Additional file 1 of Reconstructing the ancestral gene pool to uncover the origins and genetic links of Hmong–Mien speakers

Additional file 1: Table S1. Quality control information of whole genome sequencing of Yao samples. Table S2. Total length of Archaic segments and Ancestry segments at the individual level among HM. Table S3. Higheast Altai Neanderthal segments in 80 Yao samples. Table S4. Higheast Denisova segments in 80 Yao samples. Table S5. Unique Altai Neanderthal segments in 80 Yao samples. Table S6. Unique Denisova segments in 80 Yao samples. Table S7. Y-haplogroups inferred by Y-LineageTracker software based on Panel 1 dataset. Table S8. The distribution of Y-haplogroups in sequencing data samples. Table S9. Hmong-Mien language distence matrix. Table S10. mtDNA-haplogroups inferred by Haplogrep2 software based on Panel 1 dataset. Table S11. The distribution of mtDNA-haplogroups in sequencing data samples. Table S12. Pairwise-FST between two populations based on Panel 2 dataset in the context of East Asia. Table S13. Inferring the origin of the South China components in the Han Chinese population through f4. Table S14. 8 ancient DNA samples sharing the most genetic drift with the Hmong-Mien ancestral population. Table S15. The F3 results of 8 ancient DNA samples sharing the most genetic drift with the Hmong-Mien ancestral population. Table S16. Top 0.1% signal of the pairwise FST of HM and Han. Table S17. KOBAS pathway analysis on the genes in which highly differentiated SNVs between HM and Han are located. Table S18. Top 0.1% signal of the pairwise FST of aHM and Han. Table S19. KOBAS pathway analysis on the genes in which newly identified signal SNVs of aHM are located. Table S20. IHS results of the HM population group. Table S21. IHS results of the aHM population group. Table S22. SNVs distributed in a gradient among aHM, HM and Han. Table S23. KOBAS pathway analysis on the genes that regulated by eQTLs from HM special SNVs. Table S24. Proportion of carrying recent derived alleles. Table S25. 3-degree or closer relationship pairs in 80 Yao samples. Table S26. HLA types of all samples in Panel 1 dataset. Table S27. Frequency statistics of each HLA type in each population.