Human genetic variation: The first 50 dimensions

Dienekes' Anthropology Blog ^ | 01 Dec 2010 | Dienekes Pontikos

[Palter]

Here is a huge data dump for anyone interested in human variation. Part of the reason I started the Dodecad Project was to be able to analyze data on my own, rather than having to squint to make sense of a plot, to speculate about what might show up at higher dimensions, or with more clusters, to wonder how the inclusion of additional populations would affect the results, and so on.

The following dataset represents the culmination (so far), of my efforts.

Number of SNP markers: ~177,000 as in here

Populations: 139

Individuals: 2,230

In the RAR file (~11MB) you will find 49 scatterplots (5000x5000 pixels each) representing the first 50 dimensions of a multi-dimensional scaling analysis of this dataset, together with information about the samples and their sources. There is a plot of the 1st and 2nd dimensions, 2nd and 3rd, 3rd and 4th, and so on, until the 49th and 50th.

I don't believe Picasa allows such huge pics, so I've made a few smaller (still 1600x1600 pixels each) ones to give you an idea of what to expect. Note that the legend in these small ones is partly visible.

In all plots, population labels have been placed on the population averages; this usually correspond to blobs of datapoints belonging to that population, but occasionally they are shifted due to the presence of outliers.

Before I proceed, it might be worth to give a visual representation of the three poles of human variation in its broadest context; these are Basques/Sardinians, Mbuti/Biaka Pygmies, and She. Well, these are marginally more toward the three poles than many others, but they will do:

Mbuti image by Mikael Strandberg; She image from Portraits of Chinese ethnic groups and links therein.

1 vs 2

3 vs 4

5 vs 6

7 vs 8

Inspection of these plots gives you an idea of why Clusters Galore works so well. It can detect "clusteredness" of individuals along multiple dimensions. It does not look at a series of 2D plots, but it considers proximity of individuals to each other along multiple dimensions, and adapts to the shape, size, and orientation of the clusters.

[Palter]

WikiGene.

[wendy1946]

There is said to be less variation in the entire human race than in a typical group of 50 African monkeys of the same species, indicating a very recent bottleneck of some sort for the human race. Of such variation as there is, the major divide is East/West and not North/South, i.e. the black and white races are genetically closer to each other than either is to the yellow. That’s probably because Semitic, Hamitic, and Japhetic (IE) peoples are actually descended from Noah and his sons while East Asians survived the flood on mountain tops and anything which could float for a year or so, as per their own literature.

[muawiyah]

The other theory is that the African people who became ancestral to both the Chinese and the Europeans didn't arrive in Europe until about 35,000 years ago (or maybe even more recently).

That makes East Asians and Europeans equally descended from one group of Africans.

That group itself is somewhat removed from the other African groups.

The solution to the Amer-Indian conundrum is simply that North American Indians have a degree of European ancestry from a single group dating back about 14,000 years. Try:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1199377/

I didn't find any mention of the Sa'ami in this study ~ that's a shame since they appear to have been the first inhabitants of Scandinavia.

[STD]

The other theory is that the African people who became ancestral to both the Chinese and the Europeans didn't arrive in Europe until about 35,000 years ago (or maybe even more recently).

Nope an earlier post has them sneaking into Greece.

[muawiyah]

Yes, they slipped over Greece and were eaten on their way out to Turkey!

That's not a theory ~ that's a recipe!

[STD]

Those heathens will eat anything

[SunkenCiv]

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[martin_fierro]

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[gleeaikin]

I looked up She, and found them in China speaking a Hmong-mien language. Are these the same Hmong who helped our special troops in the mountains of Vietnam?

In any consideration of the splite in human subgroups, one must think about the possible impact of the great Toba megavolcano 74,000 years ago. Which way did the major ash fall go, what areas of the world suffered the most from several years of “nuclear winter”? These and related factors must have had a big impact if the human population was reduced to no more than 5 or 10,000 people as some scientists propose to explain the lack of genetic variability.

[668 - Neighbor of the Beast]

Self-ping for genetics, clusters.
Thanks for posting this!

[Publius6961]

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[FastCoyote]

This stuff is too cool.