How do I verify if an atDNA match is for my father’s maternal or paternal ancestors?

+14 votes
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I have tested myself, my father, my mother, and two 1st cousins - my father’s brother’s son and my mother’s sister’s son. Do I have enough test data to verify matches 4 to 5 generations back and prove our common ancestor is on my father’s paternal or maternal side?  

I understand how triangulation can verify that a segment of a chromosome shared between 3 people came from a common ancestor.  But can that test help me to map which half of a chromosome pair is matching?  Can I determine if a possible match is from my father’s paternal side or his maternal side using my parent’s and 2 cousin’s atDNA test data?

My parents have also been tested for Y-DNA and Mitochondrial DNA.
in The Tree House by Jeffrey McGrew G2G3 (3.5k points)
edited by Ellen Smith

If you, Jeffery, have an XY karyotype then you have almost certainly inherited the Y chromosome (YChr) and some autosomal chromosomes (atChr) from your father and some X chromosome (XChr) or some parts of X chromosomes (XChrs), mitochondrial DNA (mt), and some atChr from your mother.

If your father has a XY karyotype then he has almost certainly inherited the YChr and some atChr of his father and some XChr or some parts of the XChrs, mt, and some atChr of his mother. You can not recover information about his father's mother's Xchrs and mt; you can not recover his father's Xchr and mt.

If your father's brother's son has an XY karyotype then the following: your father's brother's son likely carries an identical YChr to you and your father; he probably contributes nothing new to your information about your patrilineal YChr, but you can confirm your patrilineal genetic relation to him and your father. His mt and his XChr/XChrs is from his mother, so he contributes new information about her family but nothing new about your father's mother. Your father and his brother likely got different atChr, so he likely contributes new information about your father's father and mothers' atChrs.

If your father's father has an XY karyotype then you need his YChr, his XChr/XChrs, his atChrs, and his mt to reconstruct his complete genome. You have his YChr as does your father; you can use your YChr to triangulate matches with your paternal grandfather. You do not have your father's father's XChr/XChrs or mt. You have strictly less atChr from your paternal grandfather than your father has atChr from your paternal grandfather; your father's brother's son has strictly less atChr from your paternal grandfather than your father has atChr from your paternal grandfather; it is unlikely that you can completely reconstruct your paternal grandfather's atChrs; however, you can likely use your atChrs, your father's atChrs, and your father's brother's son's atChrs to triangulate matches with your paternal grandfather with some false negatives.

If your father's mother has an XX karyotype then you need her XChrs, her mt, and her atChrs to reconstruct her genetics. Your father has one of her XChr or has a XChr mixed from each of her XChrs, so your father can be used for triangulating XChr matches with your paternal grandmother with false negatives; you do not have all of your father's mother's XChrs. Your father has her mt, so he can be used to triangulate mt matches with your paternal grandmother. Your father's mother is much like your father's father in terms of atChrs; there is enough information to triangulate to them or from them, but there isn't enough direct information available to discern in all cases which atChrs came from which grandparent; this may be discernible by analytical methods using sex-linked inheritance to associate specific autosome half-segments to specific paternal parents.

To triangulate matches to your father's paternal side XOR your father's maternal side, your best bet is XChr matching. If they match your father's XChr or mt then they're on his mother's side; if they match your father's YChr then they're on his father's side; if they match his atChr then they could be either side.

There is indirect information to get from further analysis which would require growing your sample size by using the facts established in the above theoretical derivation to compare, classify, and test relations. The basic notion is to establish matches using (XChr OR mt) XOR YChr, and make note of the autosomal matches that can be affirmatively triangulated to your father's mother XOR your father's father. You'll then need other people with overlapping atChr at those segments; you'll need to compare them to your (YChr XOR (XChr or mt)) AND atChr matches to differentiate the pool into those that match one half and those who match the other half; with a little luck, you'll end up with your father's mother's XChr or mt matches in one pool and you'll end up with your father's father's YChr matches in the other pool. As long as the pool doesn't end up mixed then you can associate the autosome and autosome segment with the respective grandparent; it isn't strictly conclusive, but it is supported by the evidence.

Thank you Ian for the in-depth explanation. I got a little confused when you introduced "XOR". Could you define what it refers to? That would help clear up the last two paragraphs for me. Thanks again for your time and efforts.
XOR is the logical connective meaning "exclusively This or exclusively That"; alternatively, "only This or only That". A XOR B entails either that you have A but not B or you have B but not A. A binary choice of mutual exclusivity. E.g. Definitely knowing which side your relative is related to you from your father XOR mother.

3 Answers

+14 votes
 
Best answer
When you locate the common ancestral couple (which is actually what you get when you triangulate as opposed to a single ancestor), the only way to know if that match is from the male or female of the couple is to match someone further up the tree from one of the people.

Right now, with testing yourself, your parents, and two first cousins, you know the common ancestral couple (i.e. your grandparents).  As Peter said, you've got to test cousins further up the line to be able to tell if the shared DNA is from your grandfather or grandmother.
by Darlene Athey-Hill G2G6 Pilot (413k points)
selected by Jeffrey McGrew
+8 votes
One way is to use GEDmatch's phasing utility.   You will end up with two files.   One is your atDNA from your father and the other is your atDNA from you mother.  If GEDmatch's 'are my parents related' utility says they are not, then you can be sure his matches are only on his side.

Then get second cousins to atDNA test who are related to you through your father's mother's ancestry.  Then also test second cousins related via your father's father's ancestry.  That will determine which shared segments are due to shared ancestry on your father's mother's side vs. your father's father's side.
by Peter Roberts G2G6 Pilot (543k points)
I'm still learning about phasing, myself. Are the two outputs from that utility somehow more useful than the actual DNA data for the parents? I don't see how that could be.

 

It's a good point, though, to see if mom and dad are related, but I guess that would show up in THEIR matches anyway, wouldn't it?
If parents (or grandparents or aunts or uncles or great aunts or great uncles) are alive then everyone should be sure to test them.  DNA tests make great holiday gifts and right now there are excellent holiday sales.  Family Tree DNA is best because they store the person's DNA for additional testing and they offer more than just autosomal DNA testing.  I also believe they have the best customer service.
+2 votes
As I understand it, the short answer is "no", on all counts, except for certain cases where the Y-DNA and Mitochondrial DNA can do the job.

1) Your own personal test is basically redundant with those of your parents', as far as I know. It's cool to see what you got from who, but I don't think it adds anything in terms of confirming or triangulating anybody.

2) In isolation, your parents' DNA can help your cousins tell which side some of their DNA comes from (and therefore, which side of the family many of their matches are on), but that's a "one way street". Their value to YOU is in the extra DNA from your grandparents that they have - they might be able to triangulate with people that your parents can't, just as my own brother matches some of our 4th cousins that I don't match. They also confirm your grandparents, but you'd get that with any further confirming and triangulating anyway.

3) To do what I think you're talking about, as far as seeing if a match is on a given grandparent's side, you would need your parents' cousins, not your cousins.

4) 4 generations back (from your parents, so 5 back from you) is 3rd cousins, so if there are matches in their generation (or above) you don't even need to triangulate for confirmation (roughly speaking) - which means you only need ONE matching second or third cousin. With the right matching distant cousins (at least TWO), you might be able to confirm further back than even 5 generations, through triangulation (again, that's 5 gen back from your PARENTS, so pretty far back!). But, again, you need specific additional distant cousin matches for that, vs what you're talking about (which only confirms as far as your grandparents).

I hope that helps!
by Frank Stanley G2G6 Mach 6 (64.2k points)

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