Austronesian Populations Research Articles

Ritual tooth ablation in ancient Taiwan and the Austronesian expansion

The earliest farming communities in Taiwan practiced a distinctive bio-cultural marker of identity, in the form of deliberate anterior teeth extraction. This distinguishing body transformation can be traced back to 4800 years BP in Taiwan and associated with the first Austronesian communities, and it has endured among contemporary Austronesian speakers in Taiwan and extending across the Asia-Pacific region. Through a comprehensive exploration of archaeological and ethnographic evidence, our study highlights how this practice developed in Taiwan over nearly five millennia and furthermore establishes its role in relation to issues of group identity. The results can expand our understanding of cultural practice, identity-forming processes, and migration routes of ancient Austronesian populations across the Asia-Pacific region.

Ethnicity-based classifications and medical genetics: One Health approaches from a Western Pacific perspective.

A new era presently dawns for medical genetics featuring individualised whole genome sequencing and promising personalised medical genetics. Accordingly, we direct readers attention to the continuing value of allele frequency data from Genome-Wide Association Surveys (GWAS) and single gene surveys in well-defined ethnic populations as a guide for best practice in diagnosis, therapy, and prescription. Supporting evidence is drawn from our experiences working with Austronesian volunteer subjects across the Western Pacific. In general, these studies show that their gene pool has been shaped by natural selection and become highly diverged from those of Europeans and Asians. These uniquely evolved patterns of genetic variation underlie contrasting schedules of disease incidence and drug response. Thus, recognition of historical bonds of kinship among Austronesian population groups across the Asia Pacific has distinct public health advantages from a One Health perspective. Other than diseases that are common among them like gout and diabetes, Austronesian populations face a wide range of climate-dependent infectious diseases including vector-borne pathogens as they are now scattered across the Pacific and Indian Oceans. However, we caution that the value of genetic survey data in Austronesians (and other groups too) is critically dependent on the accuracy of attached descriptive information in associated metadata, including ethnicity and admixture.

Whole mitochondrial genome analysis of Tai-Kadai-speaking populations in Southwest China

As a single matrilineal gene, human mitochondrial DNA plays a very important role in the study of population genetics. The whole mitogenome sequences of 287 individuals of the Tai-Kadai-speaking population in Guizhou were obtained. It was discovered that there were 82, 104, and 94 haplotypes in 83 Bouyei individuals, 107 Dong individuals, and 97 Sui individuals, respectively; and the haplotype diversity in Bouyei, Dong, and Sui groups was 1.000 ± 0.02, 0.9993 ± 0.0015, and 0.999 ± 0.002, respectively. The result of neutrality tests of the Tai-Kadai-speaking population in Guizhou showed significant negative values, and the analysis of mismatch distribution showed an obvious unimodal distribution. The results implied that Guizhou Tai-Kadai-speaking populations had high genetic diversities and may have experienced recent population expansion. In addition, the primary haplogroups of studied populations were M*, F, B, D, and R*, implying that they may origin from Southern China. The matrilineal genetic structure of the Tai-Kadai-speaking populations in Guizhou was analyzed by merging the mitogenome data of 79 worldwide populations as reference data. The results showed that there were close relationships between studied populations and other Tai-Kadai as well as some Austronesian populations in East and Southeast Asia. Overall, the mitogenome data generated in this study will provide important data for the study of genetic structure of Tai-Kadai speaking populations.

Population data and genetic characteristics of 12 X-STR loci using the Investigator® Argus X-12 Quality Sensor kit for the Kedayan population of Borneo in Malaysia.

DNA profiling of X-chromosomal short tandem repeats (X-STR) has exceptional value in criminal investigations, especially for complex kinship and incest cases. In this study, Investigator® Argus X-12 Quality Sensor (QS) kits were successfully used to characterize 12 X-STR loci in 199 unrelated healthy Kedayan individuals living in Sabah and Sarawak, Malaysia. The LG1 haplogroup (DXS8378 - DXS10135 - DXS10148) has the largest HD (0.9799) as compared with all other closely linked haplotype groups examined (LG2; DXS7132-DXS10074-DXS10079, LG3; DXS10103-DXS10101-HPRTB and LG4; DXS10134-DXS7423-DXS10146). Data from statistical analysis showed that high combined of PDM, PDF, MEC_Krüger, MEC_Kishida, MEC_Desmarais, and MEC_Desmarais_duo values (0.999999994405922, 0.99999999999999, 0.999990463834938, 0.999999975914808, 0.999999975985006, and 0.999996491927194, respectively) in the Kedayan. In a two-dimensional scaling (MDS) plot and dendrogram constructed using allele frequencies at the 12 X-STR loci, Kedayan appear to be most closely related to their other Austronesian populations including the Malays and Filipinos as compared with other reference population groups. Findings from the present study thus demonstrate high genetic variability across the 12 tested X-STR loci and can be used for population studies and forensic applications.

