The Genographic Project: on to the autosome!

By Razib Khan | July 25, 2012 11:20 am

The Genographic Project is now moving beyond uniparental lineages with Geno 2.0. Spencer Wells kindly invited me to a conference call last month where he outlined a lot of the details, so I’ll hit the salient points for readers of this weblog:

* They’re unveiling a new SNP-chip and a new project which moves beyond the Y and mtDNA to the autosome. But they’re also expanding their coverage of uniparental markers.

* Though there are “only” autosomal 130,000 markers, Wells and his collaborators have selected a subset of markers which are highly informative of population structure (e.g., high Fst). Their SNPs are biased toward those with moderate levels of polymorphism across many populations to maximize the power of diagnosis of differentiation.

* They tried really hard to get rid of ascertainment bias. This means that in many previous chips there is a tendency to work off the polymorphism in Europeans, and then examine worldwide variation using this ruler. The problems with this method are obvious. One of the scientists on this project outlined how they worked to look for SNPs which are very informative for populations where ascertainment bias is a particular problem, Oceanians and Amerindians. I was impressed by their punctilious attitude on this question.

* The major downside is that they don’t have many trait informative SNPs on the marker. This means that they’re only interested in phylogenetics and phylogeography, rather than the evolution of specific suites of traits.

I’m sure that Wells will say a lot more. But there are a few extra aspects of the current trajectory which are exciting to me. First, they’re going to push their genotype results public at some point. Second, they’ll be encouraging utilization of the Geno 2.0 chip by giving them to specific researchers and groups. Third, their population coverage is very thorough. They have some publications in the pipeline, and it’s the last point that has me excited. I saw some slides of the coverage in India, and I’m 99% sure that this data set is the source of the claim from this group that India’s caste system predates the Indo-Aryans.

Addendum: Also, in some ways they are now moving into 23andMe’s space in scientific genealogy. If you are curious, please see Your Genetic Genealogist, as she has a much more thorough post.

MORE ABOUT: Geno 2.0

Comments (4)

  1. wijjy

    I don’t think you can ever get rid of ascertainment bias, you can just introduce different sorts, with SNPs likely to be informative for your particular question. Still if these can be mapped back onto the 1000 genomes data it is certainly going to be an improvment on the current SNP sets.

    However you choose SNPs, some sort of bias will be introduced. The most important thing is that the process by which SNPs were chosen is transparent and any fudging documented. In this way the ascertainment process can be modelled.

  2. RKM

    I am not surprised about the caste system in India predating the Indo-Aryans. It is most likely the legacy of the spread of early agriculturalists (Metspalu component k5) into the subcontinent and the consequent genetic and cultural exchanges with hunter-gatherer groups (Metspalu component k6). This was likely the basis of the jati system that predominates the subcontinent and is the equivalent to the caste system. The Indo-Aryan varna system (brahman, kshatriya, vaishya, shudra) was an adstratum placed on the pre-existing jati system. Moreover, the genetic legacy of the Indo-Aryans (Metspalu component k4) is pretty much restricted to the northwest and in brahmin communities outside the northwest.

    Metspalu, M et al The American Journal of Human Genetics 89, 731-744, December 9, 2011

  3. Justin Giancola

    I’m sure I’m not the first to say this, but what seems likely is that the Aryans just injected themselves into the top of the castes, or, maybe they superpositioned themselves on top of an indigenous kingly class, creating brahmans. The other three are sort of basic to all the East Asian caste systems to my knowledge; I’m not sure if the others have the equivalence of brahmans?

  4. G Coldham

    I hope this Geno 2.0 will cause a “gene-quake” for all those who want to enter into genetic genealogy.
    Probably nobody knows what is going to tumble out of this —but no doubt some extraordinary stuff !!!


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About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at


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