Is the Caucasoid Race closer related to Negroid race or to the Mongoloid race?

[Sandis]

Nice work Komintasavalta! I see consistency between your results and what Supercomputer posted from formal stats.
It is just another proof that scaled coordinates are basically consistent with formal stats.
One minor thing though. In your clustering Southeast Asians are clustered together with East Asians.
I wonder what Southeast Asian and Northeast Asian are in Cavali-Sforza study.
For example Han Chinese. Are they Northeast Asian or Southeast Asian?

Cavalli-Sforza separated Northern Chinese and Southern Chinese. N. Chinese was included in the East Asia cluster and S. Chinese in the Southeast Asia cluster.
You can read it here:

https://books.google.lv/books?id=Frw...page&q&f=false

Pages 229-233: Genetics of East and Central Asia
Pages 234-236: Genetics of Southeast Asia

From his works:





Northern Chinese are in this tree, clustered together with Japanese:

[Zanzibar]

They're percentages calculated by adding together the columns East_Eurasian, Southeast_Asian, and Ancient_North_Eurasian, except the column for ANE was divided by 4.

Actually there's only one Nenets individual on that list, who got around the same percentage of Mongoloid as the single Ket individual, so maybe it's not representative.



Yeah, Karitiana, Surui, and Mixe all got 66% Mongoloid on my list.

It would be great if we also have Kazakh, Kyrgyz, Altaian individuals in the spreadsheet so it can be determined how much Mongoloid they really are.

I believe that in a Global East Eurasia-West Eurasia-Africa PCA, Native Americans would plot close to the Kyrgyz and Altaian as they have similar amounts of Mongoloid and Caucasoid ancestry. For example this PCA seems to does a good job where Amerindians would plot among Old World Populations: Clovis, Pima are the Natives here. As you can see, they cluster somewhere between Kyrgyz and Altaians in the PCA.



And also this PCA: Totonacs are an Amerindian ethnic group from Southern Mexico. The PCA comes from this DNA study. The Bolivians according to this paper has some European admixture while the Totonacs are 100%/close to 100% Amerindian. CHB/JPT are Han Chinese from Beijing, Japanese from Tokyo while CEU are Americans of European descent from Utah and YRI are Yorubas from West Africa. https://www.researchgate.net/publica..._the_New_World

Look at how far the Bolivians and Totonacs plot far away from the Chinese and Japanese samples towards the Whites of Utah. It is showing their ANE ancestry affect on them compared to 100% East Eurasians like Chinese and Japanese.



Also one more: This PCA from the Malaspinas DNA paper on Botocudo genomes: https://www.sciencedirect.com/scienc...60982214012743. Here it shows Amerindians plotting close to South-Central Asians from Kyrgyzstan and Nepal due to similar amounts of East and West Eurasian ancestry:

[Komintasavalta]

I divided G25 modern averages in clusters:

curl -Ls 'drive.google.com/uc?export=download&id=1wZr-UOve0KUKo_Qbgeo27m-CQncZWb8y'>modernave
R -e 't=read.csv("modernave",header=T,row.names=1,check.names=F);k<-cutree(hclust(dist(t)),k=16);write.table(k,"clusters",sep=" ",quote=F,col.names=F)'

Then I did a PCA of the clusters for Europeans, Central Asians, North Asians, East Asians, Southeast Asians, and Americans:



In my graph, the percentage shown next to PC1 is bigger than the percentage shown next to PC2 because there's so many European and East/Southeast Asian populations in the plot. The percentage becomes smaller if I include less European populations. One horizontal square still represents the same distance as one vertical square.

Nganasans look like they're on a cline that goes from Southeast Asians to Americans. The Uralic cline from Saami to Nganasans is closer to Americans than the Turkic cline from Tatars to Yakuts. Maybe it's because of higher ANE ancestry in Uralics.

However in G25, Surui are about as far from Nganasan as from Han or Mari:

Distance to: Surui
.019 Karitiana
.089 Mayan
.386 Eskimo
.401 Greenlander_East
.441 Greenlander_West
.451 Chukchi
.473 Tlingit
.543 Shor
.559 Selkup
.559 Kazakh
.562 Ket
.562 Khanty
.563 Buryat
.564 Nivkh
.565 Nenets
.566 Todzin
.568 Mansi
.601 Han_Shandong
.604 Onge
.606 Nganassan
.616 Saami
.616 Mari

[reboun]

It depends on individual.

[Zanzibar]

I divided G25 modern averages in clusters:

curl -Ls 'drive.google.com/uc?export=download&id=1wZr-UOve0KUKo_Qbgeo27m-CQncZWb8y'>modernave
R -e 't=read.csv("modernave",header=T,row.names=1,check.names=F);k<-cutree(hclust(dist(t)),k=16);write.table(k,"clusters",sep=" ",quote=F,col.names=F)'

Then I did a PCA of the clusters for Europeans, Central Asians, North Asians, East Asians, Southeast Asians, and Americans:



In my graph, the percentage shown next to PC1 is bigger than the percentage shown next to PC2 because there's so many European and East/Southeast Asian populations in the plot. The percentage becomes smaller if I include less European populations. One horizontal square still represents the same distance as one vertical square.

