Extended Data Fig. 9: Identification of archaic introgression in MSEA populations.
From: Genome diversity and signatures of natural selection in mainland Southeast Asia
a, Comparison of the archaic-introgression sequences (from Neanderthal and Denisovan) between MSEA and global populations in 1KGP. EAS-East Asians (CDX and KHV were excluded since they due belong to MSEA), AMR-Americans, SAS-South Asians and EUR-Europeans. The y-axis indicates the mean detected Neanderthal sequences (or Denisovan sequences) per individual from different populations, stratified by super populations. We compared MSEA with EAS and SAS, and evaluated significance using two-sided unpaired t-test. For each boxplot, we drew a box from the first quartile to the third quartile. A horizontal line across the box indicates the median. The whiskers go from each quartile to the minimum or the maximum. b, Mean amounts of the detected introgressed sequences per individual in the 1KGP populations, categorized by affinity to the Altai Neanderthal and Altai Denisovan genomes. c, Intersection of the Neanderthal introgression callsets between Sprime and IBDmix. The callsets were merged for all identified introgression segments in MSEA individuals. d, Violin plots of the Neanderthal sequences per individual in MSEA populations identified by Sprime and IBDmix. For each boxplot, we drew a box from the first quartile to the third quartile. A horizontal line across the box indicates the median. The whiskers go from each quartile to the minimum or the maximum.
