Tracing the Genetic Origins of the Austronesians: DNA Evidence from the Fujian–Taiwan Connection

\n

Tang Jiaxin 1, Wang Chuanchao 2
(1. Graduate student, School of Sociology and Anthropology, Xiamen University; 2. Professor, Institute of Anthropology, Xiamen University)

\n\n\n\n

The Austronesian-speaking peoples, as the name suggests, are the communities that speak Austronesian languages. The term was first applied in the 19th century by Western colonial scholars to the sea peoples of the vast Pacific archipelagos south of the equator, who were found to share related languages; linguistically, these maritime populations were grouped together as the “Austronesian-speaking peoples.” Today the Austronesian language family comprises roughly 1,000 to 1,200 languages spoken by more than 400 million people, making it one of the largest ethno-linguistic groupings recognized in world ethnography. These populations are distributed mainly across Taiwan (China), Southeast Asia, and the three great archipelagos of Melanesia, Micronesia and Polynesia, ranging from Easter Island in the east to Madagascar off the coast of Africa in the west.

\n\n\n\n

For more than a century, archaeologists such as Lin Huixiang, Kwang-chih Chang and Peter Bellwood have carried out fruitful research on the origins and dispersal of the Austronesians. The academic community generally accepts a migration scenario in which Austronesian ancestors moved from the coastal regions of mainland South China to Taiwan and thence into Oceania. Linguists, however, remain divided over the homeland of the Austronesian languages themselves: over nearly a century of scholarship, hypotheses ranging from Polynesia, the Southeast Asian archipelago and mainland Southeast Asia to even the Americas have been proposed and tentatively argued, yet no consensus has been reached on the true cultural cradle of the world’s most widely distributed maritime peoples.

\n\n\n\n

In recent years, advances in genetic technology have brought DNA evidence to bear on Austronesian studies, clarifying a series of long-standing questions about Austronesian origins and dispersal. Because DNA data are complex, however, their interpretation in reconstructing prehistoric population history is not free from error, and not every result or conclusion withstands scrutiny; these issues deserve continued discussion and re-examination.

\n\n\n\n

Biochemical and Immunological Markers

\n\n\n\n

Population-genetic tracing of ethnic origins began with serological and immunological markers, such as blood-group systems including ABO, MNSs, Lewis, Rhesus, Kidd, Kell, Duffy and Diego. The underlying assumption was that populations with more similar allele frequencies are more closely related. From 1939 onward, several papers reported blood-group studies of Taiwan’s Austronesian populations. For example, the team of Luigi Luca Cavalli-Sforza typed the Toroko population of Taiwan in 1985 and found that they clustered genetically with populations from South China, Thailand, Vietnam, the Philippines and Taiwan proper, while being more distant from Malays, Borneans, Polynesians, Micronesians and Melanesians.

\n\n\n\n

Toward the end of the last century, Lin Ma-li and colleagues at Taiwan’s Mackay Memorial Hospital sampled and HLA-typed several indigenous groups of Taiwan. They argued that Taiwan’s indigenous peoples are among the most genetically homogeneous populations in the world, possibly isolated from other groups for more than 12,000 years and developing independently on the island. They further proposed that 85% of Taiwan’s Hokkien and Hakka people carry indigenous Taiwanese ancestry, and that over 90% bear ancestry from the Baiyue peoples of South China rather than being pure descendants of northern Han migrants, implying close affinities with Southeast Asia. Inferring population relationships from a limited set of HLA loci is problematic, however: HLA variation is strongly influenced by climate, environment and pathogens; HLA cannot reveal a population’s place of origin or the timing and direction of migrations; and with only a handful of loci, claims about whether a population is “pure” or about its relatedness to others cannot be reliably established. The “12,000 years” figure was not calculated from genetic data but was a personal estimate. Taiwan scholars such as Chen Shu-cho have published critiques of Lin’s sampling, statistical methods and ethnic classification criteria, arguing that figures such as 85% and 90% lack scientific basis.

