Dated co-occurrence of Homo erectus and Gigantopithecus from Tham Khuyen Cave, Vietnam

Old World Fruit Bats (Pteropodidae, Chiroptera) from the Pleistocene of Vietnam

Isolated teeth of a lesser short-nosed fruit bat Cynopterus brachyotis (Müller, 1838), a fulvous fruit bat Rousettus leschenaultii (Desmarest, 1820), and a dawn bat Eonycteris spelaea (Dobson, 1871) are described from the Middle Pleistocene Tham Hai cave locality in northern Vietnam (Lang Son Province). These are the first fossil findings of the Old World fruit bats in Vietnam. The Middle Pleistocene association of Pteropodidae from the Tham Hai locality may largely reflect the composition of species that roosted in local caves.

Preliminary description of a late Middle Pleistocene mammalian fauna prior to the extinction of Gigantopithecus blacki from the Yixiantian Cave, Guangxi ZAR, South China

In recent years, nearly 20 cave sites with rich assemblages of mammalian fossils have been found and excavated in the Chongzuo area, Guangxi Zhuang Autonomous Region, China. Their ages are distributed throughout the entire Pleistocene Epoch. These discoveries have greatly facilitated our understanding of the evolution of the Stegodon-Ailuropoda fauna and the environmental context of human evolution in southern China. Here, we present a preliminary report on a diverse late Middle Pleistocene mammalian fauna from the Yixiantian Cave in southern China, which is a typical representative of the Stegodon-Ailuropoda fauna (sensu lato). The fossil mammals are represented by isolated dental remains only. In 2010 and 2011, two seasons of systematic excavations at the Yixiantian Cave yielded a total of 4,958 identifiable mammalian teeth. They were identified as belonging to 37 species and 6 orders of mammals. In addition, the tooth type of all the teeth representing each species was also determined where possible. A single fragmentary molar was identified as belonging to Gigantopithecus blacki, indicating that its population had declined sharply at this time and was on the brink of extinction. Description of the Yixiantian fauna will not only help better characterize the composition of the Stegodon-Ailuropoda fauna during the late Middle Pleistocene, but also clarify our understanding of the paleoenvironmental context at a time just prior to the extinction of G. blacki.

The first maternal genetic study of hunter-gatherers from Vietnam

The current limitation of ancient DNA data from Vietnam led to the controversy surrounding the prehistory of people in this region. The combination of high heat and humidity damaged ancient bones that challenged the study of human evolution, especially when using DNA as study materials. So far, only 4 k years of history have been recorded despite the 65 k years of history of anatomically modern human occupations in Vietnam. Here we report, to our knowledge, the oldest mitogenomes of two hunter-gatherers from Vietnam. We extracted DNA from the femurs of two individuals aged 6.2 k cal BP from the Con Co Ngua (CCN) site in Thanh Hoa, Vietnam. This archeological site is the largest cemetery of the hunter-gatherer population in Southeast Asia (SEA) that was discovered, but their genetics have not been explored until the present. We indicated that the CCN haplotype belongs to a rare haplogroup that was not detected in any present-day Vietnamese individuals. Further matrilineal analysis on CCN mitogenomes showed a close relationship with ancient farmers and present-day populations in SEA. The mitogenomes of hunter-gatherers from Vietnam debate the "two layers" model of peopling history in SEA and provide an alternative solution for studying challenging ancient human samples from Vietnam.

The First Record of Eothenomys (Arvicolinae, Cricetidae, Rodentia) from the Pleistocene of Vietnam

The Oriental vole Eothenomys eleusis (Thomas, 1911) is identified from the Middle Pleistocene Tham Hai cave locality in northern Vietnam (Lang Son Province) based on isolated teeth. This is the first record of the Pleistocene Arvicolinae in Vietnam and the first fossil find of Eothenomys outside of China.

