D.I.Y. population structure analysis

By Razib Khan | December 26, 2011 1:09 pm

I badger readers here to actually use all the analytic tools which researchers put out into public circulation, rather than just offering cheap opinions. Obviously it’s way more fun and informative to have discussions with someone who can check their own hunches by doing a few “runs” overnight. Secondly, if you have minimal technical skills all it requires is an investment of time. If you can’t be bothered to invest the time if you have a modicum of nerd-quotient then it says something about how passionate you are about these issues in my opinion (granted, life gets in the way, but as someone who routinely felt lucky to sleep 3 hours on many nights over the past 3 months, please spare me).


Maju, the author of For what they were… we are, has now taken the plunge (with the help of my tutorial, which I need to clean up and fix in some details). Please check out his results (which are preliminary). Also, don’t be bashful about contacting researchers for files if you want something that’s not easily accessible in online reposities; that’s how Zack and Dienekes have gotten a hold of some data sets. There’s no need for hundreds and hundreds of people running ADMIXTURE and posting PCA plots. Rather, it is useful as a supplement to the academic community if there are at least some dozens of individuals who engage in exploratory analyses as well as replicating the results of researchers.

CATEGORIZED UNDER: Anthroplogy
MORE ABOUT: Admixture
  • http://blogs.forbes.com/johnfarrell John Farrell

    I need to try this! Thanks for reposting your tutorial.

  • Antonio

    Hi Razib. I agree that the technical requirements are probably not very complex for many readers of your and related blogs (Though, we still have to set up everything correctly, learn how to use the software, get the raw data, prepare it for analysis, graphic the results properly, etc). Yet, there is another reason that have prevented me – and possibly others – from running my own analysis: lack of knowledge about genetics. Sure, it can be learned, once you have the needed free time, but that is often lacking. Moreover, while the basic autosomal comparisons are quite simple, to do analysis at say X level we always need to know X+ K , which I most certainly don’t. Thus sometimes I am just afraid of loosing my own time trying to setting everything up just to find out that I don’t know enough of the topic to get most of the analysis.

  • Antonio

    Anyway, thanks very much for the tutorial. I will likely try this at some point. Best, Antonio.

  • Grey

    Agree on all points however as a pre New Year’s resolution cheap opinion related to a previous mention of Mamluks…

    If you consider Dioneke’s “Caucasus” component and lay out some of his ADMIXTURE strips for North Africa west to east and the Middle East north to south and you look at the scale of the Caucasus component and the clines down through to Egypt:

    http://img819.imageshack.us/img819/4383/mideast.png

    then it leads me to think the “Caucasus” component may be most concentrated *now* in the isolated mountainous regions of the Caucasus but might more likely have its origins in SE Asia Minor in the general vicinity of Gobekli as the first (or one of the first) farmers from where it radiated out in all directions depending on path of least resistance and where its original concentration was diluted by later backflows.

    If so then the path of least resistance would take it west to the coast of Levant and down to Egypt – where apparently the Delta has covered over most traces of the earliest farming

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

    and down the twin rivers to the Persian Gulf. Apparently the first farmers in Mesopotamia were

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

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

    http://en.wikipedia.org/wiki/Samarra_culture#Ancient_Samarra

    etc

    developing into

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

    which developed into Sumer, which got taken over by… nomadic Akkadians.

    Given that settled farming cultures tend to come under the control of any nomadic pastoralists who happen to be in range i’m wondering if the same people that brought farming into the Balkans and Greece brought farming into the middle-east down to Egypt as well but were later overrun by nomadic tribes coming out of Arabia.

    (What this would mean if the Anatolian IE hypothesis was correct is the Indo-Iranic branch could have come through the fertile crescent and then got cut off from the root by expansion out of Arabia. It would also tidy up King Tut’s R1b.)

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Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

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 http://www.razib.com

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