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Genetics got personal in this decade

In the spring of 2010 I began to “eat my own dog-food.” By this, I mean that I entered the world of “personal genomics.” I ordered a bunch of kits from 23andMe for myself and my family.

I didn’t have too many strong expectations of surprises. One thing though I did suspect: my parents would differ some in ancestry. My mother had family lore of someone of “Chinese” background in the 19th-century.

What did I find out? First I got my Y and mtDNA results. I was at a Japanese restaurant in Japantown in San Francisco when I got the email. My Y was R1a, and my mtDNA was U2b. I was a bit surprised by the mtDNA. Bangladesh is 80% macrohaplogroup M. The Y wasn’t as surprising. I knew a substantial minority of Bengalis were R1a from the literature. But it was cool knowing for certain.

What personal genomics in the 2010s has done is making the abstract concrete. The general personal. It’s now part of the mainstream. In 2010 personal genomics was very niche, and it’s not anymore.

Another thing that 23andMe told me is that my parents are very similar genome-wide. Depending on how you calculate it they are between 10 and 20 percent East Asian (their results are highly correlated using the same parameters). This surprised me. Whatever the family legends were, my parents are pretty generic East Bengalis.

This year, DNA from an ancient woman of the Indus Valley Civilization was analyzed from Rakhighari. It turns out she was U2b!

So on the paternal side my lineage extends back to the Eurasian steppe, and the Sintashta-Andronovo cultural horizon. But on the maternal side, it is deeply rooted northwest South Asia, with the Indus Valley Civilization. That’s a pretty cool duet of facts to learn in this decade about myself.

Note: If you want to download my VCF generated from high coverage whole genome sequencing, here is the link.

12 thoughts on “Genetics got personal in this decade

  1. Now the question is how did U2(i) get into south Asia. Did it come with Iran foragers, or from an even older hypothetical Levantine Aurignacian movement or was it already in India when the proto-east Eurasians arrived?

  2. What if that Rakhighari woman was a migrant from the region of present day Bangladesh or eastern India? Rakhighari itself was the eastern most peripheral site of Harappan Civilization

  3. Didnt U2b came most likely with the “Iranian farmer component” and was the female company to yDNA J?
    It probably was successful in two waves, but with the Indo-Aryan expansion along the Gangetic river system in particular. Or is the timing off?

  4. My R1A brother from another mother. Does any Y haplogroup have such a storied history? I can’t think of one. It’s on my to do list one day, just haven’t surmounted the price tag, to get the complete Y test done. I’ve had it done fairly high resolution and narrowed down to YP263, which is a branch I believe associated with the Polabian Slavs, interesting since my paternal line is out of the German/ Dutch border area (Limburg), though I could see how we would have gotten from A to B. YP263 TMRCA is 2K years though. I guess the other thing that has prevented me from diving deeper into my Y chromosome is I am not sure if there is much else to be learned at this point. It seems like not much is known about that branch (or most others) more recently than 2K years ago.

  5. @OBS
    >Didnt U2b came most likely with the “Iranian farmer component” and was the female company to yDNA J?
    >It probably was successful in two waves, but with the Indo-Aryan expansion along the Gangetic river system in particular. Or is the timing off?

    Well, U2b is a part of the general U2i group. Based on very old (like early 2000s) studies the U2i is supposed to have been in south Asia for tens of thousands of years, probably going back to the first peopling of south Asia. However I am not sure if things have changed since then regarding the pre-history of U2i. So far none of the Iran neolithic, mesolithic and in general Iran cluster prehistoric samples have the haplogroup U2i, or U2 in general for that matter.

    That and the presence of yDNA haplogroup H (a marker unusual for east Eurasians) has recently lead me to think that the presence of yDNA H and mtDNA U2(i) in south Asia might be due to some very old, nearly 30,000 years old contact with the Levant Aurignacian people. The lack of, or the paucity of such markers in Levant today or even in the Natufian times might be because the region is used to massive population replacements/turnovers. This is the latest of my several armchair conjectures

    That Nina Paley ‘This land is mine’ video could very well be extended all the way back for Qafzeh hominids of the middle paleolithic Levant and the narrative would probably remain consistent

  6. Latest since all the ideas about dating R1b in Western Europe to pre-Ice Age times were clearly falsified, everybody should be very sceptical about “Palaeolithic” or even Mesolithic continuity everywhere. Recent results just prove that to be justified and local continuity is rather exceptional.

    IIRC Ust Ishim is sometimes seen as more closely related to South Asian (Mesolithic?) populations, so it might be right in that way, with a once wider spread West Eurasian population which was largely replaced or changed, further differentiated in most of Eurasia, including Central Asia, but was better preserved in the South.

    I think the distribution of U2 and its subclades in India is peculiar anyway and shows a relationship to Dravidians first and Indo-Aryans second, generally speaking to more Caucasoid parts of the subcontinent.

    So regardless of how long it was present at the borders or even within South Asia, I would suggest it spread and expanded mostly with Neolithic, Dravidian and Indo-Aryan colonisation. But this will be up to further samples of which I hope they will come up rather sooner than later.

    I’d assume that Dravidians too were a fusion group which might have incorporated local Caucasoid-like people first.

