I wonder if the “stringy” look of the Kalash in this plot is actually an artifact of the normalization. Playing around with the decode me kinship map most populations appear “stringy” when I plot a high variation axis against a lower variation axis. I suspect that they normalize the low variation axis to the high variation axis with the result that the populations seemed stretched along the low variation axis.

When I plot pca2 vs pca3 the variation of the kalash population along pca2 looks much more compact.

In any case, when I look at pca1 vs pca2 the decodme plot looks pretty much like the one that you posted. pca1 vs pca3 has the Kalash cluster with the other pakistan groups in a continuum along pca3 from kalash to burusho. The Uygur and Hazara are outliers separated from the rest along pca1. They still overlay each other.

I think this confirms your guess in post 23, but I don’t have enough real experience to say more. You might be able to create a free account there and look at this. Alternatively, I can try to figure out how to take a screen shot.

By the way, do you know of a paper I can look at to see how these pca plots are defined? My background is in physics so I am comfortable with the idea of eigenvectors, but I have not quite been able to deduce how to build the vectors out of snp raw data.

Anyway, on the STRUCTURE-like analyses and PCA plots involving the Kalash I’ve seen so far, the Kalash don’t show up more heterogeneous than the other Central and South Asian populations, but the reverse may be true. So the above PCA plot seems somewhat anomalous, but I think it has other explanations.

compare structure vs. frappe. i believe structure is more distorted by linkage disequilibrium, so that may explain the difference.

interesting points.

1) from what i know the kalash leave, but no one joins them. they’ve been isolated since partisans of the religion of peace forcibly converted their cultural kin across the border in afghanistan circa 1900. but before 1900 there may have been more fluidity

2) it could be that there’s clan substructure in the kalash, that they started out more like their neighbors (i think this is true) and some inbred clans have shifted more than others from initial allele frequency

The best explanation that I have been able to come up with is that recent immigration into the Kalash that adds a more typical south asian component to their population and the Kalash now cover the continuum from unadmixted to highly admixed. If we fast forward 100 years and take a pca snapshot every ten years would we see the line of Kalash grow towards the rest of the south asian populations and then get absorbed into it? Or is my does my model miss something important?

I noticed the same problem with Orcadians in the 23andme northern european PCA plot. The Orcadians form a long thin line and the rest of the northern european population forms a somewhat thicker line perpindicular to the Orcadians.

*looks at map*

Well, duh!

More seriously, it’s not quite as obvious as it seems – apparently Kashmiri Pandits don’t seem to share much with their “yellow” neighbours.

A lot of modern identities are recently (19th to 20th centuries; for some Western countries, late 18th century) constructed (as a result of the “nationalism” disease and changing borders). The situation of the “Turkish” identity of modern Turks isn’t so different from the “Uzbek” identity of modern Uzbeks.

I am not a person receptive of “anomalies”, so my thoughts are similar to yours on this issue.

i don’t want to open up this can of worms in detail, because i weary of deleting/banning commenters with strong nationalistic inclinations. but a lot of the turkic national groups of the former soviet union and east turkestan of the 19th and 20th century are relatively recent constructions from what i have read. e.g., “uzbek” was a specific term for the ruling dynasty/caste, while the commoner turks were termed “sart.”

http://en.wikipedia.org/wiki/Sart

i can accept that the hazaras have many uyghur ancestors among their male line. though i think it is clear that their maternal lineage would be slightly different. additionally, the balance between “eastern” and “western” differs somewhat. i think they’re parent populations are genetically analogous to each other so it might not work, but finding PC3 and PC4 might resolve this.

They are so many (in fact, all STRUCTURE and similar analyses I have seen involving the two populations) that I cannot list them all. But the last one that you assessed on your blog is particularly a clear example:

http://download.cell.com/AJHG/mmcs/journals/0002-9297/PIIS0002929710003642.mmc1.pdf

also, do you know if the uyghurs carry the khan Y chromosomal lineage as the hazaras do?

Good question. Your thread about Chinggis Khan has a map showing the proportions of the star-cluster chromosomes that are thought to be related to the Chinggisid family in various Eurasian populations, and luckily, it includes both Hazaras and Uyghurs:

http://blogs.discovermagazine.com/gnxp/2010/08/1-in-200-men-direct-descendants-of-genghis-khan/

As you see, Hazaras have more of it than Uyghurs, but that may be related to genetic drifts due to Hazaras being probably a very small population for most of their history. Mongolians proper have almost the same proportion of the “Chinggisid” star-cluster chromosomes with Kazakistani Uyghurs and Chinese Kazaks, so genetic drift is probably the best explanation for its particular abundance in Hazaras. Strangely, on the same map Chinese Uyghurs show no “Chinggisid” star-cluster, while Kazakistani Uyghurs have it in abundance; that is probably an error as even some Han groups have some “Chinggisid” star-cluster.