Estimates of absolute crown strength and bite force in the lower postcanine dentition of Gigantopithecus blacki

Gigantopithecus blacki is hypothesized to have been capable of processing mechanically challenging foods, which likely required this species to have high dental resistance to fracture and/or large bite force. To test this hypothesis, we used two recently developed approaches to estimate absolute crown strength and bite force of the lower postcanine dentition. Sixteen Gigantopithecus mandibular permanent cheek teeth were scanned by micro-computed tomography. From virtual mesial cross-sections, we measured average enamel thickness and bi-cervical diameter to estimate absolute crown strength, and cuspal enamel thickness and dentine horn angle to estimate bite force. We compared G. blacki with a sample of extant great apes (Pan, Pongo, and Gorilla) and australopiths (Australopithecus anamensis, Australopithecus afarensis, Australopithecus africanus, Paranthropus robustus, and Paranthropus boisei). We also evaluated statistical differences in absolute crown strength and bite force between the premolars and molars for G. blacki. Results reveal that molar crown strength is absolutely greater, and molar bite force absolutely higher, in G. blacki than all other taxa except P. boisei, suggesting that G. blacki molars have exceptionally high resistance to fracture and the ability to generate exceptionally high bite force. In addition, G. blacki premolars have comparable absolute crown strength and larger bite force capabilities compared with its molars, implying possible functional specializations in premolars. The dental specialization of G. blacki could thus represent an adaptation to further facilitate the processing of mechanically challenging foods. While it is currently not possible to determine which types of foods were actually consumed by G. blacki through this study, direct evidence (e.g. dental chipping and microwear) left by the foods eaten by G. blacki could potentially lead to greater insights into its dietary ecology.

Gigantopithecus blacki (Primates, Ponginae) from the Lang Trang Cave (Northern Vietnam): The Latest Gigantopithecus in the Late Pleistocene?

The dental remains of Gigantopithecus blacki von Koenigswald, 1935 (a complete right m2 with roots and distal fragment of left m2 crown) from the Upper Pleistocene deposits of the Lang Trang cave in northern Vietnam (Thanh Hoa Province) are described. It is the first record of Gigantopithecus in the Upper Pleistocene of Vietnam and, apparently, the second one in the Upper Pleistocene in general (considering material from Shuangtan cave in southern China). Probably, the extinction of G. blacki was confined to the Middle-Late Pleistocene transition, and the specimens from the Lang Trang cave belong to one of the latest relict populations of Gigantopithecus.

A Middle Pleistocene Denisovan molar from the Annamite Chain of northern Laos

The Pleistocene presence of the genus Homo in continental Southeast Asia is primarily evidenced by a sparse stone tool record and rare human remains. Here we report a Middle Pleistocene hominin specimen from Laos, with the discovery of a molar from the Tam Ngu Hao 2 (Cobra Cave) limestone cave in the Annamite Mountains. The age of the fossil-bearing breccia ranges between 164–131 kyr, based on the Bayesian modelling of luminescence dating of the sedimentary matrix from which it was recovered, U-series dating of an overlying flowstone, and U-series–ESR dating of associated faunal teeth. Analyses of the internal structure of the molar in tandem with palaeoproteomic analyses of the enamel indicate that the tooth derives from a young, likely female, Homo individual. The close morphological affinities with the Xiahe specimen from China indicate that they belong to the same taxon and that Tam Ngu Hao 2 most likely represents a Denisovan.

Evidence for the presence of Homo during the Middle Pleistocene is limited in continental Southeast Asia. Here, the authors report a hominin molar from Tam Ngu Hao 2 (Cobra Cave), dated to 164–131 kyr. They use morphological and paleoproteomic analysis to show that it likely belonged to a female Denisovan.

Evolutionary history of orangutan plasmodia revealed by phylogenetic analysis of complete mtDNA genomes and new biogeographical divergence dating calibration models

During the past 15 years, researchers have shown a renewed interest in the study of the Plasmodium parasites that infect orangutans. Most recently, studies examined the phylogenetic relationships and divergence dates of these parasites in orangutans using complete mitochondrial DNA genomes. Questions regarding the dating of these parasites, however, remain. In the present study, we provide a new calibration model for dating the origins of Plasmodium parasites in orangutans using a modified date range for the origin of macaques in Asia. Our Bayesian phylogenetic analyses of complete Plasmodium sp. mitochondrial DNA genomes inferred two clades of plasmodia in orangutans (Pongo 1 and Pongo 2), and that these clades likely represent the previously identified species Plasmodium pitheci and Plasmodium silvaticum. However, we cannot identify which Pongo clade is representative of the morphologically described species. The most recent common ancestor of both Pongo sp. plasmodia, Plasmodium. hylobati, and Plasmodium. inui dates to 3-3.16 million years ago (mya) (95% highest posterior density [HPD]: 2.09-4.08 mya). The Pongo 1 parasite diversified 0.33-0.36 mya (95% HPD: 0.12-0.63), while the Pongo 2 parasite diversified 1.15-1.22 mya (95% HPD: 0.63-1.82 mya). It now seems likely that the monkey Plasmodium (P. inui) is the result of a host switch event from the Pongo 2 parasite to sympatric monkeys, or P. hylobati. Our new estimates for the divergence of orangutan malaria parasites, and subsequent diversification, are all several hundred thousand years later than previous Bayesian estimates.

