Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation

Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation

Human genetic diversity is shaped by both demographic and biological factors and has fundamental implications for understanding the genetic basis of diseases. We studied 938 unrelated individuals from 51 populations of the Human Genome Diversity Panel at 650,000 common single-nucleotide polymorphism loci. Individual ancestry and population substructure were detectable with very high resolution. The relationship between haplotype heterozygosity and geography was consistent with the hypothesis of a serial founder effect with a single origin in sub-Saharan Africa. In addition, we observed a pattern of ancestral allele frequency distributions that reflects variation in population dynamics among geographic regions. This data set allows the most comprehensive characterization to date of human genetic variation.

Posted in plenty of other places, but I thought I’d get around to it.

snp2  snp

Most interesting observations from my POV are the European trace in the Uygur and in Mongolia- I would have expected central Asian purely from proximity. It also shows the Kalash are typically central Asians for alll the light hair and eyes you see in them. The Mozabite show as mainly near eastern, which is hardly surprsing as that’s where most of their maternal ancestry comes from. Transit across the Med seems to be about twice as much as much as the contributions from the African cluster. Not surprising to me is the trace middle Eastern ancestry in the Bantu samples, as I know mt DNA U is seen in them occassionally.

If you take a really close look at the American Maya samples you can see a slight trace of Oceanian blue. The European trace can be put down to recent mixture, but the Oceanian-I don’t think so. A trace remant of the older australoid population maybe.

8 responses to “Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation

  1. Most interesting observations from my POV are the European trace in the Uygur and in Mongolia- I would have expected central Asian purely from proximity.

    Uyghurs are known to be partly descendant of ancient Tocharians, who were probably the first settlers ever in such arid region, allowing them to leave a durable imprint. They have the highest R1b apportion out of West/North Europe.

    If you take a really close look at the American Maya samples you can see a slight trace of Oceanian blue. The European trace can be put down to recent mixture, but the Oceanian-I don’t think so. A trace remant of the older australoid population maybe.

    What about Filipino blood? The Philippines and Guam were virtually a province of New Spain (modern Mexico roughly) until the Latin American independence, when they became more directly tied to metropolitan Spain for the following century. There was some significative Filipino emigration to Mexico in all that time and they were well integrated and eventually absorbed, unlike the Chinese.

    The samples that show Melanesian blood are also the same that show East Asian and European admixture, so guess it may make some sense.

    But it may be also that these traces are more apparent than they should because the Mayas would have some other local dominant component distinct from the main Amerinidian one (not detected at this analysis depth). Such distortions are common in K-means (and even more at PC) analysis when not sufficient depth is reached. The problem is that the more and more deep you dive, the more and more clusters appear making the resulting graph anything but simple.

  2. “A trace remant of the older australoid population maybe”.

    Could be more recent though. It seems pretty likely that Polynesians could have reached America because they spread rapidly across the Pacific. Controversial evidence supports the idea although the evidence is usually dismissed.

  3. Polynesians reaching the Americas, sounds a bit like Thor Heyerdahl, except his thought it the other way round!

    The Kalash are South Asian not Central Asian as is shown by the analysis. The European green is not very conclusive. The differences between Europeans is mainly north and south. The Russians should have had more northern component different from the Tuscans and other southern populations.

    The Bantu brown stain is probably from East African Bantu speakers, Kenyans etc not Zulus or Xhosa. The presence of Arabians in Zanibar was quite recent into the 1960s. The Tuscans show that brown stain as well. Etruscans maybe?

    Luis the Tocharian hypothesis to the ancestry of Central Asians like Uighurs is not proven. They certainly have Caucasoid admixture or East Asian admixture depending on what angle you look at it; eastern, Chinese or western European. Europeans are always drooling over fair haired sand mummies and plaid cloth. It is not wise to draw conclusions from post mortem mumified corpses whether Eqyptian, Badarian or Central Asian. Ramesis did not have red hair, and neither did most Bog bodies. R1a and R1b originated near Central Asia.

    • Ramesis did not have red hair

      Actually the forensic examination of Ramses concluded he was naturally red haired in his youth- they yanked out a hair to study it’s roots. His mummyb has hennaed hair though- different cause to the bog bodies which is acid destruction of brown pigment.

  4. …dismissed evidence is the basis of history it
    seems. the polynesian effect is probably earlier than now admitted, a whole sea age/rope age
    in 4k bc has slipped its knots by historians but shows up in the language record and now haplogroup.
    polynesians navigators, like the arab astronomers, were the best of their time,
    and rode the winds of trade, conquest, and
    slavery while the egyptians were in spankers.

  5. The European green is not very conclusive. The differences between Europeans is mainly north and south.

    All Europeans show as a tight cluster when compared with any other populations: Europeans are extremely homogeneous. The differences can only be percieved when you do European-only studies and then they are as much south-north as west-east. That if you want to arbitrarily limit your understanding to the two-dimensional (hypersimplistic) PC graphs, when you get into K-means structure you see very interesting and mostly logical clusters, like in Bauchet 2007.

    The presence of Arabians in Zanibar was quite recent into the 1960s.

    Not from the 1960s. Arabs and especially Persians founded the Zandj states in the late Middle Ages. That’s not so recent. After a brief Portuguese interlude, Oman displaced Portugal again in the area until the 19th century.

    Luis the Tocharian hypothesis to the ancestry of Central Asians like Uighurs is not proven.

    Ah, no? In what regards to me it’s as well proven as anything can be.

    They certainly have Caucasoid admixture or East Asian admixture depending on what angle you look at it; eastern, Chinese or western European.

    Not Western European: there’s nearly not R1b1b1 in Western Europe.

    Europeans are always drooling over fair haired sand mummies and plaid cloth.

    I couldn’t care less but the Kizyl fresco depicts them as fair haired , so guess the fatual data is coincident in that. What I laugh a lot at is when they claim they had “blue eyes” because neither the mummies nor the tapestries allow to judge such extreme. The related Pazyrk horseman though has black curled hair but even more clear Caucasoid features (prominent nose, large eyes, big moustache) than the Kyzil fresco.

    It’s quite clear that West Eurasians were dominant in Central Asia as far as Altai and Uyghuristan before the Turkic expansion. Wether they were blond or brunette is trivial in my opinion.

    Ramesis did not have red hair…

    I can’t say for sure but red hair is not unknown of in West Asia or North Africa anyhow (think Chemical Ali, for instance), just somewhat rarer than in Europe, where it is pretty rare anyhow (excepting Ireland and Scotland that had some sort of Epipaleolithic founder effect, it seems).

  6. LOL, not “Chemical Ali” but ‘Izzat Ibrahim al-Douri, the current Baath leader of Iraq, sorry.

  7. Pingback: Human genetic variation and population structure: statistical construct or real? « Anthrogenetics' Blog

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