Shutler R, Marck JC. On the dispersal of the Austronesian horticulturalists. Archaeology Phys Anthropol Ocean. 1975;10:81–113.
Bellwood P. A hypothesis for Austronesian origins. Asian Perspect. 1984;26:107–17.
Blust R. The Austronesian homeland: a linguistic perspective. Asian Perspect. 1984;26:45–67.
Gray RD, Drummond AJ, Greenhill SJ. Language phylogenies reveal expansion pulses and pauses in Pacific settlement. Science. 2009;323:479–83.
Tabbada KA, Trejaut J, Loo JH, Chen YM, Lin M, Mirazón-Lahr M, et al. Philippine mitochondrial DNA diversity: a populated viaduct between Taiwan and Indonesia?. Mol Biol Evol. 2010;27:21–31.
Delfin F, Salvador JM, Calacal GC, Perdigon HB, Tabbada KA, Villamor LP, et al. The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups. Eur J Hum Genet. 2011;19:224–30.
Delfin F, Min-Shan Ko A, Li M, Gunnarsdóttir ED, Tabbada KA, Salvador JM, et al. Complete mtDNA genomes of Filipino ethnolinguistic groups: a melting pot of recent and ancient lineages in the Asia-Pacific region. Eur J Hum Genet. 2014;22:228–37.
Chang K-C. Taiwan archaeology in Pacific perspective. In: Kwang-Chih C, Li, K-C, Arthur P, editor. Anthropological studies of the Taiwan area: accomplishments and prospects. Department of Anthropology, National Taiwan University; 1989.
Li H, Wen B, Chen SJ, Su B, Pramoonjago P, Liu Y, et al. Paternal genetic affinity between Western Austronesians and Daic populations. BMC Evol Biol. 2008;8:146.
Jinam TA, Hong LC, Phipps ME, Stoneking M, Ameen M, Edo J, et al. Evolutionary history of continental southeast Asians: “early train” hypothesis based on genetic analysis of mitochondrial and autosomal DNA data. Mol Biol Evol. 2012;29:3513–27.
Su B, Xiao J, Underhill P, Deka R, Zhang W, Akey J, et al. Y-Chromosome evidence for a northward migration of modern humans into Eastern Asia during the last Ice Age. Am J Hum Genet. 1999;65:1718–24.
Hill C, Soares P, Mormina M, Macaulay V, Clarke D, Blumbach PB, et al. A mitochondrial stratigraphy for island southeast Asia. Am J Hum Genet. 2007;80:29–43.
Soares P, Trejaut JA, Loo JH, Hill C, Mormina M, Lee CL, et al. Climate change and postglacial human dispersals in southeast Asia. Mol Biol Evol. 2008;25:1209–18.
Karafet TM, Hallmark B, Cox MP, Sudoyo H, Downey S, Lansing JS, et al. Major east-west division underlies Y chromosome stratification across Indonesia. Mol Biol Evol. 2010;27:1833–44.
Trejaut JA, Poloni ES, Yen JC, Lai YH, Loo JH, Lee CL, et al. Taiwan Y-chromosomal DNA variation and its relationship with Island Southeast Asia. BMC Genet. 2014;15:77.
Melton T, Clifford S, Martinson J, Batzer M, Stoneking M. Genetic evidence for the proto-Austronesian homeland in Asia: mtDNA and nuclear DNA variation in Taiwanese aboriginal tribes. Am J Hum Genet. 1998;63:1807–23.
Yao YG, Watkins WS, Zhang YP. Evolutionary history of the mtDNA 9-bp deletion in Chinese populations and its relevance to the peopling of east and southeast Asia. Hum Genet. 2000;107:504–12.
Yao YG, Kong QP, Bandelt HJ, Kivisild T, Zhang YP. Phylogeographic differentiation of mitochondrial DNA in Han Chinese. Am J Hum Genet. 2002;70:635–51.
Yang MA, Fan X, Sun B, Chen C, Lang J, Ko YC, et al. Ancient DNA indicates human population shifts and admixture in northern and southern China. Science. 2020;369:282–8.
Wang T, Wang W, Xie G, Li Z, Fan X, Yang Q, et al. Human population history at the crossroads of East and Southeast Asia since 11,000 years ago. Cell. 2021;184:3829–3841.e3821.
Ko AM, Chen CY, Fu Q, Delfin F, Li M, Chiu HL, et al. Early Austronesians: into and out of Taiwan. Am J Hum Genet. 2014;94:426–36.
Wang CC, Yeh HY, Popov AN, Zhang HQ, Matsumura H, Sirak K, et al. Genomic insights into the formation of human populations in East Asia. Nature. 2021;591:413–9.
Cabrera VM. Human molecular evolutionary rate, time dependency and transient polymorphism effects viewed through ancient and modern mitochondrial DNA genomes. Sci Rep. 2021;11:5036.
