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

[alchemist223]

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

In a 2022 Current Biology paper, Zhang et al. 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., 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.

https://www.cell.com/current-biology/abs...all%3Dtrue

[miquirumba]

I think that more papers, with a critical character like this, should be published, questioning the theses of authors based on fraudulent data or samples with low coverage. There are hundreds of H and H2 samples of maternal haplogroups in the AADR that failed sequencing or contamination errors return the reference rCRS sequence or a close prediction. Reference genomes for ancient samples should be as distant as possible from the populations of the sequenced samples to avoid bias and errors caused by transforming no calls into reference bases

[TanTin]

There are not much details in the publication, however in the Supplemental Information there is a PDF file:
Document S1. Experimental Procedures and two tables

Conclusions
Our analyses show that, contrary to claims by Zhang et al, at least some of the East Asian
ancestry in Native Americans likely split off from Northeast Asians after the split with the
ancestors of Southeast Asians including MZR. While it remains possible that Native Americans
harbor some Southeast Asian ancestry, analyses of MZR data provide no evidence for this.

In general the coverage of this sample MZR is low
SNPs hit on autosomal targets (Computed using easystats on 1240k snpset) = 50259
SNPs hit on autosomal targets (Computed using easystats on HO snpset)  = 25228

50 k is only 5% coverage , less than 5%
With such low coverage it is useless to talk about D statistics and other calculations.  More the missingness of the data - more error and discrepancy.

I guess  Zhang et al  did their best to provide some results for such low coverage data.  All other claims are useless, because low coverage data is not reliable for anything.

[TanTin]

The MZR  sample is not problematic at all.  There are hundreds low coverage like this in the dataset.
However the main issue with this sample is it contradict the other study results:

Neanderthal ancestry through time: Insights from genomes of ancient and present-day humans
https://www.science.org/doi/10.1126/science.adq3010

According to Lasi et all,

The EarlyOoA cluster has large amounts of unique Neandertal ancestry, a significantly different matching profile to the sequenced Neandertals, and the weakest correlation in the locations of introgressed segments with other population clusters. These observations are consistent with the insight that some Neandertal ancestry in these older individuals is not shared with modern humans after 40,000 years (7–9).

The expectations for MZR are to have higher levels of  Neandertal ancestry compareble with other ancestral .