The proteome of Middle Pleistocene Xujiayao and common Denisovan morphology

Abstract

The taxonomy and phylogeny of late Middle Pleistocene hominins in East Asia remain highly debated1. Xujiayao, a key representative assemblage with many fossils and a clear stratigraphy dating to around 199–138 thousand years ago, has been extensively studied, but its evolutionary position remains uncertain. Here, to clarify this, we analysed Xujiayao material through both palaeoproteomic analysis and morphological comparisons with other East Asian late Middle Pleistocene archaic Homo. Proteomic analysis of two specimens identified 18 endogenous proteins, and the Denisova-specific COL1A2-996 R>K mutation strongly supported their affiliation with the Denisovan lineage. Extended analysis identifies a set of shared morphological traits between Denisovan fossils (Xujiayao and Harbin) and other East Asian late Middle Pleistocene archaic Homo (such as Jinniushan, Dali and Hualongdong), indicating that they all belong to the Denisovan lineage. This analysis provides a comprehensive view of Denisovan features, showing both traits reminiscent of Homo erectus (such as a thick cranial vault) and those characteristic of modern humans (for example, a strongly arched temporal squama). They also share features with late Neanderthals, such as the structure of the temporal labyrinth and the presence of a suprainiac fossa. Notably, Denisovans are distinctive, with a low cranial profile with near-parallel lateral walls, a massive supraorbital torus, a flat zygomaxillary region and weak prognathism. Denisovans from the Xujiayao and other East Asian sites are morphologically distinctive, with a low cranial profile with near-parallel lateral walls, a massive supraorbital torus, a flat zygomaxillary region and weak prognathism.