Double Visual Phasing

Many articles have been written lately about visual phasing. This is a method developed by Kathy Johnston. I would like to write about double visual phasing. Previously, I had tested my father in law and his two sisters and tried visually phasing them. Here is the result of my attempt to visually phase their Chromosome 15:

Chromosome 15 – Richard and Sisters

I can tell that I did this a while ago as it was done in MS Word which I don’t use now for visual phasing. L is Lorraine, R is Richard and V is Virginia.

What is Double Visual Phasing?

This is a term I made up. I’m guessing that others have tried this, but I have not seen any Blogs on the subject. Richard has a second cousin named Fred. He is related on the Pouliot side (in orange above). Fred has had his sister Sleuth tested and his brother Don. If I phase Fred and his two siblings who are related to Richard and his two siblings, I’ll have double phasing. As they both share a Pouliot grandparent, it will be interesting to compare the results.

A Brief Genealogy

For the purposes of this Double Visual Phasing, here are the people involved:

Let’s Visually Phase Fred and His Two Siblings on Chromosome 15

The first step is to compare the three siblings to each other at Gedmatch.com using the Chromosome Browser:

I used MS Excel for this and I adjust the columns to the segment changes. Note that all the segments don’t line up perfectly, but I’ll say they are close enough. Next I add locations in millions:

I also put in darker vertical markers. I’m hoping that the places where the segments don’t align perfectly do not indicate additional crossovers.

Next I need to show who the crossovers belong to:

From this, it looks like Fred has four crossovers, Sleuth has two and Don has only one. Fred’s first crossover is at position 22M.

Next, I can assign colors based on Fully Identical Regions (FIRs). In these regions, there will be a match on both one maternal and one paternal grandparent. These grandparents will be represented by two of the same colors in that region extending to the person’s next crossover.

Where there is no match, I can assign two different colors and extend those to each persons’ crossover.

I make sure that the boundaries for each person line up with their crossovers. So on Fred’s map his first FIR with Don is short as it is within Fred’s two crossovers.

Mapping Half Identical Regions (HIRs)

Here I get one chance to map an HIR. My inclination is to map the HIR on the right between Sleuth and Don. My reasoning is that Sleuth is already at her last crossover at that point, so I’ll extend her segments all the way to the right. I already know from my previous map for my father in law’s family that Fred has some matches with my father in law and his two sisters on the left side of Chromosome 15 shown in Orange. So that information may help me map the left side of Chromosome 15:

Chromosome 15 – Richard and Sisters

Here is Fred and family’s partially completed Chromosome 15 with the HIR added for Sleuth:

However, there are blanks. Also we haven’t figured out which side is maternal and which side is paternal.

Two other testers

There are also two other testers: Patricia and Joe. They are my father in law’s first cousins. They are related like this:

The next thing I do is to compare all these eight people in gedmatch.com to each other. I download the results into a spreadsheet. Here are the matches on Chromosome 15:

I have the matches between siblings filtered out so they don’t show. I have Fred, Don, and Sleuth in the first column and the others in the second column. Every match represents DNA from Joseph Pouliot (or his wife Josephine Fortin – let’s not forget her). The way I have it mapped right now, the most important match is Joseph to Don and Sleuth. The only place that match could be is on the blue portion:

This is good news, because this sets the paternal and maternal sides for Fred, Sleuth and Don. It also sets where their paternal grandparents are. Here are Fred’s grandparents:

That means that blue is Pouliot and pink is Ford. Like my father in law’s family, Fred has a French Canadian side and an Irish side.

Next, we should be able to fill in the left side of the puzzle using the other matches:

A few observations:

  • The same match that Fred had with my father in law’s family helped finish my father in law’s visual phasing and Fred’s visual phasing.
  • All four of Fred’s grandparents DNA is represented between the three siblings. The one exception is a small portion of green from 22 – 27 M on the maternal side
  • The purple segment that Fred has from 22 – 27 seems quite small. It is a little unusual to have a small internal segment like that. By internal, I mean a segment that is not right on either end of the chromosome
  • Without the match between Joe, Sleuth and Don, I don’t know if I would have been able to complete this Chromosome
  • I don’t know about Fred’s maternal [Irish] side. He may already have matches that would identify the Halloran and Drennan DNA.

