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 First 1st Cousin DNA Results: Part 3 – The X Chromosome

In my first Blog about Cousin Rusty’s DNA matches, I discussed some maternal matches. I also looked at how first cousin DNA matches worked. In my second Blog about Rusty, I looked at the more complicated matching of nephew to aunt. In this Blog, I would like to look at the X Chromosome.

Here is how Rusty matches my family on the X Chromosome as shown in the Gedmatch Browser:

These are his matches with:

  1. Mom
  2. Sister Heidi
  3. Me (Joel)
  4. Sister Sharon
  5. Brother Jonathan

Here is an X Chromosome Map produced by M MacNeill before my brother Jonathan’s DNA results were in. He made this using our raw DNA results.

The blue is the maternal side where there are matches with Rusty. The red is what my sisters inherited on the Hartley side. MacNeill did not designate the blue by grandparent. The choices for maternal grandparents here are Alexander Rathfelder and Emma Lentz. Let’s try to figure out which is which.

Speaking of Emma and Alexander, here they are with their five children:

Rusty’s mom is the girl on the left and my mom is the girl on the right.

The X Path

The X Chromosome follows a particular path from our ancestors. The rule is that the X DNA never travels from male to male. So that means that two males in a path will break the X chain. Here are my top picks for X Chromosome matches:

The matches in the browser were through the green people up to Rathfelder and Lentz. Judy has the potential to match on the Lentz/Nicholson side. Joshua could also have shared X, though he is further down the ladder. Carolyn could match on the Nicholson side.

Carolyn’s Nicholson X DNA

I’ll look at Carolyn’s X DNA matches.

She matches:

  1. My Mom
  2. Sharon from 106672721 to 113198089 (7.056 cM)
  3. Jonathan from 139830607 to 143171128 (11.542 cM)
  4. Judith
  5. Joan

Based on Sharon’s small match, I would initially say that the darker blue is Lentz and the lighter is Rathfelder on the MacNeill Map. However, the problem with that theory is that I should match Carolyn also in that area. If I reduce the match level, I do have a match there with Carolyn:

Mapping Jonathan’s X

In order to be sure, we need to map Jonathan’s X. He has a larger X match with Carolyn than Sharon does – even though it looks smaller on the browser. Here is some previous X Mapping I had done for my sister Sharon (S), me Joel (J) and my sister Heidi (H).

It looks like I had already guessed that orange would be Lentz. Recall that Sharon’s (S) match with Carolyn was 106-113 and mine was 109-113 within the orange segments. When I compare Jon to his siblings, it looks like he has 3 crossovers:

As we are only looking at Jon’s maternal Chromosome, we are looking at the blue areas on the Chromosome Browser where he matches his siblings and the non-blue areas where he does not match his siblings.

This was pretty easy. I started on the right. Jon matches all his siblings, so that has to be green. Going from right to left, the segments alternate between green and orange. The only ambiguous part is on the left hand side where Heidi has a small orange Lentz segment. However, if I lower the thresholds for Jon’s match with Heidi, I get this left side match which clears up the ambiguity:

Gedmatch normally has a SNP cutoff at 500, but apparently they have not lowered that for the X One to One match and must still have a 700 SNP cutoff.

Now back to Jon’s match with Carolyn. I had noted above that it was at position 140 to 143. That just fits in to Jon’s Lentz mapped orange segment as shown by the red arrow below:

This confirms that yellow should indeed be assigned to Lentz. That means that green has to be Rathfelder – the only other maternal grandparent.

Now I’ll bring Rusty back into the picture with his matches to my family:

  • Rusty’s match with my mom is line 1
  • Heidi is line 2. You can see her Lentz indent on the left of her match with Rusty.
  • Joel is line 3. You can see the space left by Lentz in the middle of my large match with Rusty
  • Sharon is 4. Her match with Rusty stops at her Lentz (orange) segment
  • The newly mapped Jonathan is 5. He matches Rusty on his green Rathfelder segments.

So would we be able to guess Rusty’s X Map?

Rusty’s X Chromosome is either mostly or all Rathfelder. The part I’m unsure of is between 120 and 140 cM. The reason that I think that it might be Rathfelder is because Carolyn matches Judith and Joan in that segment and Rusty does not match any of those three by the X Chromosome. However, as Carolyn’s Nicholson matches go back at least another generation, that is not proof.

Looking at the ??????? Gap

I’m curious as to what is happening where Rusty and my mom don’t match. The answer to this goes back a generation. Alexander Rathfelder’s parents were Rathfelder and Gangnus. My mom and Rusty’s mom had two different X Chromosome maps showing how they got their X DNA from their grandparents. However, on their paternal side, their Rathfelder father gave them a full X Chromosome unchanged from his mother Maria Gangnus.

