Large-scale mitogenome analysis reveals complex maternal genetic connections between Sino-Tibetan- and Altaic-speaking populations

The Sino-Tibetan and Altaic groups have played central roles in shaping the human demographic history of populations at the crossroads of East Asia and Siberia. However, their matrilineal relationships and links to complex cultural interactions remain poorly resolved. Here, we reported 344 newly sequenced complete mitogenomes from representative populations and integrated them with a curated dataset of more than 53,000 reference sequences. We uncovered a highly structured maternal genetic landscape, in which Sino-Tibetan and Altaic groups shared some maternal lineages despite distinct demographic trajectories, including East Asian haplogroups D4 and A. Sino-Tibetan-speaking populations showed elevated frequencies of B4, F1, and M7, whereas Altaic-speaking populations were enriched for C, H, and U. These observed genomic diversity patterns were jointly shaped by linguistic affiliation and geography. High-resolution phylogeographic analyses further showed that Tibeto-Burman groups from the Qinghai-Tibetan Plateau (QTP) carried distinctive maternal components, including region-specific sub-lineages within A, M9, and R32. Phylogenetic reconstructions dated the maternal lineages shared by Sino-Tibetan- and Altaic-speaking populations to 56.87–10.86 thousand years ago (kya), indicating that these early divergences formed the primary genetic foundation of both groups, whereas later Neolithic expansions contributed only modestly. Mongolic groups from the Inner Mongolian Plateau shared some maternal lineages with QTP populations, largely dating to 26.83–12.72 kya, indicating deep maternal connections despite substantial geographic separation.