Concerns about ancient DNA sequences reported from a Late Pleistocene individual from Southeast Asia

Abstract

In a 2022 Current Biology paper, Zhang et al.1 reported DNA sequences from an approximately 14-thousand-year-old female skeleton from Red Deer Cave referred to as ‘Mengzi Ren’ (MZR). MZR’s data are the first DNA sequences reported from pre-Holocene Southeast Asia, revealing genetic affinities dissimilar to all previously published ancient DNA data. Here, we show extremely high error rates, an abnormal error distribution and evidence of contamination by modern human sequences in the published DNA sequences of MZR. Even ignoring these issues, we fail to replicate key population genetic findings of Zhang et al.1, namely that Native Americans are equally related to MZR and ancient Northeast Asians. These results raise concerns regarding the paper’s conclusions about population history, such as the claim that there was “an express northward expansion of AMHs starting in southern East Asia through the coastal line of China … eventually crossing the Bering Strait and reaching the Americas,” and also about the general usability of the published sequences.