Here is Maria:

So due to the fact that Rusty’s mom and my mom both have the same paternal grandmother DNA on the entire length of their X Chromosome, that means that Rusty cannot have Rathfelder aka Gangnus DNA from 120 to 140. If he did, then he would have to show a match to my mother.

The result of our little thought experiment is that Rusty has to have Lentz DNA. Here is a possible scenario of what could have happened. This shows Rusty with his maternal grandparents. Then we see Rusty’s mom and my mom with their X Chromosome grandparents. Maria Gangnus is Alexander Rathfelder’s mother and Emma Lentz’s parents are George Jacob Lentz and Annie Nicholson.

What we know for sure is that Rusty’s mom and my mom both had a full X Chromosome from their paternal grandmother, Maria Gangnus. The only place for there to be difference is on my mom’s and Rusty’s mom’s maternal X Chromosome. Suppose that Rusty’s mom got her DNA from her maternal Nicholson grandmother and my mom got her DNA from her maternal Lentz grandfather. That would be why Rusty’s Lentz DNA would not match my Lentz DNA or my sibling’s Lentz DNA. We only got the X DNA that we received from our mothers and these mothers got DNA from different maternal grandparents in this location. We now know what Rusty’s X Chromosome map looks like. We don’t know what our mother’s maternal X DNA looks like. We only know they had DNA from different maternal grandparents from 120M to 140M.

First 1st Cousin DNA Results: Part 2 – Trying to Explain Aunt/Nephew Matches

First, Another Look at First Cousins

In my last Blog I took a first look at my 1st cousin, Rusty’s DNA. I went into some detail on how he matched on a few of the lines we have in common. I looked at how Rusty compared to me and my siblings on Chromosome 16. Here is a visual summary of that comparison:

The first image is a chromosome map of the DNA that my 3 siblings and I got from our four grandparents. The red and yellow grandparents are the maternal ones shared with Rusty. The second image shows Rusty’s matches with me and my 3 siblings. Note that the long segments shared are similar to the Lentz segments on the left and the Rathfelder segments on the right. Note that as Rusty and my siblings are of the same generation, we share the same long segments with our grandparents. From this, I was able to create a maternal Chromosome Map for Rusty.

As there were a lot a matches, I would assume that the DNA profiles of my mom and Rusty’s mom were somewhat similar to each other on Chromosome 16.

Rusty Compared to His Aunt – My Mom

In the above example, the common ancestors of Rusty and me are our two maternal grandparents. When I compare Rusty and my mom, I will be looking at two different generations.

Here Rusty and my mom share the same common ancestors as me and my mom. However, do Rusty’s and my mom’s shared segments represent my mom’s parents’ or my mom’s grandparents’ DNA?

Does rusty share DNA with my mom’s grandparents (his maternal great grandparents)?

My thinking is that when I compare Rusty to my mom the DNA compared goes up a generation from when I compare Rusty to myself and my siblings. Here is Rusty again at Chromosome 16 compared to my mom:

My mom has a full Lentz and a full Rathfelder Chromosome from her parents. Yet there is a place in the middle of Chromosome 16 where Rusty and my mom do not match. That makes me think that we are comparing my mom’s grandparents with Rusty’s great grandparents. Let’s assume that to be the case. That means we need to bring in another generation.

With what we know of Chromsome 16, Rusty and my mom must share all of the same Lentz next generation up. That would be either Jacob Lentz or Annie Nicholson. The same must be true for the Rathfelder side from position 56M to 88M. However between about 50M and 56M Rusty and my mother must get their DNA from different paternal grandparents of my mom.

a look at chromosome 10

Here is the way I have mapped my mom’s chromosomes using Kitty Munson’s Chromosome Mapper:

The DNA match in purple is my from my mom’s Nicholson only side. It is mapped to William Nicholson and Martha Ellis who were the parents of my mom’s grandmother Annie Nicholson.

First, let’s look at my mom’s matches on Chromosome 10. I had discussed this Chromosome in my previous blog also.

#1 is mom’s match with Carolyn which maps to the Nicholson side. #2 is mom’s match with Rusty. #3 is a small match with Catherine which I’ll ignore for now.

Here are Rusty’s matches:

#1 is Carolyn. #4 in my mom. 2, 3, 5 and 6 are me and my siblings – not so important for this comparison. #7 is Linda (Nicholson descendant) and #8 is Catherine (Rathfelder descendant).

A possible explanation of a maternal aunt/nephew match

I have to admit that this gets a bit confusing.