A New Species of Typhlomys (Platacanthomyidae, Rodentia) from the Middle Pleistocene of Northern Vietnam

A pygmy dormouse Typhlomys stegodontis sp. nov. is described on the base of the maxillary fragment and isolated teeth from the Middle Pleistocene Tham Hai cave locality in northern Vietnam (Lang Son Province). This first finding of the fossil Platacanthomyidae in Vietnam fills the Middle Pleistocene gap in the paleontological record of the family.

Enamel proteome shows that Gigantopithecus was an early diverging pongine

Gigantopithecus blacki was a giant hominid that inhabited densely forested environments of Southeast Asia during the Pleistocene¹. Its evolutionary relationships to other great ape species, and their divergence during the Middle and Late Miocene (16-5.3 Mya), remains disputed^2,3. Hypotheses regarding relationships between Gigantopithecus and extinct and extant hominids are difficult to substantiate because of its highly derived dentognathic morphology and the absence of cranial and post-cranial remains^1,3-6. Therefore, proposed hypotheses on the phylogenetic position of Gigantopithecus among hominids have been wide-ranging, but none have received independent molecular validation. We retrieved dental enamel proteome sequences from a 1.9 million years (Mya) old Gigantopithecus blacki molar found in Chuifeng Cave, China^7,8. The thermal age of these protein sequences is approximately five times older than any previously published mammalian proteome or genome. We demonstrate that Gigantopithecus is a sister clade to orangutans (genus Pongo) with a common ancestor about 10-12 Mya, implying that the Gigantopithecus divergence from Pongo is part of the Miocene radiation of great apes. Additionally, we hypothesize that the expression of alpha-2-HS-glycoprotein (AHSG), which has not been observed in enamel proteomes previously, had a role in the biomineralization of the thick enamel crowns that characterize the large molars in the genus^9,10. The survival of an Early Pleistocene dental enamel proteome in the subtropics further expands the scope of palaeoproteomic analysis into geographic areas and time periods previously considered incompatible with genetic preservation.

Disentangling isolated dental remains of Asian Pleistocene hominins and pongines

Scholars have debated the taxonomic identity of isolated primate teeth from the Asian Pleistocene for over a century, which is complicated by morphological and metric convergence between orangutan (Pongo) and hominin (Homo) molariform teeth. Like Homo erectus, Pongo once showed considerable dental variation and a wide distribution throughout mainland and insular Asia. In order to clarify the utility of isolated dental remains to document the presence of hominins during Asian prehistory, we examined enamel thickness, enamel-dentine junction shape, and crown development in 33 molars from G. H. R. von Koenigswald's Chinese Apothecary collection (11 Sinanthropus officinalis [= Homo erectus], 21 "Hemanthropus peii," and 1 "Hemanthropus peii" or Pongo) and 7 molars from Sangiran dome (either Homo erectus or Pongo). All fossil teeth were imaged with non-destructive conventional and/or synchrotron micro-computed tomography. These were compared to H. erectus teeth from Zhoukoudian, Sangiran and Trinil, and a large comparative sample of fossil Pongo, recent Pongo, and recent human teeth. We find that Homo and Pongo molars overlap substantially in relative enamel thickness; molar enamel-dentine junction shape is more distinctive, with Pongo showing relatively shorter dentine horns and wider crowns than Homo. Long-period line periodicity values are significantly greater in Pongo than in H. erectus, leading to longer crown formation times in the former. Most of the sample originally assigned to S. officinalis and H. erectus shows greater affinity to Pongo than to the hominin comparative sample. Moreover, enamel thickness, enamel-dentine junction shape, and a long-period line periodicity value in the "Hemanthropus peii" sample are indistinguishable from fossil Pongo. These results underscore the need for additional recovery and study of associated dentitions prior to erecting new taxa from isolated teeth.

