joel@jmhartley.com – Page 68 – Hartley DNA & Genealogy

December 13, 2016December 19, 2016

Visual Mapping of Butler Chromosome 5 Reveals an Identical By Chance (IBC) AKA False Match

I would like to try to map my in law’s Butler DNA on Chromosome 5. This is based on a rare paternal match that was found at AncestryDNA and cross-referenced at Gedmatch based on similar names and matches.

I have already mapped Chromosome 11 here. I would now like to map Chromosome 5 with the help of one match that my father in law Richard has with a Rooney descendant named Jeanette. That Rooney match is on Richard’s paternal grandmother’s side (Kerivan)

Mapping Chromosome 5

Chromosome 5 is one of the larger chromosomes with 1 being the largest. Now I compare the three Butler siblings: Lorraine; Richard; and Virginia and I add in crossover lines.

I have the locations of the proposed crossovers at the top. Note the smallest match between Lorraine and Virginia. I think that I have the resolution too low for that match, so I will take it out as there is no indication of a change from HIR to FIR (Half Identical Region to Fully Identical Region) or match to non match status in the other sibling comparisons. That will simplify things in the area of 35/38.

Just pretend the match between Lorraine and Virginia at 34 is not there. I will now assign the crossovers to the siblings. The first crossover goes to Richard as he is represented in a FIR (green) to HIR (yellow) change in the 1st comparison and in the HIR to FIR in the 3rd comparison.

The crossover tallies are in:

Richard (R) – 5
Virginia (V) – 4
Lorraine (L) – 2

Actually, I would not be surprised if Lorraine had an additional crossover at the very far right end of the Chromosome, but as it is so small, I am ignoring it for now.

Recall that Richard’s Kerivan Line match was 66-75M. That is probably within the segment R-V ending at 75.5M above. When I compare Lorraine and Richard at full resolution at Gedmatch I get this for Chromosome 5:

This defines Richard’s crossover (from HIR to FIR) and is at about 61M as every ^ is 1M. That means that my assumption about the Rooney/Kerivan match was correct. I am curious to see if I will be able to map the Butler paternal side with just one match.

time to map based on no match, HIR’s and Fir’s

I’ll just start with the large FIR between Lorraine and Richard.

The green FIR above translates to the same blue grandparent DNA on one side and the same green grandparent DNA on the other side for Lorraine and Richard. Then we need to expand these regions of DNA to the crossover lines for Lorraine and Richard:

Lorraine had no crossover to the left to keep her 2 grandparents’ DNA from expanding there. Richard goes to the right to his last crossover. Then we can add in other FIRs and put in opposite colors for the areas where siblings don’t match (red on the chromosome browser above).

This is what I call the Swiss Cheese phase of visual mapping.

comparing gedmatch cousin matches

At this point I would like to compare Gedmatch matches. There is one thing already that doesn’t make sense. According to Gedmatch, Richard has a Kerivan match between 66 and 75M. However, the mapping shows that Lorraine and Richard are in a FIR there. That means that if Richard has this match, then Lorraine should also. Let’s check Lorraine again. I still get no match. When I lower Lorraine’s threshold to 5 cM, I only get a small match with Jeanette on Chromosome 20. That could mean that Richard’s match with Jeanette on Chromosome 5 is by chance. That was disappointing, but informative.

That leaves us the maternal side. Are there matches there?

Here are the matches that I show for our 3 Butler siblings on Chromosome 5. Virginia shows a match on the maternal side with her 1st cousins Patricia and Joseph (in pink). This could be helpful. But in this case, it appears that it isn’t. That is because in this segment, Virginia doesn’t match her two siblings. Should I give up? I have one more idea. As I mentioned above, Virginia has a maternal match from 88 to 118. However, John matches Richard and Lorraine in that same area. That means that John’s match in that area has to be paternal. John is a nephew, so he shares maternal and paternal matches. Unfortunately, as Richard and Lorraine are FIR in this segment, it tells us no more.

update based on reader comment

I had a comment questioning my apparently too hasty assertion that the John match above (from 81-115M) to Richard and Lorraine was paternal. I did put a little thought into that comment. M MacNeill has kindly phased John’s raw DNA on a different chromosome (Chromosome 1) and came up with this result.

This gets to the old adage about a picture being worth 1,000 words. As John is in a different generation (as is Marie, my wife – his cousin) it gets confusing. However, the above image shows the DNA John got from his four great grandparents on his paternal side.

The segment we are looking at above is between 75.5 and 117. In that stretch all 4 grandparents are represented by four different colors. This is part of what makes the analysis difficult. If there was an HIR in that region, the analysis would have been easier as there would have been only 3 grandparents to consider in that segment.

We know that John matches Virginia on a maternal match, but we don’t know which grandparent it represents. That leaves one other maternal grandparent and two paternal grandparents (from the viewpoint of the above map). John’s match with Richard and Lorraine from 88 to 115M could therefor be with one of Richard and Lorraine’s maternal grandparents or with either of the two paternal grandparents. This tells me that there is a bigger chance of the match being on the paternal side, but that the maternal side is not ruled out.

Updates on the Update

Since my update, I had a few important responses on the ISOGG Facebook Page that I would like to preserve in this Blog. Kathy Johnston, from whom I learned the visual mapping technique responded with a possible visual mapping:

I liked how she put in the Patricia and Joseph match suggesting that the purple could be the maternal side. I also received a response from M MacNeill who has been so helpful in working on the raw phasing of the Hartley and Butler families:

Here is a screenshot of comments relating to the image above:

Summary and Conclusions

I could map out one further HIR, but I won’t at this point
I had high hopes in mapping some paternal segments to specific grandparents on Chromosome 5, but it didn’t work out
I did find an apparent Identical by Chance (IBC) or what I call a false match between Richard and Jeanette at Chromosome 5. It appeared to be real before I mapped it out.
Future identified cousin matches may resolve the mapping of Chromosome 5
I appreciate comments from readers that help me to re-think my conclusions

December 12, 2016

Looking At French Canadian Pouliot DNA

My wife’s great grandmother was Emma Pouliot b. 1874 in Quebec. The exact location was St.-Étienne-de-Bolton, Brome, Quebec. According to her death record, she was from Eastman, Quebec. Could it be possible that she was born in Brome and later moved to Eastman?

The place with the stick pin is Brome, while Eastman is a few towns to the Northeast. The line below is the U.S boundary. This is what Emma Pouliot looked like:

I’d like to look at Pouliot DNA in this Blog. One reason that I’d like to look at Pouliot DNA is because of my wife’s Aunts. I had them tested at AncestryDNA and most of their Shared Ancestor Hints (SAHs) were from the Pouliot Line.

The Pouliot DNA Project

I’ve been involved in two other DNA projects. Both of them have been in populations that intermarried. On my grandmother’s side the Frazers intermarried as they usually looked to marry someone from the Church of Ireland in an area that had mostly Roman Catholics. On my wife’s mother’s side the Dicks intermarried with other Newfoundlanders. French Canadians have been known to intermarry due to the colonial nature of the area. There were only so many original settlers. Here are some of the Pouliot descendants I have so far:

I have been in touch with Robert in the left column in the past due to good DNA matches. Those on the right are closer relatives to my father in law Richard. They have all had their DNA tested. One group has for a common ancestor Emma Pouliot. Fred and Sleuth who are second cousins of my father in law Richard have the common ancestors of Joseph Pouliot and Josephine Fortin.

Pouliot DNA

Here is how the testers compared. I didn’t include my wife as all her Pouliot DNA is from her dad.

This shows that everyone matches – except for Fred and Robert.

Triangulation Groups

I like to look at Triangulation Groups (TGs) as these indicate common ancestors. Once we find these, we can confirm existing genealogy and suggest new genealogy in some cases. To do this, I can compare the segments of the nine that tested above. I’ll look at Robert as he is most distantly related. He is a 4th cousin, twice removed to those in my father in law’s generation.

