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Fig. 2 Exploratory analyses of relationships of ancient Southeast Asian genomes to those of present-day populations.
Ancient samples are projected on the first two components of PCAs for (A) worldwide populations and (B) a subset of populations from EA and SEA. (C) fastNGSadmix plot at K = 13 (11). We refer to the following present-day language-speaking groups in relation to our ancient samples: Austroasiatic (bright green), Austronesian (pink), and Hmong-Mien (dark pink), along with a broad East Asian component (dark green). P.M., proto-Malay; M.N., Malaysian negrito; P.N., Philippines negrito; And. Is., Andaman Islands; NA, not applicable.
We also find a distinctive relationship between the group 1 samples and the Ikawazu Jōmon of Japan (IK002). Outgroup f3 statistics (11, 16) show that group 1 shares the most genetic drift with all ancient mainland samples and Jōmon (fig. S12 and table S4). All other ancient genomes share more drift with present-day East Asian and Southeast Asian populations than with Jōmon (figs. S13 to S19 and tables S4 to S11). This is apparent in the fastNGSadmix analysis when assuming six ancestral components (K = 6) (fig. S11), where the Jōmon sample contains East Asian components and components found in group 1. To detect populations with genetic affinities to Jōmon, relative to present-day Japanese, we computed D statistics of the form D(Japanese, Jōmon; X, Mbuti), setting X to be different present-day and ancient Southeast Asian individuals (table S22). The strongest signal is seen when X = Ma911 and La368 (group 1 individuals), showing a marginally nonsignificant affinity to Jōmon (11). This signal is not observed with X = Papuans or Önge, suggesting that the Jōmon and Hòabìnhians may share group 1 ancestry (11).
D-statistics of the form D (Papuan, Tiányuán; Y, Mbuti), where Y is a test population, are consistent with present-day East Asian populations and most populations of ancient and present-day SEA being more closely related to Tiányuán than to Papuans (Fig. 1) (11, 18). However, this D statistic is not significantly different from 0 for Y = Jehai, Önge, Jarawa or group 1 (the ancient Hòabìnhians) (table S12). D statistics of the form D(Önge, Tiányuán; X, Mbuti), where X is Jarawa, Jehai, or group 1, show that these populations share more ancestry with Önge than with Tiányuán (Fig. 1) (11). Using TreeMix and qpGraph (16, 19) to explore admixture graphs that could potentially fit our data, we find that group 1 individuals are best modeled as a sister group to present-day Önge (Fig. 3, and figs. S21 to S23 and S35 to S37). Finally, the Jōmon individual is best-modeled as a mix between a population related to group 1/Önge and a population related to East Asians (Amis), whereas present-day Japanese can be modeled as a mixture of Jōmon and an additional East Asian component (Fig. 3 and fig. S29).
Fig. 3 Admixture graphs fitting ancient Southeast Asian genomes.
TreeMix and qpGraph admixture graphs combining present-day populations and selected ancient samples with high single-nucleotide polymorphism coverage (11). (A) A graph including group 1 samples (Ma911 and La368) fits them as sister groups to present-day Önge. (B) A graph including the highest-coverage group 1 (La368) and group 2 (La364, Ma912) samples shows that group 2 receives ancestry from both group 1 and the East Asian branch. (C) Using qpGraph, we modeled present-day East Asians (represented by Amis) as a mixture of an Önge-like population and a population related to the Tiányuán individual. (D) The Jōmon individual is modeled as a mix of Hòabìnhian (La368) and East Asian ancestry.
The remaining ancient individuals are modeled in fastNGSadmix as containing East Asian and Southeast Asian components present in high proportions in present-day Austroasiatic, Austronesian, and Hmong-Mien speakers, along with a broad East Asian component. A PCA including only East Asian and Southeast Asian populations that did not show considerable Papuan or Önge-like ancestry (fig. S11) separates the present-day speakers of ancestral language families in the region: Trans-Himalayan (formerly Sino-Tibetan), Austroasiatic, and Austronesian/Kradai (20). The ancient individuals form five slightly differentiated clusters (groups 2 to 6) (Fig. 1B), in concordance with fastNGSadmix and f3 results (Fig. 2 and figs. S12 to S19) (11).
Group 2 contains late Neolithic and early Bronze Age individuals (4291 to 2184 cal B.P.), from Vietnam, Laos, and the Malay Peninsula who are closely related to present-day Austroasiatic language speakers such as the Mlabri and Htin (Fig. 1) (11). Compared with groups 3 to 6, group 2 individuals lack a broad East Asian ancestry component that is at its highest proportion in northern EA in fastNGSadmix. TreeMix analyses suggest that the two individuals with the highest coverage in group 2 (La364 and Ma912) form a clade resulting from admixture between the ancestors of East Asians and of La368 (Fig. 3 and figs. S24 to S27). This pattern of complex, localized admixture is also evident in the Jehai, fitted as an admixed population between group 2 (Ma912) and the branch leading to present-day Önge and La368 (fig. S28). Consistent with these results, La364 is best modeled as a mixture of a population ancestral to Amis and the group 1/Önge-like population (Fig. 3). The best model for present-day Dai populations is a mixture of group 2 individuals and a pulse of admixture from East Asians (fig. S39).
Group 6 individuals (1880 to 299 cal B.P.) originate from Malaysia and the Philippines and cluster with present-day Austronesians (11) (Fig. 2). Group 6 also contains Ma554, having the highest amounts of Denisovan-like ancestry relative to the other ancient samples, although we observe little variation in this archaic ancestry in our samples from MSEA (11).
Group 5 (2304 to 1818 cal B.P.) contains two individuals from Indonesia, modeled by fastNGSadmix as a mix of Austronesian- and Austroasiatic-like ancestry, similar to present-day western Indonesians, a finding consistent with their position in the PCA (Fig. 2) (11). Indeed, after Mlabri and Htin, the present-day populations sharing the most drift with group 2 are western Indonesian samples from Bali and Java previously identified as having mainland Southeast Asian ancestry (21) (fig. S13). Treemix models the group 5 individuals as an admixed population receiving ancestry related to group 2 (figs. S30 and S31) and Amis. Despite the clear relationship with the mainland group 2 seen in all analyses, the small ancestry components in group 5 related to Jehai and Papuans visible in fastNGSadmix may be remnants of ancient Sundaland ancestry. These results suggest that group 2 and group 5 are related to a mainland migration that expanded southward across MSEA by 4 ka ago and into island Southeast Asia (ISEA) by 2 ka ago (22–24). A similar pattern is detected for Ma555 (fig. S33) in Borneo (505 to 326 cal B.P., group 6), although this may be a result of recent gene flow.
Group 3 is composed of several ancient individuals from northern Vietnam (2378 to 2041 cal B.P.) and one individual from Long Long Rak (LLR), Thailand (1691 to 1537 cal B.P.). They cluster in the PCA with the Dai, Amis, and Kradai speakers from Thailand, consistent with an Austro-Tai linguistic phylum, comprising both the Kradai and Austronesian language families (20, 25). Group 4 contains the remaining ancient individuals from LLR in Thailand (1570 to 1815 cal B.P.), and Vt778 from inland Vietnam (2750 to 2500 cal B.P.). These samples cluster with present-day Austroasiatic speakers from Thailand and China, in support of a South China origin for LLR (26). The genetic distinction between Austroasiatic and Kradai speakers is discussed further in (11).[/a]