  7. Or to say it differently: There were multiple waves from West-Central Eurasia coming into South Asia, which is part of the reason why the West Eurasian component in the IVC was not completely of the kind we see further West, the Neolithic settlers incorporated, fused with more distant related WEA Mesolithics already living there.
    But the final spread of WEA ancestry, including U2, happened later, with the Neolithic and subsequent colonisations. I just doubt it happened before the “rice cultivation revolution” that Caucasoid people went deep and large scale into the more tropical parts of the country. That’s why AASI survived in such relatively higher percentages, at least that’s what I think right now, until more definitive results come in.

  8. Dravidan itself has at least two components so saying that it is more associated with Dravidians isn’t saying much.

    https://upload.wikimedia.org/wikipedia/commons/8/82/Most-of-the-extant-mtDNA-boundaries-in-South-and-Southwest-Asia-were-likely-shaped-during-the-1471-2156-5-26-2.jpg

    Looking at this it is obviously widespread and doesn’t seem to show specific bias towards populations with a high Iran neolithic type ancestry. Probably indicative of older settlement.

    >Latest since all the ideas about dating R1b in Western Europe to pre-Ice Age times were clearly falsified, everybody should be very sceptical about “Palaeolithic” or even Mesolithic continuity everywhere. Recent results just prove that to be justified and local continuity is rather exceptional.

    That was a specific case with a type of dating method with R1b which was rejected in favour of something else, can’t remember the details. If the same is true for U2i then we should be seeing more recent reference dates, and yet I have seen people, professionals, refer to Rakhigarhi female’s maternal lineage as being indigenous in the AASI sense and not the Iran neolithic sense.

    >IIRC Ust Ishim is sometimes seen as more closely related to South Asian (Mesolithic?) populations

    There are no published south Asian mesolithic samples, but in raw PCA distance he isn’t too far from Onge and Hoabinhians.

    “sample”: “LAO_Hoabinhian:Average”,
    “fit”: 12.2633,
    “RUS_Ust_Ishim”: 100,
    “closestDistances”: [
    “RUS_Ust_Ishim:Ust_Ishim: 12.26328”

    “sample”: “Onge:Average”,
    “fit”: 14.7989,
    “RUS_Ust_Ishim”: 100,
    “closestDistances”: [
    “RUS_Ust_Ishim:Ust_Ishim: 14.79888”

    All 3 are from very different time periods.

    What I see is no U2 in Iran neolithic and presence of U2 in Aurignacian culture of Europe. However no known Levant Aurignacian samples exist as of yet. So I just guessed that the U2 in south Asia comes from a divergent Aurignacian U2 subclade like a hypothetical one from Levant Aurignacians who separated from European Aurignacians a very long time ago.

  9. I knew the distribution maps and to me it looks like a later expansion during the “rice revolution” which allowed higher productive cultures to colonise the inland of South Asia effectively. Along the Gangetic system in particular. The haplogroup might be older in the subcontinent, but most of its spread is more recent I suppose.
    Dravidian to me is the Iranian farmer component. They mixed with local NW Indian Mesolithic Caucasoids and AASI.
    How many layers from the different incursions from the North West exist in India will be seen. But U2 is from one of those,which one remains open.
    But the modern spread has a pattern imho, making more sense if its associated with rice cultivation and Dravidian and Indo-Aryan expansions from the North-West, the Indus region.

  10. >Dravidian to me is the Iranian farmer component. They mixed with local NW Indian Mesolithic Caucasoids and AASI.

    Is this an introduced of a new population. “local NE Indian Mesolithic Caucasoids”. Based on what is published so far, before the Iran HG movement, north India would have been inhabited by AASI Australoids only. Do you have anthropological proof of Caucasoids in north India before the Iran migration (because there are no genetic samples in south Asia before the bronze age)? I only know of Ganga mesolithic series which on peripheral view seems to be like Cro-magnids with prognathy- basically Australoids/not Caucasoids (https://imgur.com/a/IqS9J7k). If there was a Levantine movement into south Asia 30,000 years ago, they wouldn’t necessarily make the locals more Caucasoid-like since Aurignacians themselves would have looked like Kostenki 14.

    >But the modern spread has a pattern imho, making more sense if its associated with rice cultivation and Dravidian and Indo-Aryan expansions from the North-West, the Indus region.

    True, population movements, especially of agricultural types would mask former patterns.

  11. I don’t remember the exact sites, but yes, there were older forms of rather Caucasoid people in the area of Northern India. With India I mean always historical India, including Pakistan and Bangladesh of course, not just modern India in its current borders.

    Also, and this is more important than whether they were “Caucasoid proper” by phenotype, they were different from AASI. The local trpical inhabitants were more divergent than what we see in more Northern Eurasia in that time genetically and phenotypically. This means they have a long history of their own, independent from the West Eurasian populations, from which U2 is derived from – at which time exactly for India is open to debate though.

  12. Which sites are these? the details are important in these cases. The only pre-neolithic sites that I know of in northern India specifically are the Ganga mesolithic series (from Mahadaha, Sarai Nahar Rai and Damadama) and their similarities to cromagnids were superficial according to the archaeologists involved with the sites.

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