The first maternal genetic study of hunter-gatherers from Vietnam

[crashdoc]

Abstract
The current limitation of ancient DNA data from Vietnam led to the controversy surrounding the prehistory of people in this region. The combination of high heat and humidity damaged ancient bones that challenged the study of human evolution, especially when using DNA as study materials. So far, only 4 k years of history have been recorded despite the 65 k years of history of anatomically modern human occupations in Vietnam. Here we report, to our knowledge, the oldest mitogenomes of two hunter-gatherers from Vietnam. We extracted DNA from the femurs of two individuals aged 6.2 k cal BP from the Con Co Ngua (CCN) site in Thanh Hoa, Vietnam. This archeological site is the largest cemetery of the hunter-gatherer population in Southeast Asia (SEA) that was discovered, but their genetics have not been explored until the present. We indicated that the CCN haplotype belongs to a rare haplogroup that was not detected in any present-day Vietnamese individuals. Further matrilineal analysis on CCN mitogenomes showed a close relationship with ancient farmers and present-day populations in SEA. The mitogenomes of hunter-gatherers from Vietnam debate the “two layers” model of peopling history in SEA and provide an alternative solution for studying challenging ancient human samples from Vietnam.

Published: 12 July 2023

https://link.springer.com/article/10.100...23-02050-0

In the article they make much of the R0 haplogroup of the two hunter gatherers (CCN24 & CCN55) and they also place them in a mtdna tree that they generated.

I have created this thread as a warning for those who would blinding take what they say for cash.

First, their mtdna tree is garbage, not properly rooted and as a results, recurrent snps make a mess of it.

Second, as you can see in the supplementaries https://static-content.springer.com/esm/...3_ESM.xlsx , both individuals are contaminated.

We can also see the details of their haplogrep that gave an R0 result.

Haplogrep works by finding the best matching line away from rCRS (H2a2a1), see for instance: https://haplogrep.i-med.ac.at/phylogenie...ogroups/R9

As a result of contamination from an M8 (probably C) line the real R9 result gets lost because both lines fight away from each other starting from R towards M8 (maybe C) and the other branch towards R9 (maybe R9c1b1).

The first thing that catches the eye is that they both have 73G, so they definitely can't be R0.

Then among the others snps, we can discern 2 lines, one from the actual hunter gatherers and the other presumably from the modern individual dna from whom the samples are contaminated:

73G -> out of R0 (both have it)

14783C -> M (both have it)
4715G -> M8 (CCN24 so both have 1 M8 defining snp)
7196A -> M8 (CCN55 so both have 1 M8 defining snp)
14318C -> C (which is below M8, CCN55)
16209C -> C1d2a (CCN55) was there a Columbian man on the extraction team? Or maybe coincidence as with other recurrent snps that I have not shown.

13928C -> R9 (both have it)
7684C -> R9c1b1 (CCN55)

On yfull mtree R9c1b1 has a TMRCA of 8900ya and is present in Vietnam & Thailand.

[miquirumba]

have you fasta files or raw data?
it's easy running MUSCLE into MEGA to force an haplogroup alignment and detect quickly false or contaminated reads

[crashdoc]

have you fasta files or raw data?
it's easy running MUSCLE into MEGA to force an haplogroup alignment and detect quickly false or contaminated reads

No they have not made the files available as far as I know.  I am only using their results in the supp file.

[Psynome]

Low quality paper, unfortunately. The two layer hypothesis has essentially been confirmed...in fact modern mainland SEA populations are more like a 3+ major layer mix. In chronological order: Hoabinhian forager, then Proto-Austroasiatic farmer, then Tai and Austronesian farmer related.

Then add smaller amounts of Chinese, Indian etc depending on the region. In Vietnam Chinese is more relevant.

[alchemist223]

Honestly thought that maternal haplogroup assignment was suspect.

[okarinaofsteiner]

Low quality paper, unfortunately. The two layer hypothesis has essentially been confirmed...in fact modern mainland SEA populations are more like a 3+ major layer mix. In chronological order: Hoabinhian forager, then Proto-Austroasiatic farmer, then Tai and Austronesian farmer related.

Then add smaller amounts of Chinese, Indian etc depending on the region. In Vietnam Chinese is more relevant.

Within the framework of the two-layer hypothesis, this is basically a founding layer of "Ancient Southern East Eurasians" ("Para-Onge"/Hoabinhian-related forager), with several different waves of pre-Indianization "Ancient Northern East Eurasian" ancestry. Although you could treat the Proto-Austroasiatic "first farmer" population as being a roughly 2:1 mix of "Southern Northern East Eurasian" and "Para-Onge Hoabinhian-related".

From Razib Khan's substack- the "Papuan/Australian" and "Hoabinhian" split should probably be further up- either at the same level as the "Ancient SE Asian" and "Ancient NE Asian" split or slightly before it.