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bioRxiv · 10.64898/2026.09.18.752559

Adaptive introgression in Tibetans spans focal and distributed architectures

Liang, S.-A.·Zhu, Q.·Gao, X.·Xiao, Y.·Liu, K.·Xie, Z.·Deng, L.·Ge, X.·Su, B.·Fu, Q.·Zheng, Y.·He, Y.·Xu, S.·Chen, L.
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Abstract

The Denisovan-derived EPAS1 haplotype is a paradigmatic example of adaptive introgression, but whether archaic ancestry contributed beyond such large-effect loci remains unclear. We analyzed genomes from 1,039 Tibetans, Han Chinese, archaic hominins and ancient Tibetan Plateau individuals. Denisovan-derived adaptive variation was highly localized around EPAS1, whereas Neanderthal-derived variation was distributed across the genome; temporal and elevational patterns reinforced this contrast. Despite individual-level heterogeneity, Neanderthal-introgressed gene repertoires repeatedly converged on immune, metabolic and signal-transduction pathways. A Tibetan-enriched Neanderthal PPARGC1A haplotype was associated with lower fasting glucose and showed concordant support from an independent East Asian type 2 diabetes GWAS. These findings reveal that adaptive introgression can contribute to complex human adaptation through functionally convergent combinations of archaic variants, rather than only through shared large-effect haplotypes.

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Liang, S.-A., Zhu, Q., Gao, X., Xiao, Y., Liu, K., Xie, Z., Deng, L., Ge, X., Su, B., Fu, Q., Zheng, Y., He, Y., Xu, S., Chen, L.. 2026-09-21. Adaptive introgression in Tibetans spans focal and distributed architectures. https://doi.org/10.64898/2026.09.18.752559

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