Comparison of the Double Visual Phasing

  • Unlike Fred’s results, my father in law’s family does not have good Pouliot coverage (in orange) between the three siblings.
  • This explains why Richard’s family matches Fred’s family in the beginning of the Chromosome and not the end. Pouliot DNA is missing between 60 and 95M.
  • It appears that Sleuth and Richard could have matched between 95 and 100, but I didn’t find a match over 3cM. Could this be because one received DNA from Joseph Pouliot and one received DNA from his wife, Josephine Fortin? Perhaps this is also an explanation of why the match between Don and Viginia (V) stops at position 38M.

Summary

  • Double visual phasing has benefits in that there are at least six people to compare matching DNA results with each other.
  • Double visual phasing should result in a crosscheck for the visual phasing of each family and better Chromosome maps of contributing grandparent DNA.
  • There are benefits in noting which group has the better coverage of DNA of a shared ancestor.
  • Comparison of results appear to indicate deeper crossovers between ancestors

Next Up

There are matches between Fred and his two siblings and the other five tested people on every chromosome except for 18, 19 and 22. That should make mapping the chromosomes with matches relatively easy.

I would like to try double visual phasing between two sets of siblings where the siblings are from different generations. However, it may take a while to get the additional samples done.

Determining Whether a Match Is Irish Or French Canadian By Visual Phasing

In this Blog I will look at a DNA match that my in-laws have. I would like to know whether the match is Irish or French Canadian. I will use Visual Phasing of my father in law and his two sisters’ DNA match to try to figure that out.

Irish at First Look

Something caught my attention with one of my father in law’s matches at FTDNA. My father in law Richard’s match Ann had this tantalizing detail under her Ancestral Surnames:

White (County Waterford Ireland to New Brunswick Canada)

I had recently found out, with the help of DNA and DNA researchers, that my father in law’s immigrant ancestor had shipped out from Waterford to New Brunswick. I have very few DNA matches for my father in law on this Irish side that I have identified. Most of the matches are French Canadian.

Irish or French Canadian?

At first, I didn’t notice other French Canadian names in Ann’s ancestry. However, after finding out she was listed at Gedmatch and Ancestry, I looked at her Tree and did see some French Canadians.

Visual Phasing

I do have DNA from my father in law Richard and his two sisters Lorraine and Virginia. So perhaps Visual Phasing will give and answer to the question whether the match with Ann is French Canadian or Irish. Ann’s best match to Richard, Lorraine and Virginia is on Chromosome 9:

Lorraine has the largest match above followed by Richard and Virginia. It looks like Richard and Virginia have crossovers at about position 107M.

I have used MS Word for phasing, but it wasn’t the best. PowerPoint worked well, but lately I have preferred using Excel. First I cut and paste the comparison of the my 3 in-laws into Excel.

Then I add the crossover points for the three siblings:

At first I thought that the first crossover belonged to Richard. however, there is a short break in the Lorraine V. Virginia comparison, so that adds an additional first crossover for Virginia. Actually the Virginia/Richard should be Virginia/Lorraine. There are likely 2 close crossovers there. I ignored the last small match between Lorraine and Virginia as there wasn’t anything going on in the comparisons above and below that match. Next I add the locations of the crossovers:

Lorraine and Richard have the largest Fully Identical Region (FIR) shown in green. I map that with the same two colors for Lorraine and Richard:

Lorraine only has two crossovers, so we extend her colors all the way to her left crossover and on the right to her crossover (L):

As Lorraine only had two crossovers, this perhaps explains why she had the largest match with Ann on Chromosome 9. Next, I fill in FIRs and Regions that don’t match (shown as red in the Gedmatch comparisons) with corresponding colors:

Unfortunately, that lead to a bit of a dead end. Instead, I’ll try starting with the Richard and Virginia FIR on the bottom comparison:

This version looks better. Next we choose a Half Identical Region (HIR) shown as yellow above. The longest one starts at position 14 between Lorraine and Virginia. A HIR maps as matching only one color and not matching the other.

Above, I chose for Lorraine and Virginia to match on the green and not match on purple and yellow. That is how the HIR is represented. I can then extend Lorraine’s purple and green to her crossover (L) on the right and fill in more FIRs and non-matching areas:

Now, except for the two ends of Virginia and Richard, I have a four grandparent map represented by four colors. Next, we have to identify the grandparents.