When we compare my mother to Rusty, we are looking at my mom’s maternal and paternal chromosome. However, the match to Rusty is all on his maternal chromosome. Conceptually, I think that it would look something like this.

The top showing my mom has her 4 grandparents on her maternal and paternal chromosomes. I don’t know how my mom’s paternal side might look, so I made something up there. My mom’s four grandparents are equivalent to Rusty’s 4 great grandparents, but those 4 great grandparents are all on Rusty’s maternal Chromosome. So they are cramped in to a smaller space.Said another way, Rusty’s maternal DNA is alternating between Rathfelder and Lentz. However, that Rathfelder grandparent may be broken up further to two great grandparents of Rathfelder and Gagnus. Likewise the Lentz grandmother may be broken up to Lentz and Nicholson great grandparents.

In the first segment, my mom has Nicholson DNA due to the match with Carolyn. Rusty has a Rathfelder match in that segment. However, as my mom doesn’t also match Catherine in that segment, it must be from a different Rathfelder. My mom’s grandparents were Rathfelder and Gagnus. So here my mom has either one of those grandparents’ DNA and Rusty has the opposite. That is why I have blue for my mom there and green for Rusty.

A final note is that the last small segment match that Rusty has with Catherine cannot be right. Or it cannot be Rathfelder. That is because Rusty’s DNA is alternating  between Rathfelder and Lentz. The last segment has to be Lentz, so there is no room for Rathfelder DNA there. On the other hand, my mother’s #3 match is with Catherine, which is a Rathfelder match. She has room for that match along with her Nicholson match as she has a maternal and paternal chromosome to match on.

Summary

  • In a 1st cousin match, the DNA from my two grandparents are compared to the same DNA that my first cousin got from those same two grandparents
  • In a nephew/aunt match, the great grandparents of the nephew are compared to the grandparents of the Aunt
  • The aunt, however, has her 4 grandparents’ DNA on 2 chromosomes
  • The nephew has his 4 great grandparents’ DNA On only one chromosome
  • Those 4 great grandparents have to fit within the appropriate alternating grandparents of the newphew

The Segmentology Blog, Segments: Bottom-Up explains it well. Here is an image from that Blog:

In my example above, this Segmentology image would be like Rusty’s maternal DNA. In Rusty’s grandparent look, his maternal DNA alternates between Rathfelder and Lentz. However, in his great grandparent look, the DNA may be split up between the parents of those grandparents within the crossovers of the grandparent look.

For my mom, I am just looking at her grandparents. However, there will be two lines of grandparents: maternal and paternal for her. Also the crossover points will in most cases be different than for Rusty as he got his DNA from his mom – my mom’s sister.

 

 

My First 1st Cousin DNA Results

Not too long ago, I was at a car dealer with my wife picking up her new car. I checked my email on my phone and was surprised that I had gotten an email from FTDNA saying that my mom had a new close relative. I checked and it was my first cousin on my mother’s side, Rusty. I have been looking at DNA for quite some time now and have written over 100 Blogs, but this was my first 1st cousin DNA results. As a first cousin Rusty’s DNA matches are comparable to mine on my mother’s side.

Rusty on the Family Tree

Here is the family tree on my mother’s side with those that have had their DNA tested:

Rusty matches on my mother’s side. This includes the Rathfelder (blue), Lentz (yellow) and Nicholson (red) families. As Rusty got different DNA from his mom that my 3 siblings and I got from my mom, he will have some of the same and some different matches with all those that have tested so far.

Rusty’s 1st Cousin Matches

I’ll look at my matches with Rusty first as they are more straightforward than his matches with my mom. At least we are both in the same generation. Rusty matches me at 1,164 cM as reported at Gedmatch which is also on the high side for a first cousin. Here is how my matches with Rusty look like on the FTDNA browser:

By the looks of it, Rusty and I light up about half of the positions of the chromosomes.

Why do Rusty and I match as we do?

I like to look at DNA matches in terms of grandparents. That is because I have tried to map all my ancestral DNA to my four grandparents. For example, here is how I have used a visual method to map to my 4 grandparents on Chromosome 10. I am using Chromosome 10 as it comes up later in this Blog:

I will assume that I did the visual phasing correctly. I have the raw data to check, so it can be corrected later if it isn’t 100% right. My sister Sharon is in the first row, Heidi in the second, I’m in the third row and my brother Jon is in the fourth row. The numbers at the bottom are the rough positions of the crossovers. My siblings and I will match Rusty on the blue and purple segments only (maternal side). Looking back up at the FTDNA browser above for Chromosome 10, it shows that I match Rusty at three segments. It is clear that the third match must be a Rathfelder segment match as a little more than half of my Chromosome 10 is mapped to Rathfelder on the right side.