Orangutans venture out of the rainforest and into the Anthropocene

Conservation benefits from understanding how adaptability and threat interact to determine a taxon's vulnerability. Recognizing how interactions with humans have shaped taxa such as the critically endangered orangutan (Pongo spp.) offers insights into this relationship. Orangutans are viewed as icons of wild nature, and most efforts to prevent their extinction have focused on protecting minimally disturbed habitat, with limited success. We synthesize fossil, archeological, genetic, and behavioral evidence to demonstrate that at least 70,000 years of human influence have shaped orangutan distribution, abundance, and ecology and will likely continue to do so in the future. Our findings indicate that orangutans are vulnerable to hunting but appear flexible in response to some other human activities. This highlights the need for a multifaceted, landscape-level approach to orangutan conservation that leverages sound policy and cooperation among government, private sector, and community stakeholders to prevent hunting, mitigate human-orangutan conflict, and preserve and reconnect remaining natural forests. Broad cooperation can be encouraged through incentives and strategies that focus on the common interests and concerns of different stakeholders. Orangutans provide an illustrative example of how acknowledging the long and pervasive influence of humans can improve strategies to preserve biodiversity in the Anthropocene.

Bayesian inference reveals ancient origin of simian foamy virus in orangutans

Simian foamy viruses (SFVs) infect most nonhuman primate species and appears to co-evolve with its hosts. This co-evolutionary signal is particularly strong among great apes, including orangutans (genus Pongo). Previous studies have identified three distinct orangutan SFV clades. The first of these three clades is composed of SFV from P. abelii from Sumatra, the second consists of SFV from P. pygmaeus from Borneo, while the third clade is mixed, comprising an SFV strain found in both species of orangutan. The existence of the mixed clade has been attributed to an expansion of P. pygmaeus into Sumatra following the Mount Toba super-volcanic eruption about 73,000years ago. Divergence dating, however, has yet to be performed to establish a temporal association with the Toba eruption. Here, we use a Bayesian framework and a relaxed molecular clock model with fossil calibrations to test the Toba hypothesis and to gain a more complete understanding of the evolutionary history of orangutan SFV. As with previous studies, our results show a similar three-clade orangutan SFV phylogeny, along with strong statistical support for SFV-host co-evolution in orangutans. Using Bayesian inference, we date the origin of orangutan SFV to >4.7 million years ago (mya), while the mixed species clade dates to approximately 1.7mya, >1.6 million years older than the Toba super-eruption. These results, combined with fossil and paleogeographic evidence, suggest that the origin of SFV in Sumatran and Bornean orangutans, including the mixed species clade, likely occurred on the mainland of Indo-China during the Late Pliocene and Calabrian stage of the Pleistocene, respectively.

The Middle Pleistocene vertebrate fauna from Khok Sung (Nakhon Ratchasima, Thailand): biochronological and paleobiogeographical implications

The fluviatile terrace deposits of Khok Sung, Nakhon Ratchasima province, have yielded more than one thousand fossils, making this the richest Pleistocene vertebrate fauna of Thailand. The excellent preservation of the specimens allows precise characterization of the faunal composition. The mammalian fauna consists of fifteen species in thirteen genera, including a primate, a canid, a hyaenid, proboscideans, rhinoceroses, a suid, cervids, and bovids. Most species correspond to living taxa but globally (Stegodon cf. orientalis) and locally (Crocuta crocuta ultima, Rhinoceros unicornis, Sus barbatus, and Axis axis) extinct taxa were also present. The identification of Axis axis in Khok Sung, a chital currently restricted to the Indian Subcontinent, represents the first record of the species in Southeast Asia. Three reptilian taxa: Crocodylus cf. siamensis, Python sp., and Varanus sp., are also identified. Faunal correlations with other Southeast Asian sites suggest a late Middle to early Late Pleistocene age for the Khok Sung assemblage. However, the Khok Sung mammalian fauna is most similar to that of Thum Wiman Nakin, dated to older than 169 ka. The Khok Sung large mammal assemblage mostly comprises mainland Southeast Asian taxa that migrated to Java during the latest Middle Pleistocene, supporting the hypothesis that Thailand was a biogeographic pathway for the Sino-Malayan migration event from South China to Java.

