TABLE S1: Sample information and haplogroup for newly reported individuals in this study.

TABLE S2: Outgroup f3 statistics of the form (Studied population, Ancient; Yoruba) based on the merged Human Origins dataset with 10 top f3 values.

TABLE S3: Admixture f3 statistics of the form (Ancient1, Ancient2; Studied population) based on the merged 1240 K dataset with significant negative Z scores (Z < −3).

TABLE S4: F4 statistics of the form (Studied population, Yoruba; North Eurasia ancient, South Eurasia ancient) based on the merged Human Origins dataset with significant positive and negative Z scores (Z > 3 and Z < −3).

TABLE S5: F4 statistics of the form (Studied population, Mbuti; North Eurasia ancient, South Eurasia ancient) based on the merged 1240K dataset with significant positive and negative Z scores (Z > 3 and Z < −3).

TABLE S6: F4 statistics of the form (Studied population, Yoruba; southeast EA Ancient1, southeast EA Ancient2) based on the merged Human Origins dataset with significantnegative Z scores (Z < −3).

TABLE S7: F4 statistics of the form (Studied population, Yoruba; SEA Ancient1, SEA Ancient2) based on the merged Human Origins dataset with significant negative Z scores (Z < −3).

TABLE S8: F4 statistics of the form (Millet farmer, Yoruba; Studied population, southeast Eurasian) based on the merged Human Origins dataset with significant positive and negative Z scores (Z > 3 and Z < −3).

TABLE S9: F4 statistics of the form (Millet farmer, Mbuti; Studied population, southeast Eurasian) based on the merged 1240 K dataset with significant positive and negative Z scores (Z > 3 and Z < −3).

TABLE S10: F4 statistics of the form (SEA rice farmer, Yoruba; Studied population, southeast Eurasian) based on the merged Human Origins dataset with significant positive and negative Z scores (Z > 3 and Z < −3).

TABLE S11: F4 statistics of the form (SEA rice farmer, Mbuti; Studied population, southeast Eurasian) based on the merged 1240 K dataset with significant positive and negative Z scores (Z > 3 and Z < −3).

TABLE S12: F4 statistics of the form (EA rice farmer, Yoruba; Studied population, southeast Eurasian) based on the merged Human Origins dataset with significant positive and negative Z scores (Z > 3 and Z < −3).

TABLE S13: F4 statistics of the form (EA rice farmer, Mbuti; Studied population, southeast Eurasian) based on the merged 1240 K dataset with significant positive and negative Z scores (Z > 3 and Z < −3).

TABLE S14: Three-way qpAdm models of studied Yunnan populations in percent.

TABLE S15: Haplogroup frequencies of Y and mtDNA chromosome in studied populations.