Let’s see how Rusty matches with me and my siblings on Chromosome 10.

This points out an error in my original visual mapping. Based on these matches with Rusty I should be able to correct my Chromosome Map. First, this shows on the right segment, that Rusty matches me (#4) and not my three siblings. That means that my three siblings will have different DNA than me on the maternal side. Note above that difference is not reflected in my Chromosome Map. I have purple Rathfelder mapped to all my siblings on the maternal side. Previous work that I’ve done has shown that my three siblings have a small Rathfelder match at the right end of this Chromosome and I do not. That match is between 132 and 135M. I take that to mean that my yellow segment match above with Rusty must be on the Lentz side and not the Rathfelder side. So, back to the drawing board.

Checking my laptop, I see that I had done a raw DNA analysis on Chromosome 10 in the past. I went back and checked the raw data and found that I had missed my last maternal crossover. I just added that one in to get this corrected Chromosome 10 Map.  The map format below was developed by M MacNeill [prairielad_genealogy@hotmail.com].

The segment that I had missed was the yellow Lentz portion of DNA to the right of my Chromosome. A few points from comparing the Chromosome Map above to Rusty’s matches with the map:

  • Chromosome 10 was heavy on Lentz DNA for me and my 3 siblings (yellow vs. Rathfelder brown)
  • As a result, Rusty only matches me and my siblngs on Lentz DNA
  • Other Chromosomes would likely yield Rathfelder DNA
  • By comparing Rusty matches to my family to all my family’s Chromosome maps, I could create a spotty Chromosome map for Rusty on some chromosomes and a more complete one on others (see below)
  • Rusty’s match with me was helpful in finding a crossover I had missed on my Chromosome 10 Map on the maternal side.
A simpler Chromosome (16)

Perhaps this example is clearer. I will show my visual phasing map followed by Rusty’s matches to my siblings:

 

  1. Heidi
  2. Jon
  3. Joel
  4. Sharon

Unfortunately, the order of my siblings is different in the two representations. I am the only one in the same relative position in both representations. A few observations:

  • Rusty’s inherited DNA from his maternal grandparents lined up well with the my family’s inherited DNA on the maternal side.
  • Rusty’s matches with me and my siblings confirms the visual mapping that I have done for me and my siblings on Chromosome 10
  • Rusty appears to have two large segments of DNA on his maternal side. The larger one on the left is from the Lentz side and the slightly smaller DNA segment on the right side of Chromosome 16 is from our shared Rathfelder side.
  • Rusty’s crossover from Lentz to Rathfelder DNA appears to be at the abrupt end of his first bunch of matches to me and my siblings at about 49.7M.

This figure is a likely representation of Rusty’s Chromosome 16 on his mother’s side. That means that any matches he has on Chromosome 16 in the red part before position 49.7M will be on his Lentz side and any matches he has in the yellow part of Chromosome 16 will be on his Rathfelder side.

Rusty’s Aunt Match

According to the ISOGG web page, Rusty should match my mom (his aunt) and my 3 siblings and me as follows:

This is a visual show of how Rusty matches my mom:

He lights up the browser pretty well. At FTDNA he shows a match of 2,085 cM. This is close to what Gedmatch shows at 2,160.6 cM. Both of these matches are over the reported average of 1744 cM for an aunt/nephew relationship.

Rusty and Rathfelder DNA

Rathfelders are difficult to find. So far, I have found one other person that tested at AncestryDNA who I have been able to link up to the Rathfelders. I wrote about that Rathfelder match in two Blogs. Here is a link to the second Blog. As best as I can tell, the person I found has the following link to Rusty and my family:

I find it unusual that a couple would give the same name (Johann Georg) to two of their sons. Also to make life confusing, the father, Hans Jerg, was also known as Johann Georg. The chart above shows the person I found (Astrid) as a 4th cousin to my mom and a 4th cousin, once removed to my second cousin Catherine, my family and 1st cousin Rusty.

A Rathfelder Triangulation Group

Here is how Astrid matches my mom and Rusty on Chromosome 17.

Astrid, my mom and Rusty are in a Triangulation Group as they all match each other at least in the green area above. Assuming I have the genealogy right, this points back to an early Rathfelder ancestor:

This shows that the shared Chromosome 17 DNA came from Hans Jerg Rathfelder and his wife. This couple were among some of the early settlers of Hirschenhof which was a German colony in Latvia.

Rusty’s Lentz and Nicholson DNA

I only have one distant cousin, Al,  that matches only on the Lentz line. This person does not match Rusty at standard thresholds, so I’ll be mostly looking at Rusty’s Nicholson DNA shown in red below.