The Pouliot French Canadian Connection

One of my in-laws’ grandparents is a French Canadian Pouliot. Fortunately, my in-laws have a Pouliot cousin named Fred. Fred’s sister has also tested. Here is Fred’s matches with Virginia (78-83.5 and 107-110) and Richard (107-115).

Here is Fred’s sister’s matches with Virginia, Richard, and Lorraine.

Note that Lorraine only has one small match with Fred’s Pouliot sister. This is leading me to believe that the match with Ann is on the Irish side. Can we use these Pouliot matches to identify our blank map above? I think we can. The 2 green matches above are for Virginia and Richard at 17-31M. The only place between 17 and 31 where Fred’s sister could match Virginia and Richard, but not Lorraine is on the yellow. If the match were on the green segments, Fred’s sister would have had to have matched all three siblings at that location. Note that mapping out the smaller matches should also be on the yellow segments.

I should point out that my in-law’s had a father of Irish descent and mother of French Canadian descent. This means that both their paternal grandparents were Irish and both their maternal grandparents were French Canadian. As Pouliot is the maternal grandfather, that sets the maternal side of the map as yellow and purple. That also sets purple as the other maternal grandparent: LeFevre. Further, salmon and green now represent the paternal Irish grandparents.

So Is Ann a French Canadian or Irish Match?

Although I was leaning toward the Irish earlier, I now think that the match is French Canadian. Take another look at the match between Ann and Lorraine, Richard and Virginia:

The pattern looks a lot like the purple LeFevre segments. Lorraine’s larger match is on top. Richard’s green match stops where the purple LeFevre segment stops. Virginia’s smaller blue match starts where the purple Lefevre segment starts again. I’ll put the matches in the same order as Gedmatch to make it easier to see:

If Ann were to have matched on the green paternal grandparent area, there would have have to have been three equal matches in that region shown on the Gedmatch browser.

The fact that Ann did not match with the French Canadian Pouliot grandparent did not mean that she was an Irish match. In this case, it meant that she matched the other French Canadian Grandparent.

Summary and Conclusions

  • Visual Phasing can help map an unknown match to a grandparent.
  • That phasing needs to be in conjunction with at least one known cousin to identify a grandparent.
  • These results help to know where to invest genealogical research time. There is no sense in barking up the wrong tree.

My Father In Law’s Autosomal DNA: Separating the LeFevres from the Pouliots

It’s been a while since I’ve looked at my Butler father in law’s autosomal DNA, so it’s time to look at it in a blog. Richard descends from an Irish father and a French Canadian mother. Richard has many large matches with many with French Canadian ancestry. In comparison, he seems to have smaller and fewer matches on his Irish side. This is probably due to several reasons:

  • The French Canadians have been around for many hundreds of years in North America.
  • Their descendants have spread throughout the region and many migrated to Massachusetts where Richard is from.
  • Many of these early French Canadians were intermarried. This tends to increase the amount of shared DNA among cousins.
  • The numerous French Canadian descendants perhaps were more likely to take DNA tests.
  • Conversely, the Irish relatives tended to emigrate later in time.
  • These Irish descendants seem less likely to have taken DNA tests.

Richard’s Known Matches – French Canadian

Richard has 2 pairs of known matches with cousins of French Canadian ancestry (other than my wife). They are:

  • 2 First cousins – They are on his mother’s (LeFevre) side
  • 2 Second cousins – They are also on the mother’s side but one generation up. The common ancestor is Pouliot. Here is a diagram of Richard’s mother’s side:

Pouliot LeFevre Diagram

My Confusion

I looked at these matches and wondered how I would be able to sort out the LeFevres and the Pouliots. This was confusing as the LeFevre line had Pouliot in it.

The Easy Answer

The easy answer is there is no easy way to pull the 2 apart with what I had. This is because at the first cousin level, it is not easy to pull out one family. If you think about it, your first cousins share 2 grandparents with you. This was the case with Richard’s 2 first cousins also. As they are on the mother’s side, they are useful for determining whether matches are on the Butler or LeFevre (Paternal or Maternal) side, but not a whole lot more. But that is quite a bit. This is a way of phasing your results. This also separates the French Canadian matches from the Irish matches.