Brotherton P, Haak W, Templeton J, Brandt G, Soubrier J, Jane Adler C, et al. Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans. Nat Commun. 2013;4:1764.
Nagle N, van Oven M, Wilcox S, van Holst Pellekaan S, Tyler-Smith C, Xue Y, et al. Aboriginal Australian mitochondrial genome variation – an increased understanding of population antiquity and diversity. Sci Rep. 2017;7:43041.
Soares P, Ermini L, Thomson N, Mormina M, Rito T, Röhl A, et al. Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet. 2009;84:740–59.
Fu Q, Mittnik A, Johnson PLF, Bos K, Lari M, Bollongino R, et al. A revised timescale for human evolution based on ancient mitochondrial genomes. Curr Biol. 2013;23:553–9.
Kutanan W, Kampuansai J, Brunelli A, Ghirotto S, Pittayaporn P, Ruangchai S, et al. New insights from Thailand into the maternal genetic history of Mainland Southeast Asia. Eur J Hum Genet. 2018;26:898–911.
Duong NT, Macholdt E, Ton ND, Arias L, Schröder R, Van Phong N, et al. Complete human mtDNA genome sequences from Vietnam and the phylogeography of Mainland Southeast Asia. Sci Rep. 2018;8:11651.
Woravatin W, Stoneking M, Srikummool M, Kampuansai J, Arias L, Kutanan W. South Asian maternal and paternal lineages in southern Thailand and the role of sex-biased admixture. PLoS One. 2023;18:e0291547.
Liu J, Zeng W, Sun B, Mao X, Zhao Y, Wang F, et al. Maternal genetic structure in ancient Shandong between 9500 and 1800 years ago. Sci Bull. 2021;66:1129–35.
Miao B, Liu Y, Gu W, Wei Q, Wu Q, Wang W, et al. Maternal genetic structure of a neolithic population of the Yangshao culture. J Genet Genom. 2021;48:746–50.
Sagart L. The expansion of Setaria farmers in East Asia: a linguistic and archaeological model. In: Alicia Sanchez-Mazas RB, Malcolm DR, Ilia Peiros, ML, editors. Past human migrations in East Asia : matching archaeology, linguistics and genetics, 133–167 London; New York: Routledge; 2008.
Sagart L, Hsu TF, Tsai YC, Wu CC, Huang LT, Chen YC, et al. A northern Chinese origin of Austronesian agriculture: new evidence on traditional Formosan cereals. Rice. 2018;11:57.
Dai J, Cai X, Jin J, Ge W, Huang Y, Wu W, et al. Earliest arrival of millet in the South China coast dating back to 5,500 years ago. J Archaeological Sci. 2021;129:105356.
Gunnarsdottir ED, Li M, Bauchet M, Finstermeier K, Stoneking M. High-throughput sequencing of complete human mtDNA genomes from the Philippines. Genome Res. 2011;21:1–11.
Brucato N, Fernandes V, Kusuma P, Černý V, Mulligan CJ, Soares P, et al. Evidence of Austronesian genetic lineages in East Africa and South Arabia: complex dispersal from Madagascar and Southeast Asia. Genome Biol Evol. 2019;11:748–58.
Kong QP, Sun C, Wang HW, Zhao M, Wang WZ, Zhong L, et al. Large-scale mtDNA screening reveals a surprising matrilineal complexity in east Asia and its implications to the peopling of the region. Mol Biol Evol. 2011;28:513–22.
Trejaut JA, Kivisild T, Loo JH, Lee CL, He CL, Hsu CJ, et al. Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations. PLoS Biol. 2005;3:e247.
Bi R, Li WL, Chen MQ, Zhu Z, Yao YG. Rapid identification of mtDNA somatic mutations in gastric cancer tissues based on the mtDNA phylogeny. Mutat Res. 2011;709-710:15–20.
Feng Y, Zhang H, Wang Q, Jin X, Le C, Liu Y, et al. Whole mitochondrial genome analysis of Tai-Kadai-speaking populations in Southwest China. Front Ecol Evol. 2022;10:1000493.
Hudjashov G, Endicott P, Post H, Nagle N, Ho S, Lawson DJ, et al. Investigating the origins of eastern Polynesians using genome-wide data from the Leeward Society Isles. Sci Rep. 2018;8:1823.
Fu Q, Meyer M, Gao X, Stenzel U, Burbano HA, Kelso J, et al. DNA analysis of an early modern human from Tianyuan Cave, China. Proc Natl Acad Sci USA. 2013;110:2223–7.
Wei LH, Yan S, Teo YY, Huang YZ, Wang LX, Yu G, et al. Phylogeography of Y-chromosome haplogroup O3a2b2-N6 reveals patrilineal traces of Austronesian populations on the eastern coastal regions of Asia. PLoS One. 2017;12:e0175080.
