Ancestry painting: true but trivial, or interesting but inaccurate

By Razib Khan | April 17, 2012 9:22 pm

23andMe has done some great things, and I highly recommend its service to friends. But I’m really glad that CeCe Moore is being consulted by them in regards to improving their ancestry feature set. Below are the “ancestry paintings” for myself & my daughter.

According to 23andMe I’m 40% Asian, and she is 8% Asian. Obviously something is off here. The situation easily resolved itself when I tuned my parameters and increased my sampled populations in Interpretome. But it just goes to show you the limits of this sort of thing without fine-grained control of the details of the analysis.

 

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MORE ABOUT: 23andMe
  • Doktor Grisha

    So, you did not use the default settings in Interpretome. Well, then, Razib, publish your parameters!

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    #1, select hapmap3, smoothing down to 10, chi-square down to 0.10. left other stuff alone. using a broader set of reference populations was the essential thing though.

  • Dwight E. Howell

    While unlikely the 8% Asian would be one possibility with a 40% Asian parent.

    That’s why I’m sort of neutral to some of the data I know about my family tree. I know I have Cherokee ancestors through a female. I also know that was several generations ago so what are the odds of me or my younger relatives having any native American genes? Low but distinctly possible.

    The same sort of situation is faced by a local family that knows one female ancestor came off a plantation after the civil war. Does anyone in the family still have any of her genes? Maybe but they’ve been thoroughly diluted by now.

    Of course this also show’s why trying to build a complete family tree based on present genetics is not to be taken seriously once you go back past a certain point. You are clearly going to have ancestors whose genes never made it to you.

    This pretty much explains what I think happened to Hsn. Europe seems to be one of those places into which populations constantly flow and the local genes are constantly getting replaced or diluted until little or nothing is left. I don’t see much reason to think the people doing the replacing are in any meaningful sense superior to those being replaced as long as they keep coming in wave after wave which seems to be what actually happens and is still happening.

    Time to go to bed.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    #3, i’m 90% sure this is just a problem of lack of reference populations in the painter. mostly resolved when they were added. so it would be easy to found out about native ancestry in the case you are talking about (or lack thereof genomically).

  • Eurologist

    “While unlikely the 8% Asian would be one possibility with a 40% Asian parent. ”

    There are (possibly many orders of magnitude, depending on how you count) differences between “possible” and “unlikely” – or extremely unlikely. Ancient autosomal DNA isn’t going away quite that quickly, with increasing (or full) resolution.

  • Lank

    The lack of reference populations isn’t the only problem. The threshold for what’s classified as “European” seems to be significantly lower than for the two other categories. 23andMe’s Ancestry Painting is very bad at picking up ancient admixture events. This is less obvious for samples with, e.g., an “Asian” affinity as high as yourself. But when that’s diluted with additional European, much of what was previously classified as “Asian” becomes “European”.

    East Africans have similar issues; the amount of African in the Ancestry Painting isn’t proportional to the SSA (Yoruba) affinity, even though the African category is based on the Yoruba.

  • AG

    Meiosis (recombination), selective sequencing by 23andme,

  • April Brown

    Kind of amusing that Interpretome isn’t compatible with Internet Explorer. Bit of a silly limitation.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    #8, for client side development IE is a shitty browser. not amusing at all, cross-browser design wastes an enormous amount of time. i’d rather have this sort of niche application focus on extending the feature set on one browser than crippling itself to work on multiple browsers. chrome’s original stated purpose was to keep the major browsers ‘honest,’ but from what i recall it surpassed firefox recently, and is catching up to IE.

  • http://konradjkarczewski.com Konrad Karczewski

    Interpretome inventor weighing in here. Thanks for the shoutout! Glad to see the experimental Hapmap 3 is working for someone, it’s a bit odd because there are some pretty similar populations in there (and we’re concerned the overlap may be producing some weird results). We’re tinkering with some other reference populations, so that might help a bit. As a side note, cranking up the “Number of Samples” parameter can only help, it just takes longer because your browser is doing some more haplotype sampling.

    And yeah, we can’t deal with IE and its nuances, we just went for the most open solution, which meant Chrome (and FF where possible… all things considered, this is a side project and no one’s day job yet).

  • ackbark

    Interpretome certainly shows more variety than the 23andMe ancestry painting, but it classes the bulk of me as Tuscan rather than CEU which is more what I’d expect as all other information I have says Northwest European.

  • Eurologist

    And yeah, we can’t deal with IE and its nuances, we just went for the most open solution, which meant Chrome (and FF where possible… all things considered, this is a side project and no one’s day job yet).

    Smart decision (I was a principal in several start-ups in a prior life – I know exactly how resource-intensive this is, including QC on numerous OSs).

    Kind of amusing that Interpretome isn’t compatible with Internet Explorer. Bit of a silly limitation.

    It only takes a few minutes of your time to install a decent browser – but it may take a full-time position or more at a (presumably) underfunded organization to guarantee multiple browser compatibility.

  • April Brown

    Re: the browser stuff… well that’s all just colossally depressing. I used to work with the IE team, and was up on all this, and here is yet another example of motherhood making me dumb and ignorant.

    Back when Chrome came out as a public beta there were horrific security issues (by design), with Google using the browser to send a lot of data back to headquarters, probably in the name of usability research. I think that’s since been addressed, but clearly I’ve been out of the loop so long that I’m not much of an authority.

    I was under the impression though that IE9 was a step forward in cross platform app friendliness and not being such a resource hog. I can understand not wanting to be compatible with IE7 or IE8.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    I was under the impression though that IE9 was a step forward in cross platform app friendliness

    right. but the bar was very low. like american cars in the 1980s IE now has its past history to deal with. though whenever a new version comes out i take it for a test drive. nothing i’ve seen would make me want to switch to IE.

  • chipoltespice

    If Asian is related to Native American, segments are missed and those segments are painted the predominate ancestry. Sending to Doug McDonald will help. Due to recombination especially with a non-Asian parent, inheriting smaller Asian is not abnormal.

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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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