Looking for more than can be found in a relationship can be frustrating and confusing and that was where I was a while back. I have found that it is usually good to keep it simple – especially when figuring these things out. The problem was I was comparing apples and oranges. Or in this case 1st cousins and 2nd cousins. This is why it is sometimes suggested that a second cousin is a good choice for testing.

The Pouliot Second Cousins

As mentioned above, the Pouliot second cousins represent all the Pouliot DNA shared. On the FTDNA Chromosome Browser Richard’s DNA shared with his 2 Pouliot 2nd cousins looks like this:

Butler Pouliot Chromosome Browser

From the image above, I gather a few things:

  • This is a map of the DNA that Richard received from his Pouliot great grandfather (and Fortin great grandmother) down from his Pouliot grandmother.
  • As this represents the DNA from Richard’s grandmother, it would theoretically cover about one half of his chromosome browser. This would be the amount of DNA that he actually did get from his grandmother as compared to how he matches his two 2nd cousins.
  • Richard’s theoretical amount of DNA he got from his grandmother would cover half of the browser because the browser contains both paternal and maternal matches.

Add in the 1st Cousin

I’m only adding in one LeFevre 1st cousin as the other one didn’t test at FTDNA. Here the first cousin will be in green.

French Canadian to Richard in Browswer

From looking at the above, I observe the following:

  • The green area represents Richard’s maternal side as shown through a match with a maternal cousin.
  • This green represents LeFevre on Richard’s parent level.
  • About one half of his green match represents LeFevre and one half represents Pouliot on the grandparent level.
  • Going further up the ancestor line the green represents every other ancestor of Richard’s mother. This would be French Canadians.
  • Richard got a full chromosome from his mother, so all the DNA received from his mother would fill the above chromosome browser.
  • There are areas on Chromosomes 1, 13 and 16 where Richard’s green LeFevre cousins matches overlaps with his matches from his Pouliot cousins. These areas likely represent where the LeFevre cousins match the Pouliots. This would mean that in this area of the LeFevre cousins’ chromosomes they got their DNA from the Pouliot side. I know that I said above that it was not possible to sort out what part of the LeFevre DNA was from Pouliot, but from looking at the Chromosome Browser above, it appears that it is possible. More on this later.
  • Areas where there are breaks in the matches or where the matches go from the LeFevre cousin to the Pouliot cousins likely indicate Richard’s crossover points. These are the points where the DNA he received changed from one [maternal in this case] grandparent to another. That is, the DNA he actually received went from his LeFevre grandfather to his Pouliot grandmother.
  • As the LeFevre cousins and Richard both descend from LeFevre sisters, they share X Chromosome matches. Both those sisters got their X Chromosomes from their 2 parents. Those 2 parents were LeFevre and Pouliot.
  • Due to the X inheritance patterns there can be no X Chromosome matches between Richard and his Pouliot 2nd cousins. Richard did receive Pouliot X Chromosomes from his mother’s mother. But Richard’s cousin did not as there is no X Chromosome passed down from father to son.

Triangulation – Thinking In Three Dimensions

Triangulation is when 3 or more people all get their DNA from the same ancestor and all match each other. Our best shot at finding this is at the right hand side of Chromosome 1. It looks like these 3 people who match Richard should match each other. Two are siblings, so that is a given. Here is how Richard’s 4 cousin matches look like at Gedmatch.com:

Richard Gedmatch Chr 1

You will have to switch gears a bit here from the FTDNA browser. In this browser, the different colors stand for the size of the match. Here, #1 and #2 are the Pouliot 2nd cousins. #3 and #4 are the LeFevere 1st cousins. #4 was the cousin that didn’t test at FTDNA. As expected, in the area where the 4 cousin matches are stacked on top of each other, they also match each other. At this close of a match, they almost have to. The only other option would be if they matched somehow on Richard’s paternal Irish side, which would be unlikely. This means that the 5 cousins triangulate and they have as a common ancestor their great grandfather Pouliot. Another interesting thing about Richard’s Chromosome 1 is that with just 4 maternal cousins, he has much of his chromosome mapped out – at least the maternal side of it.