Prehistoric human migration between Sundaland and South Asia [ProBoards repost]

[okarinaofsteiner]

https://genarchivist.freeforums.net/thre...land-south

www.nature.com/articles/s42003-023-04510-0 (found here)

Interesting paper. I disagree with the conclusion on the population origin of Munda and Munda-like Austroasiatic groups in India that they came up with in the abstract, especially because the assumed admixture dates contradict linguistic and archaeological evidence Razib Khan has cited in his content (also see here).

However, the charts and figures are interesting. They used Paniya as their "Dravidian" reference and Kensiu as their "Malaysia Negrito" reference. I don't think Kensiu is the best proxy for the Neolithic SEA group that lent its language and agricultural practices to the Munda, even if Kensiu does have a lot of Austroasiatic (East Asian-related) rice farmer ancestry. But I'll leave that for the members of New Anthrogenica to discuss.

Abstract
Rapid sea-level rise between the Last Glacial Maximum (LGM) and the mid-Holocene transformed the Southeast Asian coastal landscape, but the impact on human demography remains unclear. Here, we create a paleogeographic map, focusing on sea-level changes during the period spanning the LGM to the present-day and infer the human population history in Southeast and South Asia using 763 high-coverage whole-genome sequencing datasets from 59 ethnic groups. We show that sea-level rise, in particular meltwater pulses 1 A (MWP1A, ~14,500–14,000 years ago) and 1B (MWP1B, ~11,500–11,000 years ago), reduced land area by over 50% since the LGM, resulting in segregation of local human populations. Following periods of rapid sea-level rises, population pressure drove the migration of Malaysian Negritos into South Asia. Integrated paleogeographic and population genomic analysis demonstrates the earliest documented instance of forced human migration driven by sea-level rise.

a Geographic locations of the studied populations and their sample sizes included are indicated on the map. The ethnicity label can be found in Supplementary Fig. 1. The map was constructed using ggplot2100, and the base map was retrieved through ‘map_data’ package101,102. The colour scheme represents the ancestral group as shown in plot.
b The PCA34 result for the 763 genomes are plotted with PC1 and PC2 (percentage of eigenvector). Each dot represents an individual. Each ethnic group is shown as a different colour, and the legend for each ethnic group is in Supplementary Fig. 2.
c The proportion of ancestries of the 763 individuals estimated using ADMIXTURE35 for K = 6–9 ancestral components. A bar represents an individual, and a colour indicates an ancestral component. K = 7 is the most optimal number of components based on the cross-validation error estimate (Supplementary Fig. 3). The robustness of the clustering is shown next to K. The 11 population groups were classified based on the combination of ancestral components and named under the plot. The South Asian Austroasiatic and Mainland Southeast Asian populations include the Malaysia Negrito ancestry (blue) at K = 6–7, which later is included in the new ancestral component (red) at K = 8–9. Cross-validation error of the analysis and more results are shown in Supplementary Fig. 3.

a The genetic relationships and admixture history for Southeast and South Asian are modelled using qpGraph41. The phylogenetic relationship was estimated using Treemix40 (Supplementary Fig. 9). The South Asian Austroasiatic group is the admixed population in this model and the two best ancestral populations among the 11 population groups are Dravidians (71%) and Malaysian Negritos (29%) (Supplementary Fig. 10 and Supplementary Table 4). Mainland SEA in the figure is mainland Southeast Asians.
b The changes in effective population size (X axis) over time (Y axis) for Birhor and Kensiu are estimated using MSMC. The Birhor shows an extreme increase in the effective population size to over 500,000, 12–7 thousand years ago (KYA on the X axis), and the population size is out of the Y axis range in the plot (shown the entire plot in Supplementary Fig. 6b).
c The migration rate between a pair of populations over time is estimated by MSMC-IM44. The X and Y axes indicate the time (KYA) and the migration rate at the time t, m(t), respectively. The lines show the estimated migration rate between the three pairs of populations over time as shown in the legend. The periods of the two meltwater pulses (MWP) 1A and 1B are indicated as grey bars.

Fourth, we used Multiple Sequentially Markovian coalescent (MSMC) analysis42,43 to estimate effective population size changes over time. The dramatic increase in population size of South Asian Austroasiatic groups compared to the light gradual increase in population size of Malaysian Negritos suggests the introduction of a distinct lineage into South Asian Austroasiatic groups (Fig. 3b and Supplementary Figs. 5 and 6). Therefore, the direction of admixture between the two populations is likely from Malaysian Negritos to South Asian Austroasiatic groups.