The combinatorial diversity of KIR and HLA class I allotypes in Peninsular Malaysia.

Killer cell immunoglobulin-like receptors (KIRs) interact with polymorphic human leucocyte antigen (HLA) class I molecules, modulating natural killer (NK) cell functions and affecting both the susceptibility and outcome of immune-mediated diseases. The KIR locus is highly diverse in gene content, copy number and allelic polymorphism within individuals and across geographical populations. To analyse currently under-represented Asian and Pacific populations, we investigated the combinatorial diversity of KIR and HLA class I in 92 unrelated Malay and 75 Malaysian Chinese individuals from the Malay Peninsula. We identified substantial allelic and structural diversity of the KIR locus in both populations and characterized novel variations at each analysis level. The Malay population is more diverse than Malay Chinese, likely representing a unique history including admixture with immigrating populations spanning several thousand years. Characterizing the Malay population are KIR haplotypes with large structural variants present in 10% individuals, and KIR and HLA alleles previously identified in Austronesian populations. Despite the differences in ancestries, the proportion of HLA allotypes that serve as KIR ligands is similar in each population. The exception is a significantly reduced frequency of interactions of KIR2DL1 with C2+ HLA-C in the Malaysian Chinese group, caused by the low frequency of C2+ HLA. One likely implication is a greater protection from preeclampsia, a pregnancy disorder associated with KIR2DL1, which shows higher incidence in the Malay than in the Malaysian Chinese. This first complete, high-resolution, characterization of combinatorial diversity of KIR and HLA in Malaysians will form a valuable reference for future clinical and population studies.

Paternal gene pool of Malays in Southeast Asia and its applications for the early expansion of Austronesians.

The origin and differentiation of Austronesian populations and their languages have long fascinated linguists, archeologists, and geneticists. However, the founding process of Austronesians and when they separated from their close relatives, such as the Daic and Austro-Asiatic populations in the mainland of Asia, remain unclear. In this study, we explored the paternal origin of Malays in Southeast Asia and the early differentiation of Austronesians. We generated whole Y-chromosome sequences of 50 Malays and co-analyzed 200 sequences from other Austronesians and related populations. We generated a revised phylogenetic tree with time estimation. We identified six founding paternal lineages among the studied Malays samples. These founding lineages showed a surprisingly coincident expansion age at 5000 to 6000 years ago. We also found numerous mostly close related samples of the founding lineages of Malays among populations from Mainland of Asia. Our analyses provided a refined phylogenetic resolution for the dominant paternal lineages of Austronesians found by previous studies. We suggested that the co-expansion of numerous founding paternal lineages corresponds to the initial differentiation of the most recent common ancestor of modern Austronesians. The splitting time and divergence pattern in perspective of paternal Y-chromosome evidence are highly consistent with the previous theories of ethnologists, linguists, and archeologists.

A genetic history of China

Human Evolution The history of human movements into and within China has been difficult to determine solely from archaeological investigations or genetic studies of contemporary peoples. Yang et al. sequenced DNA from 26 individuals from 9500 to 300 years ago from locations within China. Analyses of these individuals, along with previously sequenced ancient individuals and present-day genomes representing global populations, show a split between ancient humans in northern and southern China. Neolithic northern Chinese individuals are closest to modern-day East Asians, whereas ancient individuals from southern China are most closely related to modern-day Southeast Asians and show an affinity to modern-day Austronesian populations. These results indicate that there was a southward movement and admixture of peoples during the Neolithic that gave rise to modern-day populations in East Asia. Science this issue p. [282][1] [1]: /lookup/doi/10.1126/science.aba0909

Forensic parameters and ancestral fractions in the Kedayan population inferred using 21 autosomal STR loci

Few population groups in Borneo (Sabah and Sarawak) have been genetically characterized. No study has ever been done on the Kedayan population. In this project, genetic polymorphism was measured at 21 autosomal STR loci in 200 unrelated Kedayan individuals living in Sabah and Sarawak, Malaysia and their forensic statistics calculated. We also compared these new data with those from elsewhere in Southeast Asia, Europe and Africa. A PCO plot showed that Austronesian populations in the Asia-Pacific region plot closely together and well separated from the unrelated reference populations. Our statistics show that these 21 STR loci are highly informative for population studies and fully suitable for use in forensic DNA analyses.