In order for Robert to be in a TG, he would have to match two people within the same segment. Those two people would have to match each other. The other rule is that the two people that he is matching don’t count if they are siblings.

Here are my nominees for potential Robert TGs:

In the first highlighted box, Richard and Virginia are siblings, but Patricia as a 1st cousin can be a potential third in the TG. In the Red TG, we see Patricia and Joseph as siblings but their relative John makes the third with Robert. Finally Robert, Joseph and Sleuth may be in a TG.

Chromosome 3

In order for this to be a TG, Virginia and/or Richard must match Patricia in that area. Here is how Patricia matches Virginia, Richard and Robert on Chromosome 3:

Clearly they all match around the area of 130M. Here is how I think the Chromosome 3 TG would look like on the genealogy chart:

Chalk up one TG for Robert, Richard, Virginia and Joseph. Without Robert, we wouldn’t know if the common ancestor for Richard, Virginia and Patricia is Pouliot or LeFevre for this segment of Chromosome 3. Now we know. This will come in handy once I map Chromosome 3 for the Richard, Virginia, and Lorraine.

Chromosome 5

This potential TG is interesting as none of the matches are in my in law’s direct family. Here is how John matches Patricia, Joseph and Robert:

I’d say that is a match. As they say in Star Wars, “The force is strong within you”.

Chromosome 15 TG

If we could find a TG here, that would include Robert in all four of the families above. Actually, it may not be obvious above, but Jake, Richard, Lorraine and Virginia are all siblings. Marie is my wife and Richard is my father in law.

I’ll check to see if Joseph matches Sleuth around 95M.

#1 is Joseph’s match with Robert and the one we are looking for is #2 which is Sleuth’s match with Joseph of 26 cM. This should be of interest to Fred, who is Sleuth’s brother. He has done a lot of work on Pouliot genealogy.

Joseph and Sleuth can know that their Chromosome 15 matches with Robert come by way of Pouliot and not the Fortin side. With just the match between Joseph and Sleuth, we wouldn’t have known that.

I have covered all the families with TGs. That means that all these families have a paper trail and a DNA trail to a common Pouliot ancestor. Actually the common ancestors are Pouliot and Gobeil, but in the next generation down, they have the Pouliot name.

Any Potential Problems in This Analysis?

The only problem that I see would be that if we picked the wrong common ancestor. Perhaps there is another common ancestor that we don’t know about. Then this could mess up the analysis. However, my assumption is that our genealogies are fairly complete. If there were other potential common ancestors between Robert and Virginia in our Ancestry Trees, then AncestryDNA would have picked that up in the Shared Ancestor Hints. Other people in this group may want to check other lines to see if there are any other shared common ancestors that have been missed just to make sure.

Future Plans

As Lorraine and Virginia seemed to have about 80 Pouliot Shared Ancestor Hints, it seems there must be others with Pouliot ancestry that have uploaded their DNA results to Gedmatch. It would be good to find further TGs to validate existing genealogies and perhaps even find some on the Pouliot tree that did not know they were there.

December 12, 2016April 13, 2017

A Toehold On the Paternal Side Butler DNA

In my last Blog, I visually mapped my father in law and his two sisters on their Chromosome 2. I was happy with the results as I got all their segments mapped on the maternal and paternal sides. I mentioned the difficulty in finding matches on the paternal side. The paternal match that I did have was not set in stone. It was somewhat inferred by email correspondence. I think of it as a construction job. The first few pieces of wood put in are a bit shaky until the rest of the structure is built around those first few pieces.

The Problem

The problem can be seen well at AncestryDNA. I have my Butler father in law tested at FTDNA, but his two sisters are tested at AncestryDNA. Here are Lorraine and Virginia’s Shared Ancestor Hints (SAHs):

Lorraine and Virginia Share 38 SAHs. I can tell this on my laptop that has Chrome as there is a icon for the shared Shared Ancestor Hints. All of Lorraine’s SAHs are on the maternal side (or locked). Of those maternal SAHs all but 2 or three matched on the Pouliot grandparent side. The other 2 or 3 were on the LeFevre grandparent side. An additional problem is linking those SAHs to gedmatch.

For Virginia, all her matches but one were maternal or locked. The one that was paternal was on the Kerivan side. No matches were found on the Butler side.

Following Virginia’s AncestryDNA Paternal SAH

Here is Virginia’s lone paternal SAH:

As can be seen above, this match is on Virginia’s Kerivan line.

the gedmatch connection: good and bad news

The good news is that Virginia matches someone at Gedmatch that seems to have a very similar name to the match at Ancestry.com. The bad news is that I have been unable to confirm that the two people are the same. However, I did think of an additional check. Lorraine did not match this AncestryDNA person. I opened up Gedmatch, found Virginia’s match. I ran the ‘One to Many’ utility for the match above who I will call Jeanette. On Jeanette’s ‘One to Many’ match list I saw Virginia and Richard but not Lorraine. That makes me feel 95% confident that I have the right person.

Jeanette’s matches with my butler in-laws

Here is the AncestryDNA match. It must be less than expected as the SAH shows third cousin once removed and the relationship predicted by the DNA is 5th to 8th cousin.

Jeanette and Virginia at Gedmatch:

Finally, Jeanette and Richard at Gedmatch:

Visual Phasing of Butler Chromosome 11

Based on the above results I would like to map Chromosome 11 for the Butlers using a method pioneered by Kathy Johnston. In the first step, I compare the three siblings, add approximate Chromosome locations for the crossovers and assign the crossovers to siblings:

I guessed at the 112 position as this was the border between a Fully Identical Region (FIR) shown in green and a Half Identical Region (HIR) shown in yellow. I can check this using the Full Resolution option at Gedmatch when comparing Lorraine to Virginia:

Each ^ is 1M, so the actual crossover from FIR to HIR is about 113. 4. It is close to the next crossover which is at 114.5M. For the assigned crossovers above, Virginia gets 6, Lorraine gets three and Richard gets one.

phasing strategy

While performing visual phasing, it is good to have a strategy. My strategy will be to include Richard in the first segment as he only has one crossover. By the way, one crossover means that Richard will have a complete unrecombined maternal or paternal Chromosome 11 from one of his grandparents. I could start where Richard and Virginia have their first FIR together, but instead I’ll choose the first place where Lorraine and Richard don’t match as there is more coverage in that lack of match stretch. The other thing to keep in mind is that the Rooney/Kerivan match is from 118 to 124M, so we will need to work our way to that side – likely by choosing a HIR in that area.

It looks like I could have chosen the first FIR and gotten the same results. A FIR (green) with two ‘no matches’ (red areas) over it like we have here is a good combination for mapping.
The Butlers have good coverage on this Chromosome.
I can already see that in the area of 118 to 124M Virginia and Lorraine have opposite grandparent matches. This shows why Virginia matched Jeanette and Lorraine did not.

Maternal matches

Before I continue mapping, I would like to see what this Butler DNA-tested trio have for maternal matches. They have two 1st cousins and two 2nd cousins that have tested. I entered all the cousins into Gedmatch, sorted them and took out everything except for how Richard, Lorraine and Virginia matched the cousins:

John is a nephew, so could match on the maternal or paternal side. Patricia and Joseph are maternal 1st cousins. However, that would not identify a specific maternal grandparent segment. The three siblings did not have appreciable matches with either of their 2nd cousins.

More Mapping

As the paternal Kerivan match is on the right hand side of this Chromosome, I’ll add a HIR between Lorraine and Richard. I did that by moving the blue for Richard to the right for the match with Virginia and for the part that didn’t match I put in green (opposite of red).

Once I set the HIR on the right, that meant that the blue area had to be Kerivan. That is the only place that Virginia and Richard have a matching color in the area of the Jeanette Kerivan/Rooney match (118-124). That leaves the purple to be Butler – the only other paternal grandparent.

This map leaves me with that ‘Swiss Cheese’ feeling. Before I scrap this map, let’s look at the 1st cousin matches to see if they can help fill in anything. They are the pink matches – signifying maternal.

Lorraine and Patricia match from 2 to 91. I take that to be the green match. I also assume that as they are first cousins, that their match length also represents the same grandparent. I’ll go out on a limb and say that I can extend the green to position 92.

This makes sense because Patricia starts matching Virginia at 77M. Before that she doesn’t match Virginia, so the maternal segment must be red for Virginia there. Actually, Lorraine’s green should extend further (to 114M) as she has no crossover until that point.

Here I moved Virginia’s red maternal segment to the right. Because the crossover was not on the maternal side it had to be on the paternal side. That gave her a crossover from Kerivan (blue) to Butler (purple) at 27M. The Chromosome is starting to fill in. Next, in the are from 39 to 77, Lorraine and Virginia don’t match. That means that Lorraine must have a blue Kerivan segment filling in at the top. Once I fill in Lorraine’s blue Kerivan segment, Lorraine and Virginia have a FIR (from 92-112M). That means I can fill in Virginia.

Now I’m almost done. I just have the last ever-difficult HIR to complete. Here my inclination is to check Patricia and Virginia at a lower threshold. If Patricia doesn’t match Virginia at the beginning of the Chromosome, then the red must carry through to the beginning for Virginia.

I was a bit surprised that the two cousins fit a match in the beginning of the Chromosome. I shouldn’t be surprised, because small matches are typically at either end of the Chromosome. That means the half match of the HIR is on the maternal side between Virginia and Lorraine. And the crossover is also on the maternal side.

How do I identify the maternal segments for chromosome 11?

I thought of a few things. One would be ICW which is an “in common with” feature that FTDNA uses. Or I could use the feature at Gedmatch which takes two people and finds people that are in common with them. I would be more satisfied with triangulated matches. The best way I know of to find these would be to start a surname study. Pouliot would be a good choice based on all the AncestryDNA Pouliot Shared Ancestor Hints that I mentioned at the beginning of the Blog.

December 10, 2016April 13, 2017

Visual Phasing Butler DNA on Chromosome 2

The Butlers are my wife’s family. Over a year ago, I wrote a Blog called “Uncle Naffy, DNA and the Butler Brick Wall“. In that Blog, I wrote about how a match with Uncle Naffy who is believed to be a Crowley relative helped in producing a breakthrough in the Butler genealogy. Uncle Naffy is a rare paternal Butler match. Most of the Butler matches have been maternal on the French Canadian side.

Visual Mapping of Chromosomes

Since writing the Uncle Naffy Blog, I have also become aware of a tool to map Chromosomes. This visual mapping procedure was developed by Kathy Johnston. As the Uncle Naffy match was on Chromosome 2, why not map that Chromosome? In order to map my father in law Richard’s four grandparents, I need his results and two siblings. Since my Uncle Naffy Blog, I have tested Richards two sisters: Lorraine and Virginia. When I compare these three siblings at their Chromosomes 2, this is what I get:

In the green regions, the paired-up siblings share the DNA from two of their same grandparents.
In the yellow regions, the sibling pairs share one grandparent
In the red regions, the sibling pairs share no grandparents in common. That means they have their DNA from the opposite grandparent pair.
The areas between the green, yellow and red regions with the vertical lines added are the crossovers.
The crossovers are assigned to the person who has the most shared crossover regions
The numbers added are the approximate positions in millions of the crossovers

assigning the crossovers

Lorraine gets the first crossover because she is the one in common in the first two comparisons where the match goes from green to yellow. The other crossovers are from the same reasoning. Richard is in the top and bottom comparisons.

Mapping three butlers

I start by using two colors where Richard and Virginia match representing their shared Fully Identical Region (FIR) shared in green. These two colors represent the same grandparents that Richard and Virginia inherited their DNA from – one on their maternal side and one on their paternal side.

Richard is stuck between his two crossover points (R) but Virginia can go out in either direction to her two crossover points (V):

By using other green areas or Fully Identical Regions (FIRs) and areas where pairs don’t match using opposite colors, I get this:

This leaves a few holes. At this point we need to select a Half Identical Region (HIR). It would be nice to get Lorraine to the right side as she doesn’t have any more crossovers there. Lorraine and Virginia share a HIR from 128 to 204, so we will pick one color from each on Lorraine’s row and extend those to the right. As I mentioned, she has no crossovers we know about there to stop her.

I can fill in a little more using the FIRs and no-match areas.

Now we have four relative grandparents without names in a lot of these three siblings chromosomes. Using known matches, we can fill some of these in. The paternal grandparents are Butler and Kerivan. The maternal grandparents are LeFevre and Pouliot.

Adding relatives

The best known relative for this purpose is a 2nd cousin. Richard and his sisters have two known second cousins on the Pouliot side:

Here, the Pouliot matches didn’t help, due to a blank space. The Uncle Naffy match, assumed to be a Butler match helped. There was only one place that it could go. That sets the paternal side and also will make the green be Kerivan.

What now?

At this point I have two options. One, I can look for more matches or I can try to re-do the mapping. I tried looking around Ancestry for more matches. There are plenty of Pouliot matches there, but it is difficult to trace them to Gedmatch, or perhaps the Pouliot matches are not uploaded to Gedmatch. Right now, we have a proposed match identifying the paternal side. It would be nice to somehow get both sides.

Second Try at mapping Chromosome 2

In our two reference matches, we have Richard. He matches Pouliot and he matches Uncle Naffy. Also Lorraine matches both those reference matches. So let’s work on our Lorraine/Richard matches, rather than concentrating on Virginia who didn’t have too many crossovers. Between 128 and 149 Lorraine and Richard don’t match. This will be represented by two opposite colors.

Next, expand the segments to the crossovers:

That is good because our segments are now over our reference matches (Richard is over the Pouliot match and Lorraine’s represented DNA is over her Butler match). Next we can use the relationships with Lorraine on the right to create new segments from their relative grandparents (no pun intended).

Now we have another problem, we need both Lorraine and Richard to be expanded to the blue and yellow matches. Perhaps if we extend Lorraine to the left with an HIR, then Virginia will be opposite of Lorraine and Richard oppose of Virginia, it will work out to fill in the segments over our reference relative matches.

There. Now all we have to do is match the Pouliot (blue) and the Butler (yellow). The only colors the same between Lorraine and Richard above the blue is green, so that has to be Pouliot which is maternal. That means that the maternal side Butler is now top bar. The only color on the top bar (or either bar, for that matter) that is the same over the yellow Butler match is purple.

But there is more that I can do. Notice on Virginia’s Chromosome. I haven’t moved her over to her left-most crossover. This should help fill in some more.

Note that two crossovers in a row in a HIR cause a problem such as the L-L on the left side and the V-V on the right. However, I’m happy with the results. I now have the first Chromosome with 4 Butler grandparents. This is based on the presumption that Uncle Naffy is a Crowley relative who is ancestral to the Butler side. Virginia will be a good person to look for Kerivan matches. Lorraine looks like the best shot for checking Butler matches on Chromosome 2.

Finding Crossovers by comparing first cousins

It appears that we can look at these three sibling’s maternal cousins (Pat and Joe) to determine more crossovers. Here are Lorraine’s matches:

The crossover between Lorraine and Patricia is not clear by looking at the first yellow bar. But look above. This bar has a break between 67.4 and 67.9M that is not visible. That tells me that the maternal crossover for Lorraine occurs at that location.

Other crossovers

For Lorraines’ first crossover position, I will need to look at the Gedmatch expanded view. When I compare Lorraine to Virginia, I choose the full resolution box and get this:

Each up arrow (^) is 1M, so Lorraine’s crossover is at 27M. A little further on the same comparison is the change from HIR to FIR:

I would estimate this crossover at about 36.7M. These are the numbers for Lorraine and Virginia’s first crossovers:

Note that Richard’s first crossover is very close to his sister Virginia’s. Here is a closeup view of Richard’s first crossover using his comparison to Virginia:

There is a ^ mark right in the middle of the HIR for Richard and Virginia. Counting back from 40, that mark is 37. The FIR starts up again about 37.5, so that will be Richard’s first crossover.