\n\n\n\n

Taiwanese Austronesians Originated in South China

\n\n\n\n

Genetic tracing of origins and migrations relies mainly on DNA. Human DNA falls into three major classes: autosomes, sex chromosomes (X and Y), and mitochondrial DNA. Autosomes—22 pairs inherited from both parents—form the largest part of the genome. The Y chromosome is transmitted strictly from father to son and therefore records paternal history, while mitochondrial DNA is inherited maternally and, apart from rare heteroplasmy, reflects maternal history. Because these three types of DNA are inherited in different ways, they can be combined to reconstruct ancestral histories. Researchers have built a phylogenetic tree of the human Y chromosome from mutations, dividing it into twenty major haplogroups labeled A through T; among them, O-M175, C-M130, D-M174 and N-M231 are the four principal haplogroups of East Asia, together accounting for about 93% of all East Asian men. Likewise, mitochondrial haplogroups defined from sequence variation have been used to trace the routes of maternal origins and migration worldwide. The mtDNA haplogroup distribution differs markedly between northern and southern East Asia: northern populations are characterized by haplogroups A, C, D4, D5, G, M8, M9, N9 and Z, whereas southern populations are dominated by B4, B5a, F, M7 and R9.

\n\n\n\n

In 2008, Li Hui and colleagues typed Y-chromosomal SNPs and STRs in 1,509 male samples from 30 Tai-Kadai groups, 23 Malay-Polynesian-speaking groups from Indonesia and Vietnam, and 11 indigenous groups of Taiwan. They found that O1a-M119 is the principal Y haplogroup of Taiwan’s Austronesian populations, averaging 77%, while occurring at about 20.5% in Tai-Kadai populations and 21.2% in Malay populations—far higher than in other East Asian groups. O1a-M119 is widespread across East and Southeast Asia, is one of the principal paternal lineages of both Tai-Kadai and Austronesian speakers, and occurs at appreciable frequencies in various Han Chinese populations. A neighbor-joining network of O1a* Y-chromosomal haplotypes among the three population groups placed the Tai-Kadai populations at the center of the network, sharing haplotypes directly or indirectly with both Malay and Taiwan Austronesian populations, whereas Malay and Taiwan Austronesian populations shared almost no haplotypes directly. From the perspective of O1a-M119, Malay populations thus appear not to descend directly from Taiwan’s Austronesians; rather, the two may have originated independently from Tai-Kadai populations on the mainland. In addition to O1a-M119, Taiwan Austronesian populations also show notable frequencies of O3-M122 and O2a-M95. O3-M122 is the most common haplogroup in China, occurring throughout East and Southeast Asia and constituting about 50–60% of Han Chinese lineages; for example, O3a-M134, one of the three ancestral lineages of Neolithic Han Chinese, accounts for 13.5% in the Makatao and 9.1% in the Paiwan. O2a-M95 is frequent among southern minority populations of China, in mainland Southeast Asia and among Munda speakers of India, and occurs in Taiwan Austronesians mainly in the Amis, Pazeh, Makatao, Bunun and Saisiyat at proportions of 5.4–17.6%. In terms of STR genetic distances, the O3-M122 and O2a-M95 haplogroups of Tai-Kadai speakers are also closer to those of Austronesian and Malay populations respectively, again supporting the view that Austronesian and Malay populations arose independently from Tai-Kadai populations on the mainland.

\n\n\n\n

On the maternal side, Trejaut and colleagues typed mitochondrial DNA in 640 individuals from nine Austronesian groups of Taiwan and found that over 85% of mtDNA types belonged to haplogroups B4, B5a, F1a, F3b, E and M7—all common in South China and Southeast Asia except for haplogroup E. Shinoda and colleagues extracted and typed mtDNA from the teeth of 35 individuals from a Pingpu cemetery and found that the predominant types were F, B and M7, resembling populations of southern East Asia. Wang Chuanchao and colleagues successfully recovered ancient DNA from 46 skeletons of the Hanben and Gongguan sites in Taiwan dating to 1,500–3,200 years ago, and found their mtDNA types to be mainly E1a, B4a1a, F3b1 and F4b, types that are also common among present-day Taiwanese and Southeast Asian populations. The earliest genetic link between Austronesians and the mainland dates back more than 8,000 years. The mtDNA of Liangdao Man No. 1, dated to about 8,200 years ago, belongs to an ancestral type of haplogroup E1 whose mutations lie between haplogroups E and E1. Haplogroup E is a downstream branch of M9, a maternal haplogroup common in East Asia and distributed mainly on the Tibetan Plateau and its periphery; its branches E1 and E2 are widespread among ancient and modern populations of Taiwan, insular Southeast Asia and Oceania. Compared with Taiwan Austronesians and Indonesian and Philippine populations, Liangdao Man No. 1 shares the fewest variation sites with Taiwan Austronesian groups and slightly more with Indonesians or Filipinos—directly supporting a mainland origin of Austronesians and the “out-of-Taiwan” dispersal. The mtDNA of Liangdao Man No. 2, dated to about 7,600 years ago, belongs to haplogroup R9, a type found mainly among Taiwan’s Thao and among Tai-Kadai and Hmong-Mien speakers of South China, further confirming the shared ancestry of southern indigenous populations including the Austronesians of Taiwan.