Nganasans look like they're on a cline that goes from Southeast Asians to Americans. The Uralic cline from Saami to Nganasans is closer to Americans than the Turkic cline from Tatars to Yakuts. Maybe it's because of higher ANE ancestry in Uralics.

However in G25, Surui are about as far from Nganasan as from Han or Mari:

Distance to: Surui
.019 Karitiana
.089 Mayan
.386 Eskimo
.401 Greenlander_East
.441 Greenlander_West
.451 Chukchi
.473 Tlingit
.543 Shor
.559 Selkup
.559 Kazakh
.562 Ket
.562 Khanty
.563 Buryat
.564 Nivkh
.565 Nenets
.566 Todzin
.568 Mansi
.601 Han_Shandong
.604 Onge
.606 Nganassan
.616 Saami
.616 Mari

Interesting I would expected Native Americans to plot more closely with the Altaians, Khakass, Kyrgyz in that PCA due to their similar amounts of East and West Eurasian ancestries but it seems like there are probably genetic drifts and other factors that very likely cause Natives to plot really faraway from others.

Keep in mind though that American Indians are very genetically drifted so that's why the distance to other pops is very massive. If we can remove the genetic drift, maybe the distance will be much less. Probably the same case as Australoids like Papuans/Melanesians and Abos who are genetically very isolated from almost other groups as well and thus make them genetically very distant from everyone.

[michal3141]

Very strange.
Europeans in a cluster with MENAs and Iranians but Sardinians and Lapps are outside of this cluster by a big margin?
I might be slightly closer to Iranians than Sardinians but not by a huge margin.
But Southern and Western Europeans are definitely closer to Sardinians than Iranians.

[Komintasavalta]

Very strange.
Europeans in a cluster with MENAs and Iranians but Sardinians and Lapps are outside of this cluster by a big margin?
I might be slightly closer to Iranians than Sardinians but not by a huge margin.
But Southern and Western Europeans are definitely closer to Sardinians than Iranians.

Yeah, I tried choosing different ethnic groups in place of Poles here to represent Europeans, but they always clustered with Sardinians. I tried the clustering methods "ward.D2", "complete", and "single".

curl -Ls 'drive.google.com/uc?export=download&id=1wZr-UOve0KUKo_Qbgeo27m-CQncZWb8y'>modernave
awk -F, 'NR==FNR{a[$0];next}$1 in a' <(printf %s\\n Saami Iranian_Fars Syrian Sardinian Moroccan Polish) modernave>/tmp/a
R -e 'install.packages("ape",repos="https://cloud.r-project.org")'
R -e 'library("ape");png("/tmp/a.png",w=300,h=300);t=read.csv("/tmp/a",header=F,row.names=1,check.names=F);plot(as.phylo(hclust(dist(t),method="ward.D2")),cex=1.3,font=1,underscore=T);dev.off()'

[Komintasavalta]

Interesting I would expected Native Americans to plot more closely with the Altaians, Khakass, Kyrgyz in that PCA due to their similar amounts of East and West Eurasian ancestries but it seems like there are probably genetic drifts and other factors that very likely cause Natives to plot really faraway from others.

Keep in mind though that American Indians are very genetically drifted so that's why the distance to other pops is very massive. If we can remove the genetic drift, maybe the distance will be much less. Probably the same case as Australoids like Papuans/Melanesians and Abos who are genetically very isolated from almost other groups as well and thus make them genetically very distant from everyone.

Yeah, the distance between Australian and Han_Shanghai is .58 on G25, and the distance between Surui and Han_Shanghai is .61, even though Surui are the Americans who are the furthest from Mbuti.

Koinanbe (1.10) and Papuan (1.10) are even further from Mbuti than Australian (.99).



Here's a PCA of the populations closest to Koinanbe and the populations closest to Surui. Papuans (Koinanbe, Kosipe, Papuan) might be at the end of the Australo-Melanesian cline because they're more drifted than Australians.

[Sandis]

I generated a PCA using Eurogenes K15 components.
As expected, modern European populations are not far from each other except some (Saami, Chuvash, Mari).
It's strange that Amerindians and Oceanians are so close here, but there were only 2 population samples of the Oceania. It's right that Oceanians are close to Southeast Asians.
There are too little variation between Sub-Saharan African populations (San, Pygmy, Bantu). I think that's because there were too less components for them.

[Sandis]

2D PCA model for 244 populations needs higher resolution.
I later found that someone made 3D PCA from this data:



I added component labels approximately in my 2D model for better understanding: