensal animal with people, some time in the mid Holocene. However, the timing of their arrival is still a subject of major debate with published age estimates varying widely. This is largely because the age estimates for dingo arrival are based on archaeological deposit dates and genetic divergence estimates, rather than on the dingo bones themselves. Currently, estimates vary from between 5000-4000 years ago, for finds from archaeological contexts, and as much as 18,000 based on DNA age estimates. The timing of dingo arrival is important as post arrival they transformed Indigenous societies across mainland Australia and have been implicated in the extinction of a number of animals including the Tasmanian tiger. Here we present the results of direct dating of dingo bones from their oldest known archaeological context, Madura Cave on the Nullarbor Plain. These dates demonstrate that dingoes were in southern Australia by between 3348 and 3081 years ago. We suggest that following their introduction the dingo may have spread extremely rapidly throughout mainland Australia.

Home Is Where the Hearth Is: Anthracological and Microstratigraphic Analyses of Pleistocene and Holocene Combustion Features, Riwi Cave (Kimberley, Western Australia).

The manipulation of fire is a technological act. The identification of the archaeological signatures of the controlled use of fire has important implications not only for the estimations of the origins and functions of the first fireplaces but also for our understanding of prehistoric technological development and resource use. At Riwi (Kimberley region, Western Australia), excavations over two field seasons have revealed a discontinuous occupation sequence over the past 45 ka, showing numerous, different combustion features interspersed within the deposit. Anthracological and micromorphological investigations at Riwi Cave indicate that the combustion features at the site can be categorised into three types: flat combustion features (type A), dug combustion features (type B) and thick accumulations of mixed combustion residues (type C). These provide evidence for two kinds of combustion practice: (i) fires lit directly on the ground and most likely not re-used and (ii) ground ovens, the latter appearing some 10,000 years after the first evidence for occupation of the site. A comparison of the wood species identified within these combustion features with those from equivalent scattered context levels, enables an exploration of the potential factors influencing wood selection and fire use through time at the site. A detailed understanding of the relationship between wood charcoal remains and archaeological context yields significant information on changes to environmental context and site occupation patterns over time.

An Enduring Shell Artefact Tradition from Timor-Leste: Oliva Bead Production from the Pleistocene to Late Holocene at Jerimalai, Lene Hara, and Matja Kuru 1 and 2.

In this paper, we describe 485 Oliva spp. shell beads recovered from four archaeological cave sites Jerimalai, Lene Hara, Matja Kuru 1, and Matja Kuru 2, located in Timor-Leste, Island Southeast Asia. While Pleistocene-aged examples of modified marine shells used for personal ornamentation are common in African and Eurasian assemblages, they are exceedingly rare in Southeast Asia, leading some researchers to suggest that these Modern Human societies were less complex than those found further west. In Timor-Leste, the lowest Oliva bead to be recovered was directly dated to ca. 37,000 cal. BP, making it the oldest piece of personal ornamentation in Southeast Asia. Morphometric, taphonomic, use wear, and residue analyses of these beads alongside modern reference specimens, and experimentally made examples indicate that the Oliva shells were modified to be strung consecutively (as in a necklace), and while their mode of production changed remarkably little over the thousands of years they were utilised, an increase in their deposition around 6,000 cal. BP suggests that there was a change in their use coinciding with sea-level stabilisation. These tiny beads demonstrate that early Island Southeast Asian societies produced the same kinds of symbolic material culture we have come to expect from the more intensively studied African/Eurasian region, and that limited sampling and poor recovery methods have biased our perspectives of this region.