Friday, December 4, 2015

How to Find the Admixture of Shared DNA Segments

You find a genetic match and you have a family tree ancestor in common.  Hooray!  It's possible the genes you share could be from that ancestor.  Knowing the admixture of the SNPs you have in common could provide more clues.  For instance, if the ancestor in question was African, if the genes you share came from that ancestor, it should show that in the admixture.  

Tools like, ftdna and 23andme will give you an overall admixture (I am 3% Lithuanian, for instance). That overall admixture is impossible to use as a clue in gene to gene comparison of matches.  You could both share African descent, for instance - and it could be from entirely different ancestors.  Lo, the African continent happens to be pretty vast and offers billions of possible ancestors!   To find the admixture that is relevant to a particular match, you have to get more granular - down to the segments within a gene.  Only gedmatch offers the tools to do that at this time.  

These instructions will help you find out if the DNA you and you and your genetic cousin have in common has a particular admixture. It is roughly the process I used to find Millie Turner and Samuel Hussey in my genetic makeup.Although this will not prove a MRCA, it will provide more clues or evidence.  

The following caveats apply : 
  • An admixture tool is only as good as it's sample size and population.  For instance, if the sample didn't include any people of African descent, it will not pick up African admixture.  For this reason, different admixture tools interpret genes differently so you might not get a completely straight forward answer.  My experience is that you will find one or two admixture tools that do a better job than others of approximating your admixture - and that will differ from person to person.
  • When you look at the admixture of a specific gene, for yourself, for instance, you are seeing what you got from BOTH parents.  To find out which admixture on a particular gene came from which parent, you would run through these instructions first to compare yourself to one parent or the other.  
  • Not sharing the admixture of the ethnicity of the ancestor does NOT mean you do not have that ancestor in common.  It could mean that, through recombination, across generations, you just don't have any genes from that ancestor or not enough for it to accurately show up in admixture analysis.  
  • If your genetic makeup has the admixture of the ancestor in common that also does NOT mean you are definitely related to that person.  So, if you have African admixture, that does not prove you are related to the African ancestor in question.  You might have other African ancestors that you don't know about yet.  
  1. Using one to one comparison, enter your kit numbers and find out what chromosome(s) and segments you match on. In the comparison I did here for Millie Turner and Samuel Hussey, my cousin and I had chromosome 21 and 4, in common.
  2. Open the Admixture (heritage) tool
  3. In the dropdown, select the admixture tool you want to use. here's where you play with admixture tools to figure out which one works for you.  If you've never run through them before, do a few sample runs (steps 4-6) with your own kit to find the one that is most accurate to you.  I am partial to dodecad. If you have an admixture that is markedly different from mine, a different tool might work better for you.
  4. Select the 'chromosome painting' tool and click continue.
  5. Enter your kit number and select a tool.  I select Dodecad k12b - again, it depends upon which one is most accurate for your specific genetic makeup. See note on #3 above. Click continue.
  6. It will take it a while to finish.. it will go chromosome by chromosome. When it's done, you have a painting of your admixture. Save it to PDF for reference so that you don't have to run it again, if you don't want to.  I clip the full page to Evernote.
  7. Repeat steps 2-9 for your parents in order to determine which side of your family your various ethnic components came from.  Repeat them for the person you match to compare your admixture on the specific segments you have in common.  To do this : 
    1. Look through their painting for the place they match you.  You will scroll down to the chromosome, increase the resolution of the image (Ctrl + in a browser) and then scroll across to the start point of your match.  So, looking at the image at the top of this post, It shows the 29M - 36M locations.   
    2. Look through your painting for that same segment (and your parent, if one has tested). 
    3. Compare visually side by side. Use the key at the top of the chromosome painting to determine what the color represents.

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