Richard’s relatives on the chromosome browser

Here is a comparison of Richard to a nephew, two maternal first cousins and two second cousins on the Pouliot side, John as a nephew, may match on the maternal or paternal side. He is the son of another sibling of this trio not tested. Here, he appears to match on Richard’s paternal side

I’ll add in that maternal crossover for Richard:

Then the HIRs are added in for Lorraine and Virginia:

Once Richard’s crossover was found to be on the maternal side, that required his sisters’ first crossovers to be on the maternal side also.

filling in virginia’s blank spot

We just have a little area to fill in past 200M for Virginia. Is her crossover paternal or maternal? Here is how Virginia matches her nephew, and two maternal first cousins. The numbers that we will be looking for will be 224 and 227.

What we see is 224M. That means to me that there is no maternal crossover at 227 as all the matches carry on to what looks to be the end of the Chromosome. Therefore the 227 crossover must be on the paternal (Butler/Kerivan) side. Here is the completed Chromosome 2 map.

One observation is that the trio of siblings comes up short on Butler DNA (purple) for about the first third of the Chromosome.

Here are my wife’s father’s four grandparents all born in the 1870’s:

Bonus Feature: My Wife’s DNA a la Blaine Bettinger

Blaine Bettinger recently wrote a great instructive 5 Part Blog on Visual Phasing. My Blogs are my muddling and meddling with DNA. Blaine’s Blogs on the other hand are instructive. Part Four of Blaine’s Series shows how to take the results of the parent (and Aunts in this case) and apply them to the child (in this case my wife). I’ll look at Blaine’s Part Four and apply it to my wife. Here is Marie’s Dad’s Chromosome 2:

This tells me where Marie may or may not be getting DNA. She will get half of her DNA from her dad, but that will be a full Chromosome. To the extent that she gets her dad’s paternal side what she gets will be only Kerivan in the first two thirds and Butler in the last third.

Marie compared to Aunts Lorraine and virginia

Here I copied Blaine’s format, but was tempted to add some vertical lines. The browser images compare Marie to Aunt Lorraine and her Aunt Virginia.

Marie has one empty bar which we hope to fill with her 4 paternal great grandparents. Comparing Marie to Lorraine, they share a segment and then they don’t. With Marie compared to Virginia, the two keep sharing the same segment apparently. This appears to be Pouliot as Lorraine has a crossover from Pouliot to LeFevre right where she stops matching Marie. One way to check this is by comparing Marie to her dad’s maternal cousin. Marie matches that cousin in this segment which agrees with my reasoning as Pouliot is a maternal match.

For the next segment, it appears I can use the same reasoning. Marie matches Lorraine and Virginia but this time Lorraine’s match drops off right where she has a crossover from Kerivan to Butler. That makes me think that the match there is with Kerivan. Another way to look at it is that it has to be Kerivan there as Lorraine and Virginia don’t share a common grandparent on their maternal side in that location. Marie has to have the maternal Kerivan DNA in that location.

The next segment has to be Kerivan or Pouliot. Marie matches Virginia there who has Kerivan DNA, so that has to be it. That extends Marie’s Kerivan DNA. Next is the largest segment. Marie matches neither of her Aunts in that segment. The only grandparent that her Aunts don’t match in that segment is Pouliot. So far, Marie has no Butler nor LeFevre DNA:

In the next to the last segment, Marie does not match Virginia. That leaves her with Butler or Pouliot DNA. However, that is not helpful as Marie gets Butler or LeFevre from her father. Marie matches Lorraine, but that also could be Butler or LeFevre. It’s a split decision. In the last segment, there is a clue. Virginia matches Marie for Virginia’s entire maternal LeFevre segment. So that has to be LeFevre. If it was a Butler match, it wouldn’t be the entire segment as Virginia has some Kerivan in there that Marie could not have inherited from her father in that location.

Let’s try to reason through the empty space again.

Lorraine – matches on either Butler or LeFevre
Virginia – doesn’t match on Kerivan nor Pouliot which leaves, again, Butler or LeFevre
Richard – has on Butler or LeFevre

I suppose that this segment would more likely be LeFevre than Butler as larger segments are the rule more than smaller ones between father and daughter, however, I have no certaintly with that, so I will leave the segment blank for now.

The maternal cousins to the rescue

It’s time to bring back Pat and Joe. They are Marie’s father’s maternal first cousins. Here is where Marie matches them:

Due to the fact that Marie matches both of her father’s cousins at 222M before Virginia’s crossover at 225M means that Marie has a maternal match in that area. Here is Marie’s Paternal Chromosome 2 filled in:

Marie appears to be Butlerless or Butler free in Chromosome 2. This is a good example showing that Marie got exactly half of her DNA from her father and half from her mother. However, when we consider her Paternal Chromosome 2, she does not get 1/4 from each of her paternal great grandparents. She got 0% from her Butler great grandparent. She also got roughly 1/3 from her paternal grandfather and 2/3 from her paternal grandmother.

Back to Uncle Naffy

This brings the story full circle. I started this Blog based on a few large matches with Uncle Naffy. Uncle Naffy’s family stories lead me to believe that he was related to the Crowleys. A Crowley married the first Irish immigrant Butler in my wife’s line. I identified the Paternal Grandparents in the visual phasing in this Blog based on the assumption that Uncle Naffy was indeed a Crowley descendant. So, ironically, Uncle Naffy’s match results lead to the mapping of my father in law and his sisters’ Butler DNA which lead to the conclusion that my Butler wife Marie had no Butler DNA in her Chromosome 2.

Summary and Observations

The maternal side of these Butlers chromosomes are easier to map than the paternal side due to lack of verified paternal matches
The paternal side match with Uncle Naffy has not been linked to a tree, so will have to be verified at some point.
Having cousin matches made it possible to fill in this map. Otherwise it would still have blanks.
While writing this, I may have found a Kerivan ancestor match. I will follow up on that and likely write another blog on what I find.
Once some good Kerivan and/or Butler matches are found, they will likely lead to other verified matches on those lines. It is difficult to break through and get those first identifying paternal matches.
I had thought that my wife’s DNA results were somewhat obsolete after getting her parents’ results. Now I see that I can map her great grandparents thanks to Blaine Bettinger’s instructive Blog.

December 6, 2016April 13, 2017

More Dicks (and Joyce) DNA from Newfoundland

Thanks to the Newfoundland Gedmatch Facebook Group I recently ‘met’ a new Dicks descendant who had DNA tested. Trudy is from the Joyce Line of Dicks like many other in the Dicks DNA Project.

Trudy is in the bottom row of green DNA tested Dicks descendants. She is 7 generations away from Christopher Dicks b. about 1784. This is the main Dicks Line that I have been looking at. However Christopher had a brother of interest also named Henry.

Seven generations is a long way away for autosomal DNA, but we will see what Trudy’s DNA shows us. As alluded to in the Blog Title, Trudy also has Joyce ancestry.

On a certain day in the early 1800’s Rachel Dicks married James Joyce. They had at least seven descendants that had their DNA tested. And of course they had many descendants that didn’t have their DNA tested. Trudy’s closest relative in the chart above is Pauline. They are 1st cousins once removed.

Here is how Trudy matches the other Dicks descendants with tested DNA:

That is a bit small, isn’t it? This shows no matches to the Henry Dicks Line, so we won’t need to look at them in this Blog. We can stick to the descendants of Christopher Dicks b. 1784.

Triangulation Groups

I tend to focus on Triangulation Groups (TGs). These are groups of people that match each other on the same segment. When this happens, it is a sure bet that the people in the TG have a common ancestor. There should be potentially two types of TGs that Trudy would be in: new ones and existing ones. The existing ones may tell us something, but the new ones should be more interesting. In addition, there is the possibility that Trudy could be in a Joyce TG, a Dicks TG, or even one from a different surname.