Lastly, we estimated the timing of admixture events based on the migration rate inferred by MSMC-IM44. Increasing migration rates observed after the population split of the Kensiu (Malaysian Negritos) and the Birhor (South Asian Austroasiatic) groups indicate admixture between them ~12,000–9000 years ago (Fig. 3c and Supplementary Fig. 7). Similarly, an increase in migration rate between the Kensiu and Dai (Mainland Southeast Asians) groups indicates admixture ~12,000–8000 years ago (Fig. 3c and Supplementary Fig. 7). In contrast, the increase in migration rate was not observed between Birhor and any other Southeast Asian populations—the Dai, Igorot (Austronesians), or Aeta (Philippine Negritos). Therefore, the origin of the admixture found in South Asian Austroasiatic groups is the Malaysian Negritos, rather than Mainland Southeast Asians that contained the Malaysian Negrito ancestry. The admixture between the South Asian Austroasiatic and Malaysian Negrito groups could only have occurred after the split of the Austronesians and Mainland Southeast Asians, ~11,000–10,000 years ago (Supplementary Fig. 6a), since there is no admixture signal between the Kensiu and Igorot. Thus, the timing of the admixture is predicted to be ~10,000–8000 years ago. This estimated time range matches the admixture between Malaysian Negritos and Mainland Southeast Asians. The MSMC-IM results with the Dai are replicable using the Kinh (KHV) population (Supplementary Fig. 7 and Supplementary Table 3).

[okarinaofsteiner]

I don't think Kensiu is the best proxy for the Neolithic SEA group that lent its language and agricultural practices to the Munda, even if Kensiu does have a lot of Austroasiatic (East Asian-related) rice farmer ancestry.

There's an Anthrogenica post of a paper discussing this (linked the Genoplot archive this time)

Sequence analyses of Malaysian Indigenous communities reveal historical admixture between Hoabinhian hunter-gatherers and Neolithic farmers

To have a better understanding about the genetic history of these people, especially Malaysian Negritos, we sequenced whole genomes of 15 individuals belonging to five indigenous groups from Peninsular Malaysia and one from North Borneo to high coverage (30X). Our results demonstrate that indigenous populations of Malaysia are genetically close to East Asian populations. We show that present-day Malaysian Negritos can be modeled as an admixture of ancient Hoabinhian hunter-gatherers and Neolithic farmers. We observe gene flow from South Asian populations into the Malaysian indigenous groups, but not into Dusun of North Borneo. Our study proposes that Malaysian indigenous people originated from at least three distinct ancestral populations related to the Hoabinhian hunter-gatherers, Neolithic farmers and Austronesian speakers.

Our outgroup-f3 analysis is consistent with the archeological findings regarding the transition from hunting-gathering to farming lifestyle in the Gua Cha cave. While the Ma911 (Hoabinhian layer) shared most alleles with the Malaysian Negritos, the Ma912 (Neolithic farmer) was closer to the Senoi agriculturists. Our results confirm that modern Malaysian Negritos have been derived genetically from two ancient populations: the Hoabinhian hunter-gatherers and the Neolithic farmers who originated from South China or MSEA.

No mention of Kensiu in this study, but it did reference older studies that examined Kensiu population genetics.

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The paper is almost certainly mistaken about the origins of Munda speakers in India. We have enough linguistic and genomic evidence at this point to be confident that they are the result of the Austroasiatic expansion of rice farmers from Southeast Asia not earlier than ~2000BCE. They arrived with the Hoabinhian admixture that all modern Austroasiatic populations possess, and it is this which the authors seem to be mistaking for an early Holocene migration.

[Jerome]

Do you know if there was any hoabinhian migration to mainland south asia in the Mesolithic?

[Psynome]

Do you know if there was any hoabinhian migration to mainland south asia in the Mesolithic?

There is some scattered archaeological evidence of Hoabinhian presence in northeastern South Asia in the form of single outlier sites. So it is likely there was at least some  amount of mobility into South Asia. 

However, this mobility didn't have anything to do with much later Austroasiatic groups like Munda nor is there evidence I've seen of a lasting genomic impact in the region from the Mesolithic Hoabinhians, unlike the clear evidence for Austroasiatic admixture in eastern South Asia.

Check Emergence of cultural diversity in Mainland Southeast Asia: A view from prehistory (White 2011) for some maps of these outlier sites.