South-East Asia samples include shared ancestry with Jōmon

pca-south-east-asia-jomon

New paper (behind paywall) The prehistoric peopling of Southeast Asia, by McColl et al. (Science 2018) 361(6397):88-92 from a recent bioRxiv preprint.

Interesting is this apparently newly reported information including a female sample from the Ikawazu Jōmon of Japan ca. 570 BC (emphasis mine):

The two oldest samples — Hòabìnhians from Pha Faen, Laos [La368; 7950 with 7795 calendar years before the present (cal B.P.)] and Gua Cha, Malaysia (Ma911; 4415 to 4160 cal B.P.)—henceforth labeled “group 1,” cluster most closely with present-day Önge from the Andaman Islands and away from other East Asian and Southeast-Asian populations (Fig. 2), a pattern that differentiates them from all other ancient samples. We used ADMIXTURE (14) and fastNGSadmix (15) to model ancient genomes as mixtures of latent ancestry components (11). Group 1 individuals differ from the other Southeast Asian ancient samples in containing components shared with the supposed descendants of the Hòabìnhians: the Önge and the Jehai (Peninsular Malaysia), along with groups from India and Papua New Guinea.

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 presentday 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).

jomon-japanese-migrations
Model for plausible migration routes into SEA. This schematic is based on ancestry patterns observed in the ancient genomes. Because we do not have ancient samples to accurately resolve how the ancestors of Jōmon and Japanese populations entered the Japanese archipelago, these migrations are represented by dashed arrows. A mainland component in Indonesia is depicted by the dashed red-green line. Gr, group; Kra, Kradai.

(…) 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)

Interesting in relation to the oral communication of the SMBE O-03-OS02 Whole genome analysis of the Jomon remain reveals deep lineage of East Eurasian populations by Gakuuhari et al.:

Post late-Paleolithic hunter-gatherers lived throughout the Japanese archipelago, Jomonese, are thought to be a key to understanding the peopling history in East Asia. Here, we report a whole genome sequence (x1.85) of 2,500-year old female excavated from the Ikawazu shell-mound, unearthed typical remains of Jomon culture. The whole genome data places the Jomon as a lineage basal to contemporary and ancient populations of the eastern part of Eurasian continent, and supports the closest relationship with the modern Hokkaido Ainu. The results of ADMIXTURE show the Jomon ancestry is prevalent in present-day Nivkh, Ulchi, and people in the main-island Japan. By including the Jomon genome into phylogenetic trees, ancient lineages of the Kusunda and the Sherpa/Tibetan, early splitting from the rest of East Asian populations, is emerged. Thus, the Jomon genome gives a new insight in East Asian expansion. The Ikawazu shell-mound site locates on 34,38,43 north latitude, and 137,8, 52 east longitude in the central main-island of the Japanese archipelago, corresponding to a warm and humid monsoon region, which has been thought to be almost impossible to maintain sufficient ancient DNA for genome analysis. Our achievement opens up new possibilities for such geographical regions.

Related

Genomic history of South-East Asia: eastern Polynesians, Peninsular Malaysia and North Borneo

Two recent interesting genetic papers:

1. Open Access Investigating the origins of eastern Polynesians using genome-wide data from the Leeward Society Isles, by Hudjashov et al., at Scientific Reports (2018)

Abstract:

The debate concerning the origin of the Polynesian speaking peoples has been recently reinvigorated by genetic evidence for secondary migrations to western Polynesia from the New Guinea region during the 2nd millennium BP. Using genome-wide autosomal data from the Leeward Society Islands, the ancient cultural hub of eastern Polynesia, we find that the inhabitants’ genomes also demonstrate evidence of this episode of admixture, dating to 1,700–1,200 BP. This supports a late settlement chronology for eastern Polynesia, commencing ~1,000 BP, after the internal differentiation of Polynesian society. More than 70% of the autosomal ancestry of Leeward Society Islanders derives from Island Southeast Asia with the lowland populations of the Philippines as the single largest potential source. These long-distance migrants into Polynesia experienced additional admixture with northern Melanesians prior to the secondary migrations of the 2nd millennium BP. Moreover, the genetic diversity of mtDNA and Y chromosome lineages in the Leeward Society Islands is consistent with linguistic evidence for settlement of eastern Polynesia proceeding from the central northern Polynesian outliers in the Solomon Islands. These results stress the complex demographic history of the Leeward Society Islands and challenge phylogenetic models of cultural evolution predicated on eastern Polynesia being settled from Samoa.

