Fig. 3: Ancient admixture between South Asian Austroasiatic and Malaysian Negrito groups.

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.