Ancient DNA indicates human population shifts and admixture in northern and southern China.

Human genetic history in East Asia is poorly understood. To clarify population relationships, we obtained genome-wide data from 26 ancient individuals from northern and southern East Asia spanning 9500 to 300 years ago. Genetic differentiation in this region was higher in the past than the present, which reflects a major episode of admixture involving northern East Asian ancestry spreading across southern East Asia after the Neolithic, thereby transforming the genetic ancestry of southern China. Mainland southern East Asian and Taiwan Strait island samples from the Neolithic show clear connections with modern and ancient individuals with Austronesian-related ancestry, which supports an origin in southern China for proto-Austronesians. Connections among Neolithic coastal groups from Siberia and Japan to Vietnam indicate that migration and gene flow played an important role in the prehistory of coastal Asia.

Obsidian Sourcing and Characterization in the Celebes Region: An Initial Interpretation on the “Celebes Seafaring People”

AbstractThe peopling of Island Southeast Asia is told through the Austronesian migration theory. During the Neolithic Period (ca. 6000–5000 BP), the Austronesians entered the Philippines altering the cultural landscape and heralding the beginning of the Neolithic. The Austronesian people continued expanding through Island Southeast Asia, the Pacific, and as far as Madagascar. It is the most influential multiregional archaeological theory in Southeast Asia and the Pacific Region. Although archaeologists, as a whole, generally support this theory, the operations governing the Austronesian migration is still subject to intense debate. Theories suggest that migration is not as straightforward as commonly presented. In spite of their movement towards the Pacific, some Austronesian population stayed in the Celebes area and may have developed a close-knit exchange system with their neighbors powered by sophisticated ancient maritime technology and shared cultural affiliations. This paper calls this maritime network as the “Celebes Seafaring People.” The “Celebes Seafaring People” hypothesis is the first study to focus on a smaller aspect of a much larger theory, allowing a clearer perspective on the early cultures of this Region. Currently, the hypothesis encompasses three island groups: Northern Mindanao, Philippines; Sabah, Malaysia; and Talaud Islands, Indonesia. This is an initial interpretation of the “Celebes Seafaring People” hypothesis through geochemical analysis of obsidian found in the island groups in the Celebes Region. These group of people may have a complex maritime exchange network and share the same cultural affiliation during the Neolithic Period. Further investigation must done to substantiate such theoretical interpretation.

Christianity spread faster in small, politically structured societies.

Over the past 2,000 years, Christianity has grown from a tiny Judaic sect to the world's largest religious family 1 . Historians and social scientists have long debated whether Christianity spread through a top-down process driven by political leaders or a bottom-up process that empowered social underclasses 2-6 . The Christianization of Austronesian populations is well-documented across societies with a diverse range of social and demographic conditions 7 . Here, we use this context to test whether political hierarchy, social inequality and population size predict the length of conversion time across 70 Austronesian cultures. We also account for the historical isolation of cultures and the year of missionary arrival, and use a phylogenetic generalized least squares method to estimate the effects of common ancestry and geographic proximity of cultures 8 . We find that conversion to Christianity typically took less than 30 years, and societies with political leadership and smaller populations were fastest to convert. In contrast, social inequality did not reliably affect conversion times, indicating that Christianity's success in the Pacific is not due to its egalitarian doctrine empowering social underclasses. The importance of population size and structure in our study suggests that the rapid spread of Christianity can be explained by general dynamics of cultural transmission.

Predicting societal-level cultural change.

By analysing whether characteristics of Austronesian populations could predict the rate of adoption of Christianity, researchers find that political leadership and small population sizes facilitated Christianity’s spread in the Pacific.

Phylogeography of Y-chromosome haplogroup O3a2b2-N6 reveals patrilineal traces of Austronesian populations on the eastern coastal regions of Asia.