polynesian
Sampling locations and overview of genomic diversity. (a) Sources of population data used in the present study. The Philippine group names are abbreviated as follows: Aet (Aeta); Agt (Agta); Bat (Batak); Cas (Casiguran); Kan (Kankanaey); Taga (Tagalog); Tagb (Tagbanua); Zam (Zambales); and Phi (Philippines, incorporating all other groups from this region). Colours indicate regional affiliation of populations used for analysis of autosomal DNA: orange – mainland Southeast Asia and East Asia; dark blue – Taiwan; brown – Philippines Aeta, Agta and Batak negritos; light blue – Philippines non-negritos; red – western Indonesia; pink – eastern Indonesia; purple – northern Melanesia and New Guinea; black – Australia; green –Polynesia. The usage of populations varies with the type of analysis employed (Supplementary Table S1). Inset map shows the three populations from the Leeward Society Isles, and Tahiti, the major island in the Windward Society Isles. The red circles within Micronesia and Melanesia represent 20 of the atolls and islands referred to collectively as outlier Polynesia. The red stars denote the three additional Polynesian outlier populations (Rennell and Bellona, Tikopia), which together with Tonga, were used in analysis of ancient admixture by Skoglund, et al.25. Detailed sample information is given in Supplementary Table S1. The map was created using R v. 3.4.1 (R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, https://www.R-project.org/), and packages ‘maps’ v. 3.2.0 (https://cran.r-project.org/package=maps) and ‘mapdata’ v. 2.2-6 (https://cran.r-project.org/package=mapdata). (b) Inset at top right shows two alternative reconstructed sub-groupings of Polynesian languages discussed in the text. The critical differences are the position of the East Polynesian languages relative to the rest of nuclear Polynesian, and their relationship to the Central Northern Outlier languages. In the sub-grouping according to Pawley31 all the Polynesian Outlier languages group within Samoic implying an early separation of Proto-East Polynesian from the rest of the Nuclear Polynesian languages. In the alternative sub-grouping proposed by Wilson32 the Central Northern Outlier languages group with the languages of East Polynesia, within a larger clade containing the other Northern Outlier languages. (c) Principal components analysis of genome-wide SNP diversity in 639 individuals populations shown in panel A; axes are scaled by the proportion of variance described by the corresponding principal component.

2. Genomic structure of the native inhabitants of Peninsular Malaysia and North Borneo suggests complex human population history in Southeast Asia, by Yew et al. at at Human Genetics (2018)

Abstract:

Southeast Asia (SEA) is enriched with a complex history of peopling. Malaysia, which is located at the crossroads of SEA, has been recognized as one of the hubs for early human migration. To unravel the genomic complexity of the native inhabitants of Malaysia, we sequenced 12 samples from 3 indigenous populations from Peninsular Malaysia and 4 native populations from North Borneo to a high coverage of 28–37×. We showed that the Negritos from Peninsular Malaysia shared a common ancestor with the East Asians, but exhibited some level of gene flow from South Asia, while the North Borneo populations exhibited closer genetic affinity towards East Asians than the Malays. The analysis of time of divergence suggested that ancestors of Negrito were the earliest settlers in the Malay Peninsula, whom first separated from the Papuans ~ 50–33 thousand years ago (kya), followed by East Asian (~ 40–15 kya), while the divergence time frame between North Borneo and East Asia populations predates the Austronesian expansion period implies a possible pre-Neolithic colonization. Substantial Neanderthal ancestry was confirmed in our genomes, as was observed in other East Asians. However, no significant difference was observed, in terms of the proportion of Denisovan gene flow into these native inhabitants from Malaysia. Judging from the similar amount of introgression in the Southeast Asians and East Asians, our findings suggest that the Denisovan gene flow may have occurred before the divergence of these populations and that the shared similarities are likely an ancestral component.

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