My First Try at Two Sibling Visual Phasing

I recently had my wife’s Aunt Elaine’s DNA tested. She is the only sibling of my mother in law Joan. I would like to try to visually phase these two. Fortunately, they have have a half Aunt Esther. She is related on only one of their grandparent’s sides. That side is Upshall from Newfoundland. I am hoping that Esther’s DNA results will be helpful in visually phasing.

Aunt Esther’s Upshall DNA

Here is how Elaine matches Aunt Esther:

Here is how my mother in law Joan matches Esther:

It looks like Esther will be a big help in identifying Elaine and Joan’s maternal grandfather side.

Chromosome 1

I’ll just jump in and try Chromosome 1. That is the big one.

Already I have a bit of a problem. There is some green within the second HIR or Half Idendical Region (yellow area). I am ignoring it for now. This graphic shows that Joan and Elaine have no FIRs on Chromosome 1.

Next I add Esther’s DNA to the mix:

This is interesting. I see two maternal crossovers for Joan. Joan’s maternal grandparents are Upshall and Daley. Esther represents Upshall. So at 17.4M, Joan must go from Upshall to Daley. I say this because Elaine continues to match Esther (Upshall) after 17. 4M. The same thing happens at marker 117.6. Now look at Esther. She must have a maternal crossover between 70 and 117.6M.

Actually, it looks like I made a mistake. My first comparison of Joan and Elaine is the same as Esther and Joan, so I must have done it wrong. I’ll make sure I have Joan and Elaine this time and lower the levels to 3 cM and 300 SNPs. Now my results look more reasonable.

That looks a lot better. Forget my comment about there being no HIRs. There are at least five green HIRs between Elaine and Joan. Things didn’t line up perfectly, but I tried to fudge them in. Upshall is shown in orange which corresponds to the matches with Aunt Esther. Next, I add in some more Maternal segments for Elaine and Joan:

Again, the orange pretty much mimics the matches that Joan and Elaine have with Esther. The difference is with Elaine’s last orange segment. That goes more to the left as I don’t show a crossover there. There should also be a maternal crossover for Elaine to the left of her second orange segment. That means that to the left of that middle orange segment, there should be some green Daley.

The Paternal Part of the Puzzle

It would help to have some paternal matches at this point. Melissa is one match that I have mentioned in at least one previous Blog.

I like Melissa’s matches, because she doesn’t show any obvious Rayner in her ancestry. A Rayner would mess things up as that is Elaine and Joan’s maternal grandmother’s name. Jane would also be a good choice here.

Melissa adds some information. She represents the Ellis side. She matches Joan, but not Elaine. As Melissa does not match Elaine in this location, I have put down the paternal grandmother Daley in Elaine’s segment below Joan’s Ellis segment:

[Edit: the reddish paternal segment on Elaine’s bar should actually be Rayner.]

Now I have a little bit of paternal informatiion, but I appear to be at an impasse. Next, I will look at Joan’s Excel spreadsheet of matches. I see a Hayley there that matches through the Dicks Line. Dicks is a mother of Upshall, so that counts as an Upshall for my purposes.  Here is Joan’s match with Hayley:

This does not help as Esther already matches in this area. However, it does point out that I missed a crossover at the beginning of the Chromosome where the FIR (green) between Elaine and Joan goes to HIR (yellow).

I’ll take a break for now and move on to another Chromosome.

Mapping the X

I mentioned that Chromosome 1 was the largest Chromosome. The X Chromosome is fairly large also. There are some advantages to mapping the X Chromosome. One advantage is that Elaine and Joan’s paternal X is already mapped to their father’s mother (Daley).

See, I already mapped both of their paternal side X Chromosome. Joan and Elaine both get the same X Chromosome from their dad. This is the same one he got from his mom (Elizabeth Daley). Here is the genealogy:

See, that is why I check. Joan and Elaine’s dad was an Ellis and his mom was a Rayner, so I got that backward.

That leaves Upshall and Daley for the maternal side. I mapped three maternal crossovers, but there may be more that I don’t see.

Again, Esther will represent Upshall and not Daley. That is because Elizabeth died in the flu epidemic. Fred Upshall remarried a Shave and had Esther.

When I check Esther’s X against Elaine’s, I get no match. Joan and Esther, however, do match:

In fact, Joan’s matches with Esther line up with the crossovers I have. That is good news. Here I also changed the color of Rayner to be consistent with Chromosome 1.

 

I’m pretty sure the end result should look like this:

Back to Chromosome 1

In the Dicks DNA Project I have been working on, I have a Triangulation Group Summary. The mother of Fred Upshall was a Dicks, so Dicks helps to identify Upshall DNA.  Here is a partial shot of that Summary for Chromosome 1:

I have not added Elaine to the Summary yet. This shows that Cheryl, Charles, Joan and Elaine match on Chromosome 1. Here is how Cheryl matches Esther, Elaine and Joan:

Adding Cheryl and Position Numbers

I got the numbers on the top of the Joan/Elaine comparison from Gedmatch’s full resolution option on their chromosome browser. A few observations:

  • Cheryl’s matches confirm Elaine’s crossover at 94 and Joan’s at 118M
  • Cherlys’s match with Joan also indicates a likely Paternal crossover for Joan at 70M
  • Elaine and Esther match to 158M. That means that Elaine likely does not have a crossover at 152
  • Due to the centromere of Chromosome 1, the two browsers align very poorly around 152M. Note on the original comparison between Joan and Elaine how quickly the numbers go from 118 to 152M.
  • As mentioned above, Elaine’s Upshall segment should go past 152, but then there is a FIR. That means that Joan will have an Upshall segment above Elaine’s. That means that her Daley segment will look tiny, but it will actually go from 118 to 152M which is not so small.

Based on my above observations, I have this new map:

I gave Joan a paternal crossover at 70.5M. I also gave her a paternal crossover at 152M. This leads to another observation. The area between 60.5 and 70.5M is a FIR. That means that for Joan and Elaine, their paternal grandparent and maternal grandparent have to match. That means that at 60.5M, Joan’s Ellis DNA has to turn into Rayner DNA or Elaine’s Rayner DNA has to turn into Ellis DNA. Either way, there will be a Paternal Crossover for either Elaine or Joan at 60.5M. That means that there is not a maternal crossover at 60.5M for Elaine nor Joan. That will expand the maternal Daley to the left for Elaine and Joan:

This leads to more observations:

  • One I could have noted before. Betwen 17 to 26.6M Elaine and Join do not match each other. Elaine has Upshall DNA there, so Joan has to have Daley there.
  • Elaine has a Maternal Crossover at 26.6M. That means that there is no Paternal Crossover there. That means that I can move the two paternal segments to the left.
  • The fact that Elaine has a Maternal Crossover at 26.6M means that Joan has no maternal crossover there, so the Daley segment can be moved to the left also for Joan.

Moving the Daley segment to the left for Joan created a Maternal Crossover for her at 17. That means that there is no Paternal Crossover there and the two Paternal segments can be moved to the left:

So Chery’s matches were a help.

Summary and Conclusion

  • A first shot at two person visual phasing has shown promise.
  • Chromosome 1 is a difficult one, but I got a start on it
  • The X Chromosome was mapped for Elaine and Joan.

 

 

 

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