Evolution and dispersal of the genus Homo: A landscape approach

The notion of the physical landscape as an arena of ecological interaction and human evolution is a powerful one, but its implementation at larger geographical and temporal scales is hampered by the challenges of reconstructing physical landscape settings in the geologically active regions where the earliest evidence is concentrated. We argue that the inherently dynamic nature of these unstable landscapes has made them important agents of biological change, creating complex topographies capable of selecting for, stimulating, obstructing or accelerating the latent and emerging properties of the human evolutionary trajectory. We use this approach, drawing on the concepts and methods of active tectonics, to develop a new perspective on the origins and dispersal of the Homo genus. We show how complex topography provides an easy evolutionary pathway to full terrestrialisation in the African context, and would have further equipped members of the genus Homo with a suite of adaptive characteristics that facilitated wide-ranging dispersal across ecological and climatic boundaries into Europe and Asia by following pathways of complex topography. We compare this hypothesis with alternative explanations for hominin dispersal, and evaluate it by mapping the distribution of topographic features at varying scales, and comparing the distribution of early Homo sites with the resulting maps and with other environmental variables.

The Taxonomic and Phylogenetic Affinities of Bunopithecus sericus, a Fossil Hylobatid from the Pleistocene of China

Fossil hylobatids are rare, but are known from late Miocene and Pleistocene sites throughout East Asia. The best-known fossil hylobatid from the Pleistocene of China is a left mandibular fragment with M2-3 (AMNH 18534), recovered from a pit deposit near the village of Yanjinggou in Wanzhou District, Chongqing Province. Matthew and Granger described this specimen in 1923 as a new genus and species, Bunopithecus sericus. Establishing the age of Bunopithecus has proved difficult because the Yanjinggou collection represents a mixed fauna of different ages, but it likely comes from early or middle Pleistocene deposits. Although the Bunopithecus specimen has featured prominently in discussions of hylobatid evolution and nomenclature, its systematic status has never been satisfactorily resolved. The present study reexamines the taxonomic and phylogenetic relationships of Bunopithecus by carrying out a detailed comparative morphometric study of its lower molars in relation to a large sample of modern hylobatids. Our results show that differences in M2 and M3 discriminate extant hylobatids fairly well, at least at the generic level, and that AMNH 18534 is not attributable to Hylobates, Nomascus or Symphalangus. Support for a close relationship between Bunopithecus and Hoolock is more equivocal. In most multivariate analyses, Bunopithecus presents a unique morphological pattern that falls outside the range of variation of any hylobatid taxon, although its distance from the cluster represented by extant hoolocks is relatively small. Our results support the generic distinction of Bunopithecus, which most likely represents an extinct crown hylobatid, and one that may possibly represent the sister taxon to Hoolock.

Discovery of a second human molar and cranium fragment in the late Middle to Late Pleistocene cave of Ma U'Oi (Northern Vietnam)

In November 2002, during the second season of work by a Vietnamese-French-Japanese team, we discovered a human molar and a fragment of an occipital bone in the late Middle to Late Pleistocene cave of Ma U'Oi (Bacon et al., Geobios. 37 (2004) 305). The layer from which this material comes is the same as that in which a human lower molar was found in 2001. Both molars can be attributed to archaic Homo, and both exhibit archaic and modern traits.

The first discovery of a complete skeleton of a fossil orang-utan in a cave of the Hoa Binh Province, Vietnam

Here we provide a description of the first complete adult fossil orang-utan skeleton from the Asian mainland. This specimen, and remains of a juvenile orang, were collected in a late Pleistocene cavern in the Hoa Binh Province of The Socialist Republic of Vietnam. The results confirm the suggestions by Hooijer (1948) Zool. Meded. Leiden29, 175-301 and later by Schwartz et al. (1995) Anthrop. Pap. Am. Mus. Nat. Hist.76, 1-24, that ancient orang-utans had bigger teeth than those of modern Pongo pygmaeus (P. p. pygmaeus and P. p. abelii), while the dental morphology is similar. Body proportions of the adult individual of Hoa Binh show a large skull with very large teeth but proportionally a small body. This individual is also singular in having high intermembral and brachial indices, in comparison with those of modern subspecies.