Downloaded segments

First, I download the matches of all the Christopher Dicks descendants and compare them. So I’m not re-creating the wheel, I’ll reproduce my TG Summary from a past Blog:

The first interesting thing I see in my downloaded segments is here at the end of Chromosome 1:

Trudy is in a TG with Esther and Forrest. Esther is my wife’s 1/2 great Aunt. Note that Judy and Wallace are not in this TG. They have plenty of other places to have their DNA match as they are niece and uncle.

As far as I know, Esther, Trudy and Forrest all share the DNA from Christopher Dicks and his wife Margaret, so that is what it looks like this shared segment is (unless anyone else knows of a different shared ancestor in each of their ancestry).

The next interesting TG in chromosome 4

Here I see Nelson, Molly and Trudy in a TG. This TG will be a little more challenging. Howie would also likely be in the TG if we were to lower the limits. One of the challenging things about this TG is that Molly descends from two Dicks Lines:

Nelson is from the Adams Line. Trudy is from the Joyce Line. Molly is from the Joyce and Cran Line. Nelson is Trudy’s 3rd cousin, three times removed. Nelson is Molly’s 3rd cousin, twice removed. Molly is Trudy’s 4th cousin once removed and 5th cousin, once removed. My guess is that Molly is related on the Joyce line as that would be closer to Trudy, but there is no way to know with certainty.

Moving right along.

Chromosome 5 TG – The Joyce family

Here I believe I see a Joyce TG:

Pauline, Molly and Trudy all descend from the Joyce Line. Within that TG is another TG with Wallace, Joan and Esther. I had to take the match between Wallace and Esther down to find it, but it was there. Then again, we see the close Judy/Wallace relationship. They could match with Lewis DNA, for example.

Untangling Chromosome 15

Here is a TG with Trudy, Esther and Howie (Molly). Think of Howie and Molly as a tag team. As siblings, their DNA can be interchanged in many situations. Here we are missing a match between Esther and Molly. However, it would have to be there at a lower threshold.

There is a lot of mystery in this TG. I assume that the TG is Dicks. However, Molly and Howie are from 2 Dicks Lines and Esther has Dicks on her father and mother’s sides. On Esther’s mother’s side, I don’t know where her Dicks ancestors come from.

Here, the only unambiguous line (as far as I know) is between Trudy and Christopher Dicks by way of the Joyce Line. For Esther, Marilyn and Howie I am not as sure. Sandra and Cheryl listed above are both from the Adams Line of Dicks, so that is a likely source of shared DNA for those two.

TG Summary

This chart is getting large:

Trudy is in 5 TGs. I think that 4 of them are new. Two of them appear to be Joyce TGs and three Dicks TGs.

December 5, 2016

More Nicholson DNA

I am happy that my Nicholson cousin Joan had her sister Linda DNA tested. Here is my mom’s tree showing people that have tested their DNA:

Linda and Joan share a red box as they are sisters. Most of this tree is on my mother’s mother’s side. The blue is her father’s side. On my mother’s mother’s side, yellow represents Lentz, red represents Nicholson and orange represents cousins that have Lentz and Nicholson ancestry.

Comparing DNA at Gedmatch

When I compare all the people above at Gedmatch, this is what I get for overall matches:

Linda, who recently tested, matches my mom less than her sister does. However, she matches cousin Judy more. The chart also shows that 4 of the people in the group are Nicholsons and not Lentz. One is a Lentz and not Nicholson and three are Nicholson and Lentz. However, our Lentz tester, Albert, had low results – which were consistent with the distant relationship. From the above charts:

If Carolyn, Joan and Linda match each other, it may be from a Nicholson or Allen DNA
Where Carolyn, Joan, Linda, or Nigel match Joshua, Judy, or Mom, it must be from Nicholson DNA
Where Joshua, Judy or Mom match each other only, it could be from Lentz or Nicholson DNA.
Where Joshua, Judy or Mom match Albert it would represent Lentz DNA

Looking for triangulation

Next I looked at the detailed matches between all the DNA of the people above. The purpose is to find triangulation. A Triangulation Group (TG) is three or more people that have matches along the same segment of a Chromosome. This TG indicates a unique common ancestor.

Here is a summary of past five TGs I have looked at:

Lentz only – Yellow
Nicholson only – Red
Lentz/Nicholson – Orange

any new TG’s due to linda?

Here are some of the new DNA matches that I downloaded from Gedmatch at Chromosome 5 from about 39M to 84M:

It looks like there should be a TG here somewhere. Looking through my old Blogs, I see that I did previously identify a TG at Chromosome 5. It looks like we have a TG with Carolyn, Joan, Mom and Linda. But what about Joshua and Judy below? I didn’t do a detailed analysis, but the both descend from William Lentz b. 1892 and Clementina Hodder. So their match is likely on the Hodder side.

unraveling chromosome 8

Here is what I have at Chromosome 8 from about 102 to 143M

Here for some reason, we see the number 133 repeated and it is associated with Carolyn. Here is what Carolyn’s Chromosome 8 matches look like on Gedmatch’s Chromosome Browser:

Linda
Judy
Joan
Mom

Note that my mom (4) doesn’t overlap with Linda, Judy, or Joan, but matches with Carolyn up to 133M. What does this mean? I will give a possible explanation.

Remember that a TG represents a specific ancestor. However, we don’t know if it is William Nicholson or Martha Ellis in this case. Let’s suppose that the TG for Carolyn, Judy, Joan and Linda represents Martha Ellis. I have that TG represented in dark circles and lines. That means that before 133M would represent where Carolyn (and my mom) got their William Nicholson DNA that they shared with each other. That relationship I have represented above in light blue circles. The other explanation would be the exact opposite scenario where Mom and Carolyn share the Ellis DNA and the others share Nicholson DNA. In order to know for sure, we would have to have someone who is a Nicholson but not and Ellis or Ellis but not a Nicholson to check.

A less likely scenario would be that the starts and stops at 133M for Carolyn are coincidences.

Updating the Triangulation Group Summary

I didn’t add Linda in every case as sometimes her results were the same as her sister’s results.

Revising Mom’s Chromosome Map

Based on Mom’s new matches with Linda representing William Nicholson and Martha Ellis, here is her new Chromosome Map thanks to Kitty Munson’s software:

I have put mom’s ancestors in chronological order with most recent ancestors on the top. This has made the William Nicholson b. 1836/Martha Ellis segments show up in a better color also.

December 2, 2016April 13, 2017

Mapping My Chromosome 20 Using My Raw DNA Results

In a past blog, I mentioned My Big Fat Chromosome 20. That blog is also referenced on the ISOGG Chromosome Mapping Page. This particular Chromosome had puzzled me for a while due to the preponderance of matches I was getting there. I used visual phasing and determined that the overload of matches was on my paternal grandmother’s Frazer side rather than the Hartley side. I had previously supposed that the Hartley side held the key to all my matches as that side had colonial Massachusetts roots. Since that time, I had my brother’s DNA tested. He is shown as F in the bottom row below. I thought that his results might add some clarity to Chromosome 20.

Rather than clarifying things, I just got a shorter version of what I already had for Jon (F) than I had for myself (J) and my two sisters. The problem is the phenomenon of close crossovers at the beginning and end of each chromosome. Jon also has quite a few matches in Chromosome 20 (unlike my sister Sharon who had Hartley DNA in most of her paternal Chromosome 20). He has almost 30% of his phased matches there according to his match spreadsheet based on Gedmatch.

Going to the Source – Raw Data Phasing

I have been learning how to phase my raw data based on a Whit Athey article, MS Access and the work that M Macneill has done. The Whit Athey Paper describes how to manipulate the raw DNA data of one parent and four siblings to get Dad Patterns and Mom Patterns. I have found these patterns to be useful.

Dad Patterns

Even though my dad never had his DNA tested, based on the certain principles, I have come up with a spreadsheet that shows for various sections of the chromosomes matching patterns that I have with my other three siblings. I use A’s and B’s to give a generalized pattern. The patterns will be in the order of Joel, Sharon, Heidi and Jon. Here is my Dad Pattern spreadsheet showing Chromosome 20:

I find my gap to next column handy. The first thing that I notice is that there are not many large gaps. If there were very large gaps, that might indicate an AAAA pattern where all the siblings match (in this case a paternal grandparent). One thing that I added today is a Start and Stop. This is the first and last tested position of the Chromosome. This is good to know in case a pattern is hiding at the beginning or end of the chromosome. Let’s just look at the second line of the spreadsheet. This shows that there is a pattern of ABAB from position 0 to 10M. This means that the first and third people (Joel and Heidi) match the same paternal grandparent and the 2nd and 4th siblings (Sharon and Jon) match the other paternal grandparent.

In the third row of the spreadsheet, a new paternal pattern starts (at 10M). This is ABAA. Now sibling 1, 3, and 4 (Joel, Heidi, and Jon) match each other. The difference between ABAB and ABAA is in the last position where I have Jon. He switched from a B to an A and now no longer matches Sharon, but he does match his other three siblings on the paternal side. As Jon is the one that changed, he gets the paternal crossover at this position.

A few other notes

These patterns are gradual. That means that there can be only one change at a time.
If it looks like there are two or more changes, then either something was done wrong or you have to invert the A’s and B’s
For example, above in row 4, I have an AABA pattern that goes to and ABAB. On face value, it looks like three changes. However, AABA is the same as BBAB. Actually it is the first B changing to an A. This is my position A, so I have a crossover around 54M on the paternal copy of my Chromosome 20.
These areas of patterns are also used to fill in bases received from Dad or Mom in the particular areas that the patterns occur in each chromosome.
If there are only three siblings tested, these patterns are not as informative.

Mom Pattern spreadsheet

I would not want to leave mom out. Here is the pattern of her 4 children matching on the maternal side:

Like the Dad Pattern Spreadsheet, everything looks well behaved as there are no large gaps between patterns. Also there are no gaps at the beginning or end of Chromosome 20. So there you have it. That is the phased DNA for myself and my other three siblings. But it doesn’t jump out at you and I don’t have a map yet. That is where I bring in the MacNeill <prairielad_genealogy@hotmail.com> Spreadsheet.

MacNeill’s Excel Spreadsheet

I adjusted MacNeill’s Chromosome 1 spreadsheet by replacing default numbers for Chromosome 20. Then I added in the locations I had in the spreadsheet above. Those are the Start36 and Stop36 columns. The 36 refers to Build 36 locations which Gedmatch uses. After that I colored in the bars to be consistent with the visual phasing I had done previously.

Actually, I now see that I colored Sharon’s paternal bar backwards. She should have mostly Hartley (blue). This transposition also carried through to the next image, but I corrected it in the final image. I like having labels, so I copied this into PowerPoint and added some:

Next I add any appropriate cousin matches for Chromosome 20. I also made the sibling names on the left a little bigger. My mistake above on Sharon’s paternal bar is corrected and verified by her large paternal Hartley cousin match with Jim below.

I had to bring this back into PowerPoint to re-add the surnames. The places where the cousin matches start or stop may be crossovers for me and my siblings. From comparing the top part of the chart to the bottom, it should be obvious which crossovers are for me and my siblings and which are for the cousins. The good news is that the raw DNA phasing confirms my initial visual phasing done in January, 2016. The raw DNA phasing just filled in what I was unable to. The other good news was that there were significant cousin matches on both the paternal and maternal side of Chromosome 20 to make sure that all the grandparents were identified correctly. Since I did the original visual phasing last January 2016, I have gotten the DNA results of 2 more cousins. Also one additional cousin who previously had her match to only me at 23andme uploaded her results to Gedmatch.

Notes/Summary

The hard work in Raw DNA phasing is assigning all the bases of the siblings to the correct parent. Then patterns are discerned and noted.
The fun part is mapping out the results.
Raw DNA phasing and mapping is more accurate and complete than visual phasing. However, it takes a lot of work and works best when there is at least one tested parent.
The comparison of the raw DNA mapping to the actual cousin matches points out the fuzzy boundaries noted by others. This may be seen in Sharon’s short Lentz segment. Her cousin Judy match (who has Lentz ancestry) appears to exceed the length of Sharon’s Lentz segment.
Out of the four siblings, Sharon is the one who didn’t get the huge dose of Frazer ancestor matches. That means that she would be the best for looking for smaller matches at Gedmatch.com. Her smallest match is 9.3 cM (5.9 Gen) and my smallest match at Gedmatch is 10.7 cM (5.2 Gen).
At a glance, one can see who is the best person for finding matches with each of the four side of the family. For example, I received a full dose of Lentz DNA on Chromosome 20. Here is my Lentz grandmother (b. 1900) in her younger days. Her DNA is represented in yellow in the charts above.

November 29, 2016

An Ancestry/Gedmatch Success Story: Lentz DNA

This story starts with a plain genealogy match – just the tree. Al contacted me last April through Ancestry about our possible Lentz connection. I suggested a DNA test. We went back and forth and saw that our Lentz locations, names, occupations and churches sounded familiar. We decided that we had a common ancestor in John Lentz born 1792. Here a portion of my Lentz web page:

Al descended from William while I descended from Jacob. Where I left off with William Andrew, was about as far back as Al had gotten.

Lentz DNA

In early July I noticed that Al had an AncestryDNA match with my mom. It wasn’t large, but it was there:

This was good news, as my Lentz DNA documentation was sketchier than I thought it should be. Maybe sketchy isn’t the right word, but there were some ambiguities. I had trouble nailing down John Lentz as it appeared that there may have been two of them in the same area.

Here is the connection between Al and my mom:

The Lentz side is in yellow. My previous Lentz DNA testers were also part of the Nicholson family (in orange above), so Al was an important link to the non-Nicholson Lentz side. Al is in the bottom left box.

upload to gedmatch

My next step was to ask Al to upload to gedmatch. Sometimes this step is easy, sometimes not. Al had trouble uploading but just recently, I discovered that he had actually uploaded his results. When I checked the results, there was no match between Al and my mom. I had to lower the thresholds to find the match:

The interesting point here is that I would have never seen Al’s match with my mom at Gedmatch, because their match is below their threshold.

yes, but do we have triangulation?

If Al were to match with another person that matched my mom, we would have a triangulation group (TG) which would make this match all the more solid. Fortunately, one of my mom’s first cousins, once removed also uploaded her 23andme results after some initial problems many months ago. I had to lower the thresholds even further to get her match, but it was right where it needed to be for triangulation:

In order to close the loop, Judy had to match my mom at this location. This was not a problem:

My conclusion is that the TG merges in on John Lentz:

Technically, the match could be with John Lentz or his wife Elisabeth, but we will say John Lentz. Further, I am now able to identify the match on Chromosome 14 between my match and Judy as a Lentz match – or more specifically from my mom’s grandfather Jacob Lentz:

Here is Jacob with bow tie and cigar:

How AncestryDNA and Gedmatch Worked Well Together

AncestryDNA told me I had the match. They also provided a way to get in contact with someone with the same ancestry. However, Ancestry says this about the match:

They thought that Al and my mom would have what I would assume to be a 15% chance of having a recent common ancestor or couple (John Lentz and his wife Elisabeth). That is where Gedmatch came in. If I could show that Al, my mom and someone else triangulated, that should significantly up the odds that there was indeed a common ancestor. Due to Al and Judy uploading to Gedmatch, I found that to be the case.

November 29, 2016April 13, 2017

Solving Joanna’s Mystery DNA Match with Visual Mapping

Recently I had a question from Joanna, who is part of a Frazer DNA Project that I’m working on. She has a large mystery match and would like to know which side of the family the match is on. Joanna is also interested in having her chromosomes mapped using Visual Phasing. Visual Phasing is a method that Kathy Johnston has pioneered using the DNA results of at least 3 siblings. Blaine Bettinger has also written a 5 part series on this subject. Perhaps the mapping could help her find out what side of her family this mystery match is on.

Joanna’s Mystery DNA Connection with Mystery Vickey

Joanna’s siblings are Janet and Jonathan. I will check Gedmatch.com to see how the three siblings match up with Vickey.

