Response to Tabin et al-Concerns about ancient DNA sequences reported from a Late Pleistocene individual from Southeast Asia

Tabin et al suspect a high error rate and abnormal error content in the MZR genome data from our published study, from which they raised concerns about the reliability and useability of our published sequences. Given the poor environmental conditions (such as warm climate and acidic soil in the low latitude area of Southwest China), as well as the non-ideal fossil material (cranium) for DNA extraction, we argue that a relatively high level of aDNA damage, as well as possible artefacts from extraction, library construction and sequencing better explain the observed pattern by Tabin et al in MZR rather than modern DNA contamination. Particularly, we think the mutation motif of the MZR mtDNA, derived from our careful manual check, should be reliable. In addition, we provide additional analyses showing how we minimize the effect of aDNA damage in population analyses.