Austronesian diffusion is considered one of the greatest dispersals in human history; it led to the peopling of an extremely vast region, ranging from Madagascar in the Indian Ocean to Easter Island in Remote Oceania. The Y-chromosome haplogroup O3a2b*-P164(xM134), a predominant paternal lineage of Austronesian populations, is found at high frequencies in Polynesian populations. However, the internal phylogeny of this haplogroup remains poorly investigated. In this study, we analyzed -seventeen Y-chromosome sequences of haplogroup O3a2b*-P164(xM134) and generated a revised phylogenetic tree of this lineage based on 310 non-private Y-chromosome polymorphisms. We discovered that all available O3a2b*-P164(xM134) samples belong to the newly defined haplogroup O3a2b2-N6 and samples from Austronesian populations belong to the sublineage O3a2b2a2-F706. Additionally, we genotyped a series of Y-chromosome polymorphisms in a large collection of samples from China. We confirmed that the sublineage O3a2b2a2b-B451 is unique to Austronesian populations. We found that O3a2b2-N6 samples are widely distributed on the eastern coastal regions of Asia, from Korea to Vietnam. Furthermore, we propose- that the O3a2b2a2b-B451 lineage represents a genetic connection between ancestors of Austronesian populations and ancient populations in North China, where foxtail millet was domesticated about 11,000 years ago. The large number of newly defined Y-chromosome polymorphisms and the revised phylogenetic tree of O3a2b2-N6 will be helpful to explore the origin of proto-Austronesians and the early diffusion process of Austronesian populations.

Moving past the ‘Neolithic problem’: The development and interaction of subsistence systems across northern Sahul

The ‘Neolithic problem’ refers to forager/farmer interaction in northern Australia, where despite a shared environmental inheritance with their New Guinea neighbours, Indigenous Australians seemingly rejected both the domesticates and the practices of the Melanesian horticultural economy (White, 1971). This ethnographic example is often used to suggest that hunter-gatherers elsewhere may have chosen not to adopt agriculture. However, the premise of the ‘Neolithic problem’ has been criticised for its over-reliance on the ethnographic record and on an anachronistic notion of cultural evolution, which exaggerates the dichotomy between New Guinean agriculturalists and Australian hunter-gatherers. In this paper we review the historical and theoretical treatment of the ‘Neolithic problem’ and the archaeological evidence for subsistence practices in northern Sahul spanning the past 50–60,000 years. Using niche construction theory (Rowley-Conwy and Layton, 2011) to re-examine the archaeological and ethnohistoric record, it is possible to observe the development and expansion of a variety of subsistence systems. Contrary to the premise of the ‘Neolithic problem’, the past 50–60,000 years of occupation in Sahul has seen the development of a varied array of food-producing subsistence practices in both New Guinea and Australia. However, the archaeological evidence for the expansion of horticultural practices and cultivars outside of highland New Guinea suggests a spatially and temporally narrow window for the adoption of agriculture by Indigenous populations in Cape York. Instead, the interaction between different subsistence systems in northern Sahul may have centred on the New Guinea lowlands and the Bismarck Archipelago, where, in the late Holocene, local communities interacted with other Melanesian and Austronesian populations. Whilst further archaeological investigation is required, it is clear that the image of culturally-static Indigenous Australian populations often implied in the consideration of forager/farmer interactions belongs to another era of archaeological thought.

Reconstructing Austronesian population history in Island Southeast Asia.

Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the ‘Austronesian expansion,’ which began 4,000–5,000 years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, we analyse genome-wide data from 56 populations using new methods for tracing ancestral gene flow, focusing primarily on Island Southeast Asia. We show that all sampled Austronesian groups harbour ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia.

Ascertaining the role of Taiwan as a source for the Austronesian expansion

Taiwanese aborigines have been deemed the ancestors of Austronesian speakers which are currently distributed throughout two-thirds of the globe. As such, understanding their genetic distribution and diversity as well as their relationship to mainland Asian groups is important to consolidating the numerous models that have been proposed to explain the dispersal of Austronesian speaking peoples into Oceania. To better understand the role played by the aboriginal Taiwanese in this diaspora, we have analyzed a total of 451 individuals belonging to nine of the tribes currently residing in Taiwan, namely the Ami, Atayal, Bunun, Paiwan, Puyuma, Rukai, Saisiyat, Tsou, and the Yami from Orchid Island off the coast of Taiwan across 15 autosomal short tandem repeat loci. In addition, we have compared the genetic profiles of these tribes to populations from mainland China as well as to collections at key points throughout the Austronesian domain. While our results suggest that Daic populations from Southern China are the likely forefathers of the Taiwanese aborigines, populations within Taiwan show a greater genetic impact on groups at the extremes of the current domain than populations from Indonesia, Mainland, or Southeast Asia lending support to the "Out of Taiwan" hypothesis. We have also observed that specific Taiwanese aboriginal groups (Paiwan, Puyuma, and Saisiyat), and not all tribal populations, have highly influenced genetic distributions of Austronesian populations in the pacific and Madagascar suggesting either an asymmetric migration out of Taiwan or the loss of certain genetic signatures in some of the Taiwanese tribes due to endogamy, isolation, and/or drift.