On Vickey’s One to Many list, I saw Joanna and Janet, but not Jonathan. You can see why Joanna is interested as her match with Vickey is 55 cM. I didn’t want to leave out Jonathan, so I ran a One to One between him and Vickey at Gedmatch;

Jonathan does match Vickey, but he just fell off the bottom of Vickey’s One to Many List. The start of Jonathan’s match is at the start of Joanna’s orange bar above. His match with Vickey ends before his sister Janet’s match with Vickey starts. Now, in Joanna’s family we have a small, medium and large match with Mystery Vickey.

Visual Mapping of Joanna, Janet and Jonathan

As all the above matches are on Chromosome 13, it would make sense to start there. The first step is to compare the 3 siblings in the Gedmatch Chromosome Browser:

I then added crossover lines and attempted to assign the right sibling or siblings to the right crossover. This Chromosome was not simple. It looks like there are or could be close crossovers in three different places – around position 29, 33 and 98. In addition, something strange seems to be going on at the 72/73/74 location. That leaves only 2 crossovers which appear to be less than complicated. Those are: the first crossover which I have given to Jonathan and; the crossover at 62 which I gave to Janet.

Mapping the JJJ siblings

From 33 to about 73, Joanna and Jonathan have a Fully Identical Region (FIR). That means in that area, Joanna and Jonathan got their DNA from two of the same grandparents. One of those grandparents was on their Paternal side and one on the Maternal side.

Above I’ve portrayed Joanna and Jonathan’s shared grandparents as blue and red. The next step is extending the blue and red bars. I’ll keep Jonathan’s two grandparents where they are as he has crossovers on either side. However, I’ll extend Joanna’s DNA from her 2 grandparents to the right. Should I extend them to 98 or to the end?

A single or double crossover at 98?

The simplest scenario at Position 98 would be a crossover assigned to Joanna. Joanna is the common factor in the first two comparisons, so that would make sense. In that scenario, neither Janet nor Jonathan would have crossovers at 98. However, that does not appear to go along with what we know. Recall above that I looked at Vickey’s match with Joanna and Janet:

Why isn’t Janet matching Vickey for 55 cM as Joanna is? Something happened around Position 97. That something has to be a crossover for Janet. That sets a few things in motion. Now that we know Janet has a crossover, that means that Jonathan also has a crossover there. Our two options at 98 were either a single crossover for Joanna or a double crossover including Janet and Jonathan. My conclusion:

Janet has a crossover at 98
Jonathan also has a crossover at 98
Joanna does not have a crossover at 98

The immediate result is that I can send Joanna’s DNA over to the right side of the page:

In the next step, I want to take advantage of the Joanna to Janet FIR and the places where siblings don’t match at all. This is where there is red in the Browser and no blue bar below. In these areas I will use two different colors.

The Irony of Vickey’s match

Next, I’d like to use Vickey’s match with Joanna and Janet set the crossover at position 98. We will now pick a ‘side’ to the colors. We will say that Vickey is a red match. In the area between 62 and 98 Joanna and Janet are in a Half Identical Region (HIR). That means that they have one grandparent in common our their four. The irony is that we are mapping this Chromosome to find out where Vickey fits in. Yet we are first using Vickey’s match to map the Chromosome.

Here I have added in Vickey’s matches with Joanna, Janet and Jonathan. Note that Janet’s match with Vickey starts right near her crossover. Before that, Janet matched another of her four grandparents (shown in yellow). Also Jonathan’s match with Vickey ends right by his crossover where he received his DNA from another grandparent (the same yellow). Now we have Joanna and her two siblings’ Chromosome 13 roughly mapped out. We have relative positions for their four grandparents. Can we now find out which of Joanna’s grandparents the Mystery Vickey is related to?

Finding Which of Joanna’s Grandparents Matches Vickey

In January, 2016, I wrote a blog about Joanna and her Chromosome 15. Here are the results I came up with (after I went back and corrected a mistake I found):

I show this to indicate the possible grandparents that Vickey could be related to. Chromosome 15 was also a much easier Chromosome to analyze. There were only three crossovers for Joanna and her siblings on Chromosome 15. The 90-97 area was where Joanna matched a Williams relative. From 67-92, Joanna and Janet matched Frazer relatives.

For Chromosome 13, however, the [maternal] Williams relative did not match with Joanna, Janet and Jonathan. So it will not be possible to make determinations on Joanna’s maternal side. There were, however matches on the Frazer side. Betty has not uploaded her results to Gedmatch, but she is on FTDNA which has a browser and gives Chromosome match locations. Betty is our last chance to at least identify the paternal part of Joanna and her siblings’ Chromosome 13. Fortunately, Betty matches Joanna twice and Jonathan once:

Now all I have to do is see where Betty’s DNA would fit on our Chromosome 13 Map.

It looks like Betty has shown that Vickey is related somewhere along the line of Frazer – or more specifically Edward Frazer born in 1867. Here are a few notes on what I did:

I extended Jonathan’s Seymour DNA to the right as he had no Frazer match there where his two sisters did. They both matched Vickey. Then I added a blue segment above Jonathan’s yellow segment as Jonathan has a HIR with his two sisters at the end of Chromosome 13.
Question: Why didn’t I match Betty to the blue maternal side of the Chromosome? There is room for her DNA there also.
Answer: Imagine that I moved all the Betty matches up to the blue segments. That would leave a problem for Janet. In that scenario Joanna would have a blue match and Janet would also have to have the same blue match, but Janet didn’t match Betty from 75-96. Janet also did not match Vickey from 63-107. So that alternative scenario does not work out.
For more distant relationships, one would not want to make deductions based on lack of matches. However, with siblings there has to be an explanation as to why one sibling would have a match and the other would not based on the visual mapping.

Edward Frazer is wearing a top hat at the bottom right. In our Chromosome 13 Map, his DNA is shown as red and his Seymour wife as yellow.

The fact that Vickey matches on this Frazer line doesn’t mean that Vickey has to have Frazer ancestors. It just means that she and Edward Frazer must have a common ancestor. That common ancestor may be along the Palmer line, for example (Edward Frazer’s mother’s Line).

Betty to the rescue again

Let’s use Betty’s results to fill in the rest of Joanna’s family’s Chromosome 13:

Note that Betty matches Joanna from 29-43 and Jonathan from 33-43. That tells me that Jonathan has a paternal crossover at 33. Because Joanna doesn’t have a paternal crossover at 33, that means she has a maternal crossover there. The rest I fill in using the FIR and HIR regions.
The smaller segments at the beginning of the Chromosome correspond with all the crossovers at the beginning of the Chromosome. There are 5 crossovers up to position 33. In Chromosome 15 that I mention earlier in the blog, there were 3 crossovers for the whole Chromosome. After position 33 on Chromosome 13, there are fewer, more spaced out crossovers which account for the larger segments of inherited grandparent DNA.

Summary and Conclusions

Visual Mapping can be fun and helpful in finding out where mystery matches come from
Without the help of Joanna’s 2nd cousin Betty, we would not have a complete map. We would also not be able to know which grandparent Vickey was related to.
If Betty’s results were only at AncestryDNA, we would not be able to do this analysis as AncestryDNA does not give detailed information on DNA matches. The fact that she tested at FTDNA helped us come to these conclusions, even though her results were not uploaded to Gedmatch.com
Joanna may know of more test results with known relatives that could help fill out the maternal side of Chromosome 13 or we may find out more in the future.

November 21, 2016April 13, 2017

Using M MacNeills Raw DNA Phasing Spreadsheet and My Problem Chromosome 10

I have written many blogs about phasing my own raw DNA. One of the things that was bothering me while going through the process was the presentation of the results. It is possible to phase millions of bases using the raw DNA results from one parent and at least 3 siblings. But once the DNA is phased, how can those results be best portrayed? In my previous Blog on the subject, I was able to figure out a fairly simple way to show my results, but the outcome was not totally satisfactory.

