In layman language, a PCA shows how genetically related human populations (or individuals) are to one another. They are usually displayed in two dimensions and look like this:
However, by using some software online, you can view PCAs in three dimensions, which provides a much clearer image of human genetic diversity, unveiling many secrets that are hidden on 2D PCAs — like this:
It’s infinitely easier to identify the various human genetic clusters and clines on a 3D PCA. It’s also easier to see how human populations are a mix between five basal races: Sub-Saharan Africans, West Eurasians (‘Caucasoids’), East Eurasians (‘Mongoloids’), South Eurasians (‘Australoids’), and Amerindians.
How to view this 3D PCA
Open this online software:
https://web.archive.org/web/20201113044821/https://vahaduo.github.io/custompca/
- Copy coordinates listed below and paste into the “SOURCE” tab
- Open the “PCA PLOT” tab
- Hit “RUN PCA” followed by “PLOT PCA”
- For a better orientation, hit “FLIP” next to “X: PC1” and then “PLOT PCA” again.
- Hit “3D” and “2D” to switch between 3D and 2D views.
- If you make a mistake, simply refresh the page and start again.
Coordinates (Updated 04/22/2023):
COPY FROM HERE: pastebin.com/iVJQ7jLD (archive)
Each dot on this PCA represents the average population of a certain ethnic group. These groups have been carefully selected to fairly represent the range of variation from each major population cluster/cline.
Population clusters/clines are labeled in a way that I thought logical/useful. However, the clines could easily be subdivided. For example, South Indians (who mostly descend from Negrito-related hunter-gatherers that originally populated South and South East Asia) could be separated from North Indians and Pakistanis.
To see genetic variation in Africa (which is not visible on the default X, Y, Z axis settings) change the Y axis to “PCA5” and hit “plot PCA” again. This smushes all of the Eurasians together but shows that South African KhoiSan are a genetically distinct cluster.
Thuletide 
Regarding “the human race” wording.
Correct terminology would be the human species.
The “human race” are often used by people trying to trivialize race. For example “We are all the same” bullshit.
Example https://files.catbox.moe/jw3xyn.jpg
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“race” just means “biological group”
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Hey how it is if you would be make a blog/republication of this fact here
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Love me PCAs, not autistic just like ’em. Simple as.
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I’m going to have to try again with another browser, can’t get it to work on Firefox just now. I might have too many addon ‘blockers’ going on though.
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It’s interesting to me how close Russians are to Western Europeans despite the great geographical distance between them. They’re really quite close to even English/German/French.
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Caucasus is very close to Europe here.
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because caucasians are very close to europeans
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Cool stuff, thanks!
Btw, some Southern Euros seem to be closer to ME than to Northern Euros. The whole SE cluster looks like smth intermediate between NE and ME. Or maybe it just depends on how you look at it.
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It depends on how you look at it. Here is the best PCA of West Eurasians, you can see each population very clearly here: https://i.imgur.com/dF7d3Ix.png
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Yeah, this one is better – SE and NE cluster together and are almost equally distant from ME.
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Where are the Hungarians?:(
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They should be Central Europeans, between Southern Germans and West Slaves like Slovaks and Czechs.
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I wouldn’t say that humans are a mix between “five basal races”
PCA gets affected a lot by drift in this case, East Asians having enough drift that it pulls them further apart than South Eurasians from West Eurasians/Caucasoids, that does not really mean that Caucasoids are closer to South Eurasians, they are not, while Caucasoids for example are closer to Amerindians than East Asians.
Meaning, it is lack of drift/derived alleles with other pops that plot South Eurasians that way (in fact towards Africa a bit-I suspect an artifact of their archaic admix) rather than them forming their own race, although they did split quite early from Mongoloids.
Similar issues affect the placement of Amerindians, although they are a mix of East and West Eurasian as you know, mostly East ofc.
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none of that explains why you wouldnt divide humanity into five main races
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I said this in discord but I will also say it here
Just think about the differences between italians, ashkenazi jews and Iranians
They are already very different, but as you can see they are still close to each other in genetic deviation
Then look at black people vs white people vs asian people
Holy fricking crapsicles
Black people may as well have 4 eyes and tentacles for arms with how much genetic difference there is
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Interesting. Looks almost as if all the races descend from the big European-Middle Eastern cluster. Wonder how much it would change with more samples, if there’d be a full “chain” between all of them or would the clusters just become more well defined.
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What about aborignals? If they were plotted on here I reckon they would form a sixth ‘basal race’ branching out from south eurasians.
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South Eurasians / Oceanians are basically the same people, with Australians being very diverged and genetically distinct South Eurasians. It’s just a politically correct term for this: https://en.wikipedia.org/wiki/Australo-Melanesian
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Could you provide a source for your data?
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vahaduo.github.io/
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Wow, this is a fantastic resource. Thanks!
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It’s pretty useful for amateurs and the guy who made it is a talented geneticist but it shouldn’t be relied upon entirely. Also be careful when creating models. You can easily create “successful” models that are chronologically impossible if you use the wrong samples or don’t include the right samples.
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