\n\n\n\n

Genetic Links between Polynesians and Southeastern Continental Populations

\n\n\n\n

Su Bing and colleagues analyzed Y-chromosomal mutations in 551 males from 36 populations spanning South China, Southeast Asia, Taiwan, Melanesia, Micronesia and Polynesia, including 58 Taiwan Austronesian samples. They found that the Y-chromosome types of Taiwan Austronesians are absent from Polynesian populations and occur only in small numbers in Micronesians, indicating that the Y-chromosome data do not support a Polynesian origin in Taiwan. In contrast, Zeng Zhaoshu and colleagues typed Y-STRs in 293 males from nine Taiwan Austronesian groups and found that the Amis, Bunun and Saisiyat are genetically closer to Oceanic groups, suggesting that different Austronesian groups of Taiwan may have contributed differently to Oceanic populations. Mirabal and colleagues typed Y chromosomes in 158 males from Samoa and Tonga in Polynesia and compared them with populations from East Asia, Taiwan, insular Southeast Asia, Melanesia and Polynesia. Although the Samoan and Tongan Y chromosomes carry Melanesian haplogroups C2a, S and K3-P79 at proportions of 23–42%, most Polynesian Y-chromosome types are East Asian-related; notably, the O3a2c*-P164 type, rare in mainland East Asian populations, occurs at high frequency in Polynesians and in the Amis of Taiwan, indicating a genetic link between Polynesian populations and the Amis. Wei Lanhai and colleagues updated the phylogenetic tree with additional Y-chromosome SNPs and found that the former O3a2c*-P164 belongs to the newly defined haplogroup O3a2b2-N6, which originated in northern China or the southeastern coastal region of East Asia; its downstream branch O3a2b2a2-F706(×B451) appears in the eastern coastal region of mainland China, while the Y-chromosome types characteristic of Austronesian populations belong to its further branch O3a2b2a2b-B451. The paternal Y-chromosome types of the ancient individuals from the Hanben and Gongguan sites in Taiwan also belong mainly to O3a2b2-N6. The Austronesian populations represented by O3a2b2a2b-B451 thus share genetic kinship with the southeastern continental populations of Asia.

\n\n\n\n

Whole-Genome Resolution of Austronesian History

\n\n\n\n

In 1998, the first systematic study applying modern genetic markers to Chinese populations was published in PNAS. Using 30 microsatellite markers, the study analyzed the genetic structure of 28 Chinese populations, including four Taiwan indigenous groups—Amis, Atayal, Paiwan and Yami. It found genetic differentiation between northern and southern Chinese populations; polymorphism and cluster analyses showed that Taiwan’s indigenous groups cluster with South Chinese populations rather than with Australian and New Guinean aboriginal populations, indicating close genetic affinities between Taiwan’s indigenous peoples and South China.

\n\n\n\n

In 2009, Academician Jin Li and Professor Xu Shuhua of Fudan University organized the Pan-Asian SNP Consortium, bringing together more than 90 researchers from over ten Asian countries. The consortium genotyped 1,928 samples from 73 Asian populations at more than 50,000 SNP sites across the genome, delineating the fine-scale genetic structure of Asian populations and revealing a strong correspondence between genetic structure, geography and language families. Austronesian-speaking populations from Taiwan, Indonesia, the Philippines, Malaysia and Remote Oceania cluster together in the phylogenetic tree with close genetic affinities, though Austronesian groups from Java and the Sunda islands show genetic differences from other Austronesians. Phylogenetic trees alone, however, cannot resolve the details of admixture. Lipson and colleagues re-analyzed the Pan-Asian SNP data for 56 populations using the new admixture-tracing method MixMapper and found that all Austronesian populations are genetically closer to Taiwan’s indigenous groups; Austronesian populations from the western part of insular Southeast Asia also carry genetic components of present-day Austroasiatic speakers, leading the authors to infer either that Austroasiatic populations once existed in insular Southeast Asia, or that Austronesian populations migrated to mainland Southeast Asia, admixed with Austroasiatic populations there, and then continued to western Indonesia. Liu and colleagues genotyped 43 Taiwan Austronesian individuals—including Atayal, Bunun, Rukai, Paiwan, Amis, Tao and Makatao—with over 600,000 sites per sample. They found that Taiwan Austronesians have genetic substructure: the northern Atayal and central Bunun cluster together, whereas the southern Rukai, Paiwan and Amis differ; Rukai and Paiwan cluster together, while the Amis cluster with the Tao and with Kankanaey- and Ilocano-speaking populations of the Philippines. The Makatao show clear Han-related admixture, with roughly 60% of their genetic ancestry derived from Hokkien Han Chinese. Compared with the northern Atayal, the southern Amis and Rukai are genetically closer to Austronesian populations of insular Southeast Asia and Oceania, whereas the Atayal are closer to ancient and modern populations of South China.

\n\n\n\n

Since 2010, with the maturation of ancient-DNA technology, ancient genomes related to the Austronesians have been published steadily. The team of Fu Qiaomei at the Institute of Vertebrate Paleontology and Paleoanthropology of the Chinese Academy of Sciences analyzed ancient genomes from the Qihedong, Tanshishan and Xitoucun sites in Fujian and the Liangdao and Suogang sites in Taiwan, dated to 8,000–2,000 years ago; the team of Wang Chuanchao at Xiamen University analyzed whole genomes of ancient individuals from Taiwan’s Hanben and Gongguan sites dated to 1,500–3,200 years ago. These studies found genetic continuity among Neolithic Fujian individuals, late Neolithic-to-Iron Age Taiwanese populations and present-day Taiwan Austronesians, as well as close genetic affinities between Fujian and Taiwan ancients and modern Tai-Kadai speakers of South China—directly demonstrating that Austronesian populations originated in the southeastern coastal region of the mainland. Skoglund, Lipson, Posth and colleagues published successive datasets of ancient genomes from Oceania, showing that individuals from Vanuatu and Tonga dated to 3,100–2,300 years ago belong to the same genetic lineage as the ancient inhabitants of Fujian and Taiwan, with no Papuan-related ancestry; Papuan ancestry arrived in Vanuatu and Tonga only around 2,300 years ago. These analyses reveal a dramatic shift in the genetic composition of Remote Oceanic populations. Yet the intrusive Papuan languages did not replace Austronesian languages, suggesting that before the arrival of Austronesian speech, the region may have lacked a fully developed language system, making it easy for local populations to adopt Austronesian languages and retain them ever since.

\n\n\n\n

Conclusion

\n\n\n\n

The origin of the Austronesians has long been a focus of scholarly attention. Linguists have reached differing conclusions from different materials and methods, and archaeologists have corroborated or proposed new scenarios through studies of relevant sites; but because linguistics and archaeology offer limited resolution on questions of population origins, genetics must provide supporting evidence through concrete data. The strength of genetics lies in its ability to analyze the genetic information of populations—in particular, Y-chromosomal and mitochondrial DNA lineage markers that faithfully record the chronological order of population divergence events—while ancient DNA can provide direct evidence of kinship across time. Together these have empirically demonstrated that the Austronesian peoples originated in the southeastern coastal region of the mainland, greatly enriching our understanding of the formation and dispersal of Austronesian peoples.

\n\n\n\n

Many questions about Austronesian origins remain unresolved—for example, the relationship between the Neolithic rice-farming populations of the middle and lower Yangtze and the Austronesians, and whether hunter-gatherer populations already living in Taiwan were absorbed during the formation of the Austronesians. Because the soils of South China are acidic and rainy, ancient remains there are poorly preserved, and no ancient genomes from the middle and lower Yangtze have yet been published, so no data are currently available for direct comparison with the ancient populations of Fujian and Taiwan. For the time being, therefore, the Austronesian homeland can be traced back only to the southeastern coastal region. We look forward to additional ancient genomes from South China and Southeast Asia in the future, which will further clarify the origins and dispersal of the Austronesian peoples.

\n\n\n\n

Executive editor: Gao Jing

\n\n