Ancient Genomics Reveals Four Prehistoric Migration Waves into SEA and Vietnam

Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia.
(no supplement)
https://www.biorxiv.org/content/bior...78374.full.pdf
(with supplement)
https://www.biorxiv.org/content/bior...1/278374-1.pdf








Using PCA (principal component analysis) we can reduce the dimension of a data.
Normally, when we see at a graph present genetic distance we only see 2D. Howver, it actually more than only 2 features to present genetic of language family. Therefore, when using only 2 dimension, there are lots of information could be lost.

In this paper, authors use wide range of dimension from K = 2 to K = 13 to to better represent data. Let's look closer.

From paper:
"At K=6, a dark green East Asian component is maximised in the Ryukyuan and Japanese, while a pink East Asian component is now maximised in the Ami. While the dark green component is present in almost all EA, SEA and some SA populations, it is absent in the Mlabri, the Jehai, and most ISEA individuals. When looking at the ancient samples, we also observe that it is absent in In662 (Group 5) and all Group 2 samples.

At K=7, the light green component is maximised in the Mlabri, followed by other Austroasiatic SEA populations and Group 2. This component is present in all SEA populations, and is at highest frequency in the populations lacking the dark green component at K=6.

At K=13, the dark pink component is maximized in the Hmong, and allows SEA populations to be separated into two groups, represented in the ancient samples by Groups 3 and 4. This component is restricted to Tai-Kadai-speaking SEA populations, whereas the Austroasiatic populations are primarily composed of light and dark green components. However, among the SGDP populations, we can also see Austro-Asiatic speaking Kinh and Cambodian populations that also have this dark pink component."

Look at those 13 components is more better than look at only 2 components.

At page 629, we can see that:
For dark green (Japanese), Kinh > Daic > Khmer.
For dark pink (Hmong-Mien) Daic > Kinh > Khmer.
For green (Austroasiatic) Khmer > Daic approximate Kinh.
For pink (apper in all Asia) Kinh close to Daic > Khmer.
For blue (maybe Negroid) Khmer > Kinh, no apper in Daic.
For light dark green (don't know) Khmer = Kinh = Daic.
For purple (Negroid) Khmer > Kinh = Daic.

So, Kinh close to Daic can be explain that Kinh and Daic share much alleles but not that Kinh is Daic origin because, Kinh has more Japanese than Daic but smaller Hmong-Mien. Kinh has Negroid component (blue component) which is not appear in Daic, but appear in other Austroasiatic groups.

Now, look at all Vietnamese ancient group. 
Vt833(Thanh Hoá), Vt880 (Hạ Long) 2000 BC, they are close to all other Austroasiatic but has more dark pink (Hmong-Mien) than Austroasiatic in 6000 BC (La368).

Vt778, the Austroasiatic live in Nậm Tun (north VN) at 200 BC. He has dark green (Japanese) component higher than all today-Austroasiatic and today-Daic but close to today-Kinh.
He has smaller dark pink (Hmong-Mien) component than Kinh and Daic but equal to Khmer. The green and purple component of him is equal to Khmer. The most interesting thing is he has more dark green (Japanese) component than all other Austroasiatic and Daic.

For Vt777 (2200 YBP - Mái Đá Điều, Thanh Hóa) and Vt779, Vt781, Vt796, vt808 (2200 YBP - Núi Nấp, Thanh Hóa), they genetically close to Tai but they still have blue and purple component (appear in all Austroasiatic group but not apper in Daic). 

An the second interesting here, if you look at the component apper in proto-Austroasiatic (La368, Ma911), this still appear in all ancient sample at 200 BC with high ratio (around 40%). It can be the answer for this question why Kinh is close to Daic but speak an Austroasiatic language. The process of forming Kinh is long and even after the appear of first kingdom (600BC in writing history and at least 200 BC according to archeology (Cổ Loa citadel), the ratio of Austroasiatic component is still high.

So, the process of forming Kinh is first Melenasian-Papuan related group. 
Afterward, from at least 2000 BC in VN and 6000 BC in Lao, people became proto-Austroasiatic, 600 BC, they were still proto-Austroasiatic but has Hmong-Mien and Japanese/Han component. 
From 200 BC, they were genetically close to Daic but actually has more Austroasiatic than Daic (and some component has high ratio but never appear in Daic).
Finally, now, Kinh has more Hmong-Mien and less Austroasiatic.

The second image show us the genetic shift of people live in northern VN.

From 2000 BC, people in VN was Austroasiatic, close to Htin. 

Then 600 BC, the genetic shift happened and although they are still Austroasiatic but somehow in between Htin and Hmong-Mien, Japonic. It exactly what we can see in figure 1.
It means there is a process of Hmong-Mien and Japonic admixture.

From 200 BC, the genetic was shift into center of a triangle made from Austronesian, Daic, Austroasiatic.
So there was a process of Austronesian and possible Daic admixture.

Last, today Kinh close to Daic but still has differences.

So, I think the picture is more clear, proto-Austroasitic, then became more Japanese/Han and Hmong-Mien, then more Hmong-Mien (may be Taicization or Hmong-Mien admixture but second theory is unlikely) then Sinocization again.

This explain why the correlation of Kinh is significant smaller than all other Austroasiatic and Daic group. It also explain the correlation between Kinh and Khmer.