Sun J, Li YX, Ma PC, Yan S, Cheng HZ, Fan ZQ, et al. Shared paternal ancestry of Han, Tai-Kadai-speaking, and Austronesian-speaking populations as revealed by the high resolution phylogeny of O1a-M119 and distribution of its sub-lineages within China. Am J Phys Anthropol. 2021;174:686–700.
Yu HX, Zhang XP, Bai Y, Liu KJ, Li H, Li YL, et al. The formation of proto-austronesians: insights from a revised phylogeography of the paternal founder lineage. Mol Genet Genom. 2023;298:1301–8.
Crawford GW, Chen XX, Luan FS, Wang JH. People and plant interaction at the Houli Culture Yuezhuang site in Shandong Province, China. Holocene. 2016;26:1594–604.
Liu D, Ko AM, Stoneking M. The genomic diversity of Taiwanese Austronesian groups: Implications for the “Into- and Out-of-Taiwan” models. PNAS Nexus. 2023;2:pgad122.
Peng MS, Quang HH, Dang KP, Trieu AV, Wang HW, Yao YG, et al. Tracing the Austronesian footprint in Mainland Southeast Asia: a perspective from mitochondrial DNA. Mol Biol Evol. 2010;27:2417–30.
He JD, Peng MS, Quang HH, Dang KP, Trieu AV, Wu SF, et al. Patrilineal perspective on the Austronesian diffusion in Mainland Southeast Asia. PLoS One. 2012;7:e36437.
Kutanan W, Liu D, Kampuansai J, Srikummool M, Srithawong S, Shoocongdej R, et al. Reconstructing the Human Genetic History of Mainland Southeast Asia: insights from genome-wide data from Thailand and Laos. Mol Biol Evol. 2021;38:3459–77.
Kloss-Brandstätter A, Summerer M, Horst D, Horst B, Streiter G, Raschenberger J, et al. An in-depth analysis of the mitochondrial phylogenetic landscape of Cambodia. Sci Rep. 2021;11:10816.
McColl H, Racimo F, Vinner L, Demeter F, Gakuhari T, Moreno-Mayar JV, et al. The prehistoric peopling of Southeast Asia. Science. 2018;361:88–92.
Lipson M, Cheronet O, Mallick S, Rohland N, Oxenham M, Pietrusewsky M, et al. Ancient genomes document multiple waves of migration in Southeast Asian prehistory. Science. 2018;361:92–95.
Wang T, Yang MA, Zhu Z, Ma M, Shi H, Speidel L, et al. Prehistoric genomes from Yunnan reveal ancestry related to Tibetans and Austroasiatic speakers. Science. 2025;388:eadq9792.
Oliveira S, Nägele K, Carlhoff S, Pugach I, Koesbardiati T, Hübner A, et al. Ancient genomes from the last three millennia support multiple human dispersals into Wallacea. Nat Ecol Evol. 2022;6:1024–34.
Sidwell P. Austroasiatic classification. In: Jenny M, Sidwell P, editors. The handbook of Austroasiatic languages. Leiden; Boston: Brill; 2015.
Lipson M, Loh PR, Patterson N, Moorjani P, Ko YC, Stoneking M, et al. Reconstructing Austronesian population history in Island Southeast Asia. Nat Commun. 2014;5:4689.
Hudjashov G, Karafet TM, Lawson DJ, Downey S, Savina O, Sudoyo H, et al. Complex patterns of admixture across the Indonesian archipelago. Mol Biol Evol. 2017;34:2439–52.
Mörseburg A, Pagani L, Ricaut FX, Yngvadottir B, Harney E, Castillo C, et al. Multi-layered population structure in Island Southeast Asians. Eur J Hum Genet. 2016;24:1605–11.
Deng L, Hoh BP, Lu D, Saw WY, Twee-Hee Ong R, Kasturiratne A, et al. Dissecting the genetic structure and admixture of four geographical Malay populations. Sci Rep. 2015;5:14375.
Tagore D, Aghakhanian F, Naidu R, Phipps ME, Basu A. Insights into the demographic history of Asia from common ancestry and admixture in the genomic landscape of present-day Austroasiatic speakers. BMC Biol. 2021;19:61.
Norhalifah HK, Syaza FH, Chambers GK, Edinur HA. The genetic history of Peninsular Malaysia. Gene. 2016;586:129–35.
Singh PP, Vishwakarma S, Sultana GNN, Pilvar A, Karmin M, Rootsi S, et al. Dissecting the paternal founders of Mundari (Austroasiatic) speakers associated with the language dispersal in South Asia. Eur J Hum Genet. 2021;29:528–32.
Chiu H-L. Restudying the “Tso-Chen Man” and a new perspective of the Paleolithic Age. Taiwan Nat Sci. 2016;35:12–25.
Larena M, Sanchez-Quinto F, Sjödin P, McKenna J, Ebeo C, Reyes R, et al. Multiple migrations to the Philippines during the last 50,000 years. Proc Natl Acad Sci USA. 2021;118:e2026132118.
Brucato N, André M, Hudjashov G, Mondal M, Cox MP, Leavesley M, et al. Chronology of natural selection in Oceanian genomes. iScience. 2022;25:104583.
Skoglund P, Posth C, Sirak K, Spriggs M, Valentin F, Bedford S, et al. Genomic insights into the peopling of the Southwest Pacific. Nature. 2016;538:510–3.
Pugach I, Hubner A, Hung HC, Meyer M, Carson MT, Stoneking M. Ancient DNA from Guam and the peopling of the Pacific. Proc Natl Acad Sci USA. 2021;118:e2022112118.
Choin J, Mendoza-Revilla J, Arauna LR, Cuadros-Espinoza S, Cassar O, Larena M, et al. Genomic insights into population history and biological adaptation in Oceania. Nature. 2021;592:583–9.
Delfin F, Myles S, Choi Y, Hughes D, Illek R, van Oven M, et al. Bridging near and remote Oceania: mtDNA and NRY variation in the Solomon Islands. Mol Biol Evol. 2012;29:545–64.
Chambers GK, Edinur HA. Reconstruction of the Austronesian Diaspora in the Era of Genomics. Hum Biol. 2021;92:247–63.
Arenas M, Gorostiza A, Baquero JM, Campoy E, Branco C, Rangel-Villalobos H, et al. The early peopling of the Philippines based on mtDNA. Sci Rep. 2020;10:4901.
Soares P, Rito T, Trejaut J, Mormina M, Hill C, Tinkler-Hundal E, et al. Ancient voyaging and Polynesian origins. Am J Hum Genet. 2011;88:239–47.
Soares PA, Trejaut JA, Rito T, Cavadas B, Hill C, Eng KK, et al. Resolving the ancestry of Austronesian-speaking populations. Hum Genet. 2016;135:309–26.
Zhang X, Ji X, Li C, Yang T, Huang J, Zhao Y, et al. A Late Pleistocene human genome from Southwest China. Curr Biol. 2022;32:3095–3109.e3095.
Brandão A, Eng KK, Rito T, Cavadas B, Bulbeck D, Gandini F, et al. Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia. Hum Genet. 2016;135:363–76.
Matsumura H, Hung HC, Higham C, Zhang C, Yamagata M, Nguyen LC, et al. Craniometrics reveal “two layers” of prehistoric human dispersal in Eastern Eurasia. Sci Rep. 2019;9:1451.
Sneath PHA, Sokal RR. Numerical taxonomy; the principles and practice of numerical classification. San Francisco: W. H. Freeman; 1973.
Osteometrie GB. Anthropologie. Handbuch der vergleichenden Biologie des Menschen. Band I: Wesen und Methoden der Anthropologie. 1. Teil. 160–232. New York: Gustav Fischer Verlag, Stuttgart; 1988.
Shi H, Dong YL, Wen B, Xiao CJ, Underhill PA, Shen PD, et al. Y-chromosome evidence of southern origin of the East Asian-specific haplogroup O3-M122. Am J Hum Genet. 2005;77:408–19.
Yang MA. A genetic history of migration, diversification, and admixture in Asia. Hum Popul Genet Genom. 2021;2:0001.
Ning C, Li T, Wang K, Zhang F, Li T, Wu X, et al. Ancient genomes from northern China suggest links between subsistence changes and human migration. Nat Commun. 2020;11:2700.
Tsang CH, Li KT, Hsu TF, Tsai YC, Fang PH, Hsing YC. Broomcorn and foxtail millet were cultivated in Taiwan about 5000 years ago. Bot Stud. 2017;58:3.
Moodley Y, Linz B, Yamaoka Y, Windsor HM, Breurec S, Wu JY, et al. The peopling of the Pacific from a bacterial perspective. Science. 2009;323:527–30.
Zhang M, Sun G, Ren L, Yuan H, Dong G, Zhang L, et al. Ancient DNA evidence from China reveals the expansion of Pacific Dogs. Mol Biol Evol. 2020;37:1462–9.
Larson G, Liu R, Zhao X, Yuan J, Fuller D, Barton L, et al. Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA. Proc Natl Acad Sci USA. 2010;107:7686–91.
Brucato N, Kusuma P, Cox MP, Pierron D, Purnomo GA, Adelaar A, et al. Malagasy genetic ancestry comes from an historical Malay trading post in Southeast Borneo. Mol Biol Evol. 2016;33:2396–2400.