Fig. 3: Population structure.
From: The Taiwan Precision Medicine Initiative provides a cohort for large-scale studies
a, PCA analysis. The TPMI cohort was compared with TWB, SGDP and 1KGP samples. The top-left inset compares TPMI participants born before 1950 with those born after 1950; the top-right inset compares the TPMI and the 1KGP. The main figure shows TPMI, TWB and two Taiwan Indigenous tribes (SGDP). Admixture fraction plots show ancestry fractions from ten ancestral populations (K = 10), with principal component (PC) 1 on the bottom axis and PC2 on the right. b, Coancestry and fine-scale structure. The coancestry heat map shows individuals (rows, columns) clustered by shared haplotypes, with colour intensity indicating haplotype copying. Darker blue or red indicates higher coancestry; yellow or light orange indicates lower. Diagonal blocks mark within-group sharing: K1–K6 show strong within-group haplotype sharing; K1–K2 (Han Chinese-enriched) exhibit strong coancestry with each other but less with K3–K6 (Indigenous-enriched), reflecting genetic differentiation; K3–K6 form distinct blocks, with some asymmetric sharing suggesting admixture or shared ancestry. The dendrogram shows clustering consistent with subgroup distinctions. c, Admixture graph depicting relationships and gene flow among K1–K6. Solid arrows represent drift edges (genetic drift from ancestral populations); dotted arrows represent admixture, with percentages indicating fractions. Edge numbers denote drift lengths (f2 units). K1 derives around 90% of ancestry from a lineage that also contributes to K2, plus 10% admixture from a lineage related to K6, indicating close K1–K2 affinity with minor Indigenous input. K4 shows around 49% of ancestry from a K5-related lineage (shared with K3) and 51% from a branch that also contributes to K2, reflecting Han–Indigenous admixture. K6 is mostly unadmixed with a long drift branch (f2 = 70), consistent with a highly diverged Indigenous lineage. K5 seems to be ancestral to other Indigenous groups (K3, K4 and possibly indirectly K6), with considerable early divergence (drift = 36 on both edges).