Increased Y-chromosome resolution of haplogroup O suggests genetic ties between the Ami aborigines of Taiwan and the Polynesian Islands of Samoa and Tonga

The Austronesian expansion has left its fingerprint throughout two thirds of the circumference of the globe reaching the island of Madagascar in East Africa to the west and Easter Island, off the coast of Chile, to the east. To date, several theories exist to explain the current genetic distribution of Austronesian populations, with the “slow boat” model being the most widely accepted, though other conjectures ( i.e., the “express train” and “entangled bank” hypotheses) have also been widely discussed. In the current study, 158 Y chromosomes from the Polynesian archipelagos of Samoa and Tonga were typed using high resolution binary markers and compared to populations across Mainland East Asia, Taiwan, Island Southeast Asia, Melanesia and Polynesia in order to establish their patrilineal genetic relationships. Y-STR haplotypes on the C2 (M38), C2a (M208), O1a (M119), O3 (M122) and O3a2 (P201) backgrounds were utilized in an attempt to identify the differing sources of the current Y-chromosomal haplogroups present throughout Polynesia (of Melanesian and/or Asian descent). We find that, while haplogroups C2a, S and K3-P79 suggest a Melanesian component in 23%–42% of the Samoan and Tongan Y chromosomes, the majority of the paternal Polynesian gene pool exhibits ties to East Asia. In particular, the prominence of sub-haplogroup O3a2c* (P164), which has previously been observed at only minimal levels in Mainland East Asians (2.0–4.5%), in both Polynesians (ranging from 19% in Manua to 54% in Tonga) and Ami aborigines from Taiwan (37%) provides, for the first time, evidence for a genetic connection between the Polynesian populations and the Ami.

Palaeohabitat of first settlement sites 1500–1000 B.C. in Guam, Mariana islands, western Pacific

Based on computer-aided models and geoarchaeological excavations, palaeohabitat renderings can account for ancient site locations and contexts much different from today in terms of sea level, coastal dynamics, slope erosion, nearshore ecosystems, native forests, and other factors. A case study illustrates this research in Guam of the Mariana Islands of the western Pacific, with specific reference to the 1500–1000 B.C. time interval. This time interval includes the oldest known archaeological sites in the Mariana Islands, directly relevant for understanding the context of ancient Austronesian population dispersals in the larger western Pacific region. The results also help toward larger understanding of coastal adaptations in dynamic settings.

Common origin of the Austronesian and Daic Populations

Common origin of the Austronesian and Daic Populations

Tracing the Austronesian Footprint in Mainland Southeast Asia: A Perspective from Mitochondrial DNA

As the relic of the ancient Champa Kingdom, the Cham people represent the major Austronesian speakers in Mainland Southeast Asia (MSEA) and their origin is evidently associated with the Austronesian diffusion in MSEA. Hitherto, hypotheses stemming mainly from linguistic and cultural viewpoints on the origin of the Cham people remain a welter of controversies. Among the points of dissension is the muddled issue of whether the Cham people arose from demic or cultural diffusion from the Austronesians. Addressing this issue also helps elucidate the dispersal mode of the Austronesian language. In the present study, we have analyzed mitochondrial DNA (mtDNA) control-region and coding-region sequence variations in 168 Cham and 139 Kinh individuals from Vietnam. Around 77% and 95% matrilineal components in the Chams and the Kinhs, respectively, could be assigned into the defined mtDNA haplogroups. Additionally, three common East Eurasian haplogroups B, R9, and M7 account for the majority (>60%) of maternal components in both populations. Entire sequencing of 20 representative mtDNAs selected from the thus far unclassified lineages, together with four new mtDNA genome sequences from Thailand, led to the identification of one new haplogroup M77 and helped to re-evaluate several haplogroups determined previously. Comparing the Chams with other Southeast Asian populations reveals that the Chams had a closer affinity with the Mon-Khmer populations in MSEA than with the Austronesian populations from Island Southeast Asia (ISEA). Further analyses failed to detect the potential homelands of the Chams in ISEA. Therefore, our results suggested that the origin of the Cham was likely a process of assimilation of massive local Mon-Khmer populations accompanied with language shift, thus indicating that the Austronesian diffusion in MSEA was mainly mediated by cultural diffusion, at least from the matrilineal genetic perspective, an observation in agreement with the hypothesis of the Nusantao Maritime Trading and Communication Networks.