I liked how I was able to get the grandparents’ surnames at least in the first 2 bars. I also liked how I had a simple scale at the bottom. However, one of my bars went too far. Also, my simple chart started at zero and Chromosomes start at different positions. I was able to fix the bar going too far today. Excel makes these bars based on distance rather than positions, so one of my equations was wrong.

I told M MacNeill <prairielad_genealogy@hotmail.com> of my concerns and he sent me his spreadsheet. One feature I really liked about the MacNeill Spreadsheet is that it had a place for cousin matches at the bottom. Below is the first Chromosome where I used my phased raw data from my mom and 3 other siblings to create a MacNeill Chart.

Sharon’s maternal first little segment didn’t work out perfectly, but that didn’t bother me. I know that the beginning and ends of Chromosomes can have small problematic segments. Note at the bottom that my match to Carolyn in yellow shows where my maternal crossover is in the upper part of the chart where I go from red to orange.

My Chromosome 10

I am looking at my Chromosome 10 because, for one thing, I have had trouble trying to visually phase this Chromosome in the past. Here is my attempt at visual phasing from early in 2016:

Here is another try including additional cousins that tested:

Note how different the maternal (lower) side is. I switched most of the maternal grandparents around.

Here is the MacNeill spreadsheet showing just the cousin matching part:

I have some good matches here. Blue is Hartley, green is Frazer, yellow is Lentz. Red is Rathfelder. This makes it clear that my chromosome is mapped wrong. I need more Hartley and Lentz. The above chart includes my brother who I had tested not too long ago.

Here is another try with my brother’s DNA results included:

My sister Sharon (S) has a better look now on her maternal side. I got rid of the small purple segment.

Looking At the Raw DNA Phasing – Paternal Side

I have two spreadsheet summarizing the results of the many hours of work it took to phase my family’s DNA from the raw data. One spreadsheet is for the paternal side phased DNA and the other is maternal. I have patterns for both sides. They are based on the order of my siblings: me (Joel), Sharon, Heidi and Jonathan. So an ABBB pattern would mean that Sharon, Heidi, and Jonathan all get their DNA from one grandparent, and I get mine from the other. Here is the paternal spreadsheet:

These patterns go logically one to the other. The first pattern goes from AABA to AAAA at position 2,605,158. The B changed to an A in Heidi position, so the crossover goes to her at that position. I have a column called GaptoNext. This is based on the number of tested SNPs between patterns. When this number is large, I suspect an AAAA pattern. That was the case above highlighted in yellow. Except there is a problem. To go from ABAB to AAAA means 2 changes, and there should only be one change (or crossover) at a time. This caused me to look at the bases.

A Paternal pattern missed

Here is what I found.

I had missed an AABA pattern at Build 36 Position 30,683,878. I took another look by setting my MS Access query so that Sharon and Heidi would have a different base from Dad:

This shows that the there is a change from ABAB to AABA even sooner than I thought between ID 400008 and 400045. This is an ID I created that sequentially numbers the tested SNPs. You can see another way I missed this pattern, because I didn’t fill in the missing bases. TTC? should be TTCT. CCT? should be CCTC.

What does the missing pattern represent?

The pattern of ABAB TO AABA is actually my crossover (Joel). It is a bit more difficult to see than the others. That is because the ABAB pattern is the same as BABA. The change of BABA to AABA is my change of the first B to the first A. Naturally, I put myself in the first position. In rough terms, that gives me a paternal crossover at about position 30.5M. This is a good location as it does not interfere with a large match that I have with an unknown paternal DNA relative named Shamus:

Here is my corrected Dad Pattern for Chromosome 10:

I have gone from 6 to 8 crossovers as the previous correction lead to another one. I also took out one of Heidi’s crossovers that I had wrongly identified. So fixing one problem fixed a lot of others. It helps to describe the start and stop of each pattern and to describe each crossover. The important results are the person and the last Position column. These show who the crossover belongs to and where that crossover occurs on the chromosome. I then entered the paternal crossover results into the MacNeill Spreadsheet and got this:

I took out the large space between the siblings. The problem is that the space is now the same as between the maternal and paternal phased part for each sibling. Excel has no happy medium that I’ve found.

The blue is Hartley and green is Frazer. The raw phasing in the upper part of the chart matches with the cousin matches below. It is interesting that some of the cousin matches define the crossovers. For example, the Jim to Sharon match gives Sharon’s crossover. Also the Paul to Sharon match gives Sharon’s other crossover. The Paul to Jonathan match gives Jon’s first crossover.

The Maternal Side

Hopefully resolving the maternal phasing will be easier than the paternal side. My visual phasing only showed four crossovers. Here is my unfinished spreadsheet showing 5 crossovers (under the Person column):

Here, it looks like I already added an AAAA pattern to the end. That was because the AABA pattern ended at about 114M and the Chromosome itself ends at about 135M. My GapstoNext column showed that gap as almost 20,000 SNPs. My question now is: should I add an AAAA pattern to the beginning also? Perhaps. An AAAA pattern means that 4 siblings match and all got their DNA in that area from their maternal (in this case) grandmother. Those results were consistent with how I had the visual phasing done. In fact, the visual phasing indicated that the 4 siblings should all get their maternal DNA from the Lentz side up until about 60M. Let’s take a closer look. This gets at my first note above in the spreadsheet image. There were only 3 single SNPs showing the AAAB pattern and they were spaced a long way apart – over 10 Megabases each. In this case, I will disregard those 3 widely spaced patterns as some type of mistake and stay with the AAAA pattern. Once I made the change from the AAAA pattern to the AAAB pattern, that brings us up to about 60M for my (Joel’s) first crossover. That seems to fit well. That leaves us with 4 crossovers – one per sibling as opposed to the two per sibling on the paternal side.

First I’ll compact the Gedmatch browser results, then show the raw DNA Phasing results on the MacNeill Chart:

When I compare the results, I see a problem I had with the visual phasing. The next to the last crossover looked to belong to Sharon, but instead it belonged to Heidi. Also Jon’s second paternal crossover should have been marked as an “F” above. That was just a typo. The third J for Joel crossover that I had above was not a crossover. In the middle, the 2 close crossovers of J and S should be instead S and J if I’m reading the MacNeill Chart correctly. It looks like all the FIRs and HIRs, etc. match. Once I did the raw DNA phasing, it is obvious how the gedmatch browser results had to match the raw DNA phasing results. Before, I did the raw DNA phasing it was not so obvious.

I’m happy with the results. I get to pick whatever colors I want for the four grandparents. It still would be nice to have some sort of labels or color key. After a hard day of phasing DNA, it is rewarding to see the results displayed so nicely. Thank you Mr. MacNeill.

A few observations:

The 4 siblings did not inherit any Rathfelder DNA (brown) on the left side of Chromosome 10
Lentz DNA (yellow) is missing from the right side of the Chromosome for the same 4 siblings
As I have my mother’s DNA results, that would make up for the missing DNA from those 2 maternal grandparents
Short segments of Hartley DNA (blue) are missing near the beginning and near the end of the Chromosome (i.e. none of the four siblings inherited Hartley grandfather DNA in those areas).

Summary

M MacNeill has the best display that I am aware of for mapping phased DNA.
The final mapping is like the final exam where previous mistakes are brought out, but there is a chance to correct them.
The phasing process is difficult, but there are built in checks and balances to find and correct mistakes or missed patterns.
The raw DNA phasing procedure (I use the Athey method) would generally be used if a parent has been tested and the visual one is used if a parent has not been tested. However, the visual phasing as developed by Kathy Johnston is important to use as a framework for the raw DNA phasing as well as a check for the end result.
The raw DNA phasing results appear to be better than what I was able to get using the visual phasing. Not because the visual phasing method is bad; more because I have not mastered it.
If you are using someone else’s spreadsheet, it is a good idea to know how they work in case anything goes wrong.
After writing many blogs on visual and raw data DNA phasing, it is nice to see everything come together using the MacNeill Spreadsheets and Charts.