On the chart above, Judy and Joshua descend from the Lentz and Nicholson sides. Joan, Linda, Carolyn and Nigel descend from Nicholsons. That means that any match Rusty has with those on the red lines should be a Nicholson match.

Rusty’s oldest Nicholson dna

Rusty matches my mom and Nigel on Chromosome 1. This represents the DNA he got from John Nicholson who was baptized 1765 and his wife Sarah Staniforth.

The browser above shows Rusty’s DNA match with my mom (#1) and Nigel (#2). My mom and my family had a large match with Nigel. So large, in fact, that some on the ISOGG Facebook Page questioned whether that large match could be possible. Here is my Blog about Nigel. Rusty has a more moderate level DNA match and forms a Triangulation Group between himself, my mom and Nigel.

William Nicholson dna

Our shared ancestor, William Nicholson moved his family from Sheffield England to Philadelphia around 1869. Rusty matches Carolyn, Joan and Linda on quite a few Chromosomes. So if I was to map Rusty’s Chromosomes, wherever he matches these three I would map that DNA back to William Nicholson and his wife Martha Ellis. Here is a typical match that Rusty has with my mom (#1) and Joan (#2):

The green segment on Line 2 represents Rusty’s match with Joan and DNA that he got from William Nicholson and his wife.

Chromosome 10

Here is an interesting situation where Rusty matches his 2nd cousin once removed Carolyn (#1) for a longer segment (in orange) than his Aunt – my mom (#2):

The green segment is Rusty’s match with Linda (#3). Linda and Carolyn are both cousins on the Nicholson side. What does this mean? Let’s see how Carolyn matches my mom. In the places where she matches my mom, there would be triangulation:

Here, my mom matches Carolyn in the same segments where Rusty matches my mom. That leaves the blank on Line 2 above between the blue and yellow segment. Why doesn’t Rusty match my mom in the blank spot? Note that above and below on Lines 1 and 3 that has to be Nicholson DNA due to those Rusty is matching. Here is how I see it.

My mom got her DNA on her maternal side from her Lentz and Nicholson grandparents. In the area that Rusty doesn’t match her by Nicholson DNA, my mom must have Lentz DNA.

a Closer look at Chromosome 10

Here is a closer look at some of the closer Nicholson and Lentz relationships:

Here is how the DNA tested people above match each other by the numbers on Chromosome 10:

In the above spreadsheet, the three sections in gold are Triangulation Groups.

Summary and Further Study

Well this Blog wore me out a bit, so I’ll stop here. There is quite a bit to a first cousin’s DNA:

  • I found that Rusty had above average matches to me and my siblings. In addition, he had above average matches to my mom.
  • I looked at how Rusty’s match helped correct an omission I had on my Chromosome 10 Map.
  • Based on my maps, it should be easy to tell what maternal grandparent line Rusty’s matches are when they match with those on my family’s Chromosome Maps.
For Further Study
  • I may look more into what makes up an Aunt/nephew match with Rusty and my mom.
  • I’d like to look at Rusty’s X Chromosome matches.
  • Anything else that happens to come up as I’m blogging

A Shared Ancestry Hint of a French Canadian 8th Cousin and Visual Mapping

Recently I have been looking at my wife’s French Canadian Pouliot ancestry and DNA. My thought has been to find a Shared Ancestor Hint (SAH) at AncestryDNA. Then if the person in the Ancestry hint has uploaded their results to Gedmatch, I would be able to analyze those results. In this case, I would like to check using visual phasing to determine whether the match is on the Pouliot line or another line.

Here is the SAH:

Lorraine is my wife’s paternal Aunt. Here is what the DNA looks like at AncestryDNA:

Here is how the match looks like at At Gedmatch,

Actually, based on this person’s email, there are 2 matches. This is the Ancestry one. The other test was at 23andme. They are likely the same person. This AncestryDNA match got higher results perhaps due to the comparison within the same company.

The Goal: Compare Gedmatch, AncestryDNA and Visual Mapping

My goal as stated above is to map one or more of the matching Chromosomes to see if the match along the Pouliot line is likely. I do have two Pouliot 2nd cousins to Aunt Lorraine which will help. It would make sense to map the Chromosomes where they match Aunt Lorraine. Here is how Fred, who is a Pouliot 2nd cousin to Lorraine matches Lorraine on Chromosomes 4:

  1. Richard, my father in law
  2. Richard’s sister Lorraine
  3. Richard’s sister Virginia

Now To Visually Map Richard, Lorraine and Virginia On Chromosome 4

The good news is that there is a lot of Pouliot DNA for mapping this Chromosome. The bad news is that the original Chromosome match between Ann and Lorraine was fairly small.

First I compare the 3 siblings using the Gedmatch Chromosome Browser:

In the image above, I’ve added the crossovers and the approximate locations on the Chromosome where they occur. There are a lot of crossovers bunched up on the right side. Next I assign the crossovers to a particular sibling. Note that I added two crossovers that I missed in the previous image:

  • Virginia has 109 crossovers
  • Richard has 3
  • Lorraine has 4 for a total of 17 crossovers. I have a question mark my Lorraine’s last crossover as I’m not sure if there is one there or not.

Next I map the 3 siblings based on crossover, Fully Identical Regions (FIRs in green), Half Identical Regions (HIRs in yellow) and the places where the siblings don’t match in red.

I’ll start in the middle of the Chromosome where Lorraine and Virginia have a FIR going over two segments (before positions 120):

This gets us started. The DNA that these 3 siblings inherited from two of their same grandparents are represented by green and purple and extend to each of their crossover lines. Next, I look for other FIRs or places where the siblings don’t match. For example, Richard and Virginia don’t match between 59 and 84, so I’ll add two new colors to Virginia, to show the DNA she got from the other two grandparents.

Here it looks like I’m stuck for now:

Now I add a HIR. Our Gedmatch match between Lorraine and Ann was between 33 and 40, so I’ll add one for Lorraine there.

I did this by arbitrarily extending one of Lorraine’s colors to the left and choosing another color to add so Lorraine and Richard would be HIR between 31 and 84. Then I extended those colors to the left as Lorraine had no crossovers on the left side of the Chromosome. Based on this HIR, I can fill in some more on the left had side:

Now I have a lot of the left side of Chromosome 4 mapped out. I also have Fred who is a second cousin on the Pouliot side. I’ll mush all the information together and then try to figure out what color Pouliot is:

Here I’m leaning toward a purple Pouliot. The reason is that Richard has a purple segment (and Pouliot match) from 4 to 14. Richard, Lorraine and Virginia match Fred from 102-126, but Richard may not be mapped in that area yet. However, Lorraine and Virginia have purple in that segment. In addition, I don’t have positions for the two crossovers between 95 and 120. I can get those from Gedmatch by comparing Richard and Virginia’s FIR at full resolution:

The FIR starts a little after 100M and ends at about 106.5. Those two positions numbers define the two crossovers between 95 and 120. That also confirms that Pouliot is purple. This defines a grandparent and the maternal and paternal sides of the Chromosome as Pouliot is on the maternal side for these three siblings. It also defines the other maternal grandparent (LeFevre) as being the red or maroon color.

Next, I can fill in all the other Pouliot sections provided by these 3 siblings’ Pouliot cousin Fred:

A few notes on the mapping:

  • Virginia didn’t match Pouliot from 4-14 where Richard did so she gets a LeFevre segment there.
  • Virginia also does not match Pouliot from 120 to 135 where her siblings do match Pouliot. So I give her another LeFevre segment there.
  • Virginia starts matching Pouliot again at 172. This points out a crossover location that I mislabeled previously as 177. Corrected above.
  • There is still a few small segments on the right that I haven’t filled in for Virginia and Richard.
Some additional adjustments

A close look shows that between 180 and 185, Lorraine and Richard don’t match. In order to meet the FIRs, HIRs, and no-matches on the right hand side, I came up with this:

I’m not sure if this is totally right on the right hand side, but it seems close. I show Virginia as having nine maternal segments which seems quite unusual. I would like to point out that the match on Chromomse 4 between Lorraine and Ann. Ann did not match Virginia or Richard on Chromosome 4. Those results (and lack of results) are consistent with the mapping above.

Back to the Original Match Between Lorraine and Ann

A big part of this Blog was to determine whether Lorraine’s small Chromosome 4 match with Ann was on a Pouliot segment. After all that mapping, I would say that the match could not have come through Lorraine’s Pouliot side. The largest LeFevre segment between the three siblings belongs to Lorraine between 0 and 95M.

From the above analysis, I made conclude:

  • The 8.6 cM match between Ann and Lorraine is did not come down to Lorraine through the Pouliot side
  • The match is either by chance or on the LeFevre side. There are 15 names in common between Ann and Lorraine. They are all French Canadian names. My assumption would be that I could rule out a DNA match on the paternal (Irish) side.
  • Ann and Lorraine still have matches on 3 other chromosomes.

Summary and Conclusion

  • I was not surprised that this match did not match on the Pouliot side given the inter-relatedness of French Canadian genealogy
  • It was possible that this shared match on Chromosome 4 could have been from the Pouliot side, but it wasn’t.
  • It is best to not assume that a Shared Ancestor Hint and the shared DNA match go back to the same shared ancestor(s)
  • I need to build out these French Canadian lines more at Ancestry
  • The best match between Ann and Lorraine was on Chromosome 19. However, there were no 2nd cousin Pouliot matches on that Chromosome.
  • This Blog satisfied my curiosity on at least one part of the match between Lorraine and Ann and got me to map out Chromosome 4 for these 3 siblings

 

 

 

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

 

 

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.

chrom204sibs

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:

dadpatternchr20

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:

mompatternchr20

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.

chr20map1

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:

chr20map2

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.

chr20withmatches

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.

emma

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.

chr7patmatmap

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.

chromosome15macneill

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:

chr10visphase

Here is another try including additional cousins that tested:

10r1visphase

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:

cousinmatch10macneill

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:

10visphase3

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:

dadpatternchr10

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.

chr10patternmissed

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:

chr10rawpatterns

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:

shamus

Here is my corrected Dad Pattern for Chromosome 10:

dadpatternchr10corrected

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:

patchr10chart

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):

maternalchr10

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:

gedmatchcheckofrawphase

chr10phasemap

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.

More Dicks DNA – Marilyn’s Brother

I just finished 2 Blogs on the Henry Dicks Line which is a parallel line to my wife’s Christopher Dicks Line. Then I heard that Marilyn had her brother tested. Marilyn is on 2 different Christopher Dicks Lines.

Henry Dicks Line Updates

In other news, I found out that Eric’s dad, Claude, has been tested for DNA. What is more it is Claude that Eric believes to be likely related on the Henry Dicks Line. The confusing part was that Eric was in a Triangulation Group with my mother in law Joan and Joan’s half Aunt Eshter. So isn’t that confusing. That means that for now (as I understand it) Eric’s TG with my wife’s side of the family may not refer back to a Dicks ancestor. I’ll take Eric off the TG Matrix for now and put his father into the Dicks family comparisons. The good news is that there are a lot of Dicks descendants around. The bad news is that is is difficult to keep track of all of them.

I also got this note recently from Crystal from the Henry Dicks Line:

In looking at Ivy’s ancestors, We also share another ancestor. We are both related to The Vatchers as well as the Matthews and the Dicks. Burgeo is so small that you bound to be related in 2 or 3 different ways going way back!

In addition, Crystal tells me she has extra Dicks DNA on her dad’s side as shown here on this Henry Dicks Chart. Her mom’s side of the Dicks line leads up to the first pink rectangle. I have Crystal in a slightly different green to make sure I don’t forget she is in two Dicks Lines.

henrychartnew

Back to the Christopher Dicks Line and Marilyn’s Brother

Here is an updated Christopher Line Chart. All I did was add Marilyn’s brother Howie to an old chart I had:

marilynsbrotherchart

The chart is getting tiny. So I will point out that Marilyn and her brother are on the Joyce and Cran Lines. The Joyce Line is the large Line to the right of center and the Cran Line is on the right. That reminds me of something I brought up in an email. My wife’s 1/2 great Aunt Esther has 2 Dicks Lines also. One is through Christopher. The other one she doesn’t share with Joan due to the 1/2 part. However, I noted that Esther is in 3 TGs that she does not share with Joan. In those 3, she shares all 3 of them with people from the Adams Line. The Adams line is the one on the left.

esthernonjoantgs

These are the non-Joan, Esther TGs. They all have Nelson in them and two of them have Sandra. I just need to check to see if Esther’s other Dicks ancestor might fit in. “Hi Sandra, any room for Esther’s ancestor?”

However, when I look at Esther’s tree, this is what I see:

estherstree

Assuming that this tree is right, there is no room for Jane Ann Dicks in Sandra’s tree. That is because Jane Ann was b. 1841 and Sandra descends from Elizabeth Dicks b. 1809 who married Thomas Adams. Sandra would have descended from a male Dicks. I will leave this as a mystery for now. Perhaps the 3 TGs above between Esther and Nelson are non-Dicks TGs.

Marilyn’s Brother and Claude

Now I will compare all those who have Dicks ancestors. I will look especially at Marilyn’s brother and Claude (Eric’s) dad who may have Dicks ancestors. This resulted in 754 lines of matches. However, each match is listed twice, so there are only 377 matches. A lot of these matches are between close relatives. There would be a lot more matches if I had included Eric and Larry in the mix.

Chromosome 2

Here we have a complicated stretch of DNA:

tg2dicks

This may take a bit of explaining. Previously, I had this as two TGs:

  • TG2D (180-192) with Sandra, Nelson, Denise and Joan
  • TG2E (201-209) with Sandra, Nelson and Marilyn

I see now that Denise should have been in the TG2E. Now we can add Howie to TG2E also. There is another way to look at this TG. That would be that it is a larger TG and that Joan’s DNA didn’t extend to the higher end of it and Marilyn and Howie’s DNA didn’t extend to the first part of it. A few other things:

  • Kenneth and Judy are not in this TG. As they both descend from a Miller line, that would be a likely source of their DNA match.
  • Kirsten also does not appear to be in the TG. I’m not sure how to explain the matches between Kirsten and Marilyn and Kirsten and Howie. The simplest explanation would be that Marilyn and Howie are in the TG through their father’s side and match Kirsten on their mother’s side. However, I don’t know enough about everyone’s genealogy to know if that is feasible.

Here is the larger TG drawn out:

tg2chart

This was a little tricky to draw. What this is supposed to represent is that Sandra, Nelson and Denise are in the larger TG. Joan (in yellow) is in the first part of it and Marilyn and Howie are in the second part or it. I guessed that Marilyn and Howie might be in the box on the right as none of the other four Joyce line descendants are in this TG.

crossovers

I can give a likely reason Joan dropped out of this TG and Marilyn and Howie dropped in. It has to do with crossovers. Let’s look at Joan first. Joan has 2 copies of her Chromosome 2 as we all do. One is maternal and one is paternal. Joan’s Dicks DNA comes from her maternal side. Joan’s maternal DNA is made up of her mother’s two parents DNA joined together (recombined). Those 2 parents were Joan’s grandfather Frederick Upshall and grandmother Daly. Joan’s maternal Chromosome 2 is alternating between Upshall (whose mother was a Dicks) and Daly.

Here is a map of my actual Chromosome 2 showing the alternating pattern:

joelchr2

This chart was created by M MacNeill [prairielad_genealogy@hotmail.com]. It is possible to map this out if you have 2 parents tested, or if you have one tested and 2 or 3 siblings tested. There is even a way to map your grandparents with siblings and no parent tested. In the case above. Light blue represents my maternal grandmother and dark blue is my maternal grandfather. The light red is my paternal grandmother and the dark red is my paternal grandfather. Everyone’s DNA follows the same type of pattern. The actual configurations where the changes are will be different. The place where a color goes from one to another is called a crossover. Sometimes there is no crossover or recombination and you will have all your DNA on a particular copy (maternal or paternal) of a chromosome from one grandparent instead of two.

Back to the TG at Chromosome 2:

chr2joan

Notice what Joan’s matches with Sandra, Denise and Nelson have in common: they all end around 192M. That should be the place where Joan’s DNA switches from her grandpa Upshall to grandma Daly.

Here is Joan’s Chromosome 2:

joanchr2

This shows her matches with:

  1. Esther
  2. Nelson
  3. Sandra
  4. Denise

To the right of the one blue bar on top of the 2 green bars is where Joan drops out of this Dicks TG. I can almost map Joan’s Maternal grandparents from this gedmatch chromosome broswer. Here is my guess:

joanchr2map

A few notes:

  • Joan’s Daly grandmother is not from Newfoundland
  • Another possibility could be that the Upshall segment could extend to Joan’s matches with #2, 3, and 4, eliminating the first Daly segment I have.

Another interesting question is: Why doesn’t Esther match Joan where Joan matches Nelson, Sandra, and Denise? The answer would be that Esther has Upshall DNA in this area rather than Dicks and Joan got Dicks DNA in this area. It’s a bit confusing as you have to picture what is happening on each side of the match between Esther and Joan.

Marilyn and Howie’s appearance in TG2

I’d like to bring up an interesting point about siblings. Siblings represent the only relationship where you will find appreciable FIRs. FIRs are Fully Identical regions. Here is Marilyn’s match with her brother Howie on Chromosome 2:

marilynhowiechr2

This shows that Marilyn and Howie match each other along the blue line. That is from 0 to 147M. Then they don’t match from 147M to 182M. Then they match again to the end of the Chromosome 2. Above the blue bar are green and yellow areas. The yellow is how we match everyone other than siblings. The green is the FIR. That means a double match. As siblings, Marilyn and Howie share all their 4 grandparents: 2 Paternal and 2 Maternal grandparents. Looking at Marilyn and Howie’s Chromosome 2, I can know what the green, yellow and red regions mean:

  • Green – Marilyn and Howie both share a maternal grandparent and a paternal one. We just can’t tell which one right now.
  • Yellow – Marilyn and Howie both share a maternal grandparent or a paternal grandparent. Again we can’t tell which one right now.
  • Red – Marilyn and Howie share the DNA of neither their