Asymmetric Y-chromosomal and mitochondrial haplogroup structure in two pastoralist Tibetan communities of the Sanjiangyuan region

Abstract

Uniparental diversity in the Sanjiangyuan region, the pastoralist interior of the Qinghai–Tibet Plateau, is uncharacterised. We analysed Y-chromosomal haplogroups in 547 males and mitochondrial haplogroups in 623 samples from a cohort of 1 226 Tibetans in Qumalai and Tanggula, with household pedigrees for 470 Tanggula participants. Both fall within Tibetan variation yet are separable on both marker systems. Qumalai carries haplogroup D at 74.3% (effective haplogroup number 1.74), matched among the Tibetan reference samples only by Nagqu; Tanggula lies within the published range at 2.48. Two features mark the Tanggula maternal pool. The West Eurasian lineage U7, on 26 carriers, stands at 5.6% of assigned samples (26/467; 95% CI 3.5–7.7%), 10.3% of the quality-filtered set (26/252), at or above the highest value recorded on the plateau (5.3%) under every treatment, although the most conservative interval includes it; the carriers fall in 12 matrilines occupying half the households expected by chance (P < 0.0001). Haplogroup Z, present in Qumalai in every Tibetan reference sample, was not observed in Tanggula (P = 7 × 10?4 among informative assignments). Paternal haplogroup diversity differs significantly between the communities, while maternal diversity does not, at both levels and on an unbounded scale. Raw FST is not comparable across these marker systems: its attainable maximum ranges from 0.343 to 0.024 across four levels; standardised measures reverse the ordering. Sanjiangyuan Tibetans are not a genetically homogeneous unit; the large valley Amdo samples on which the published picture chiefly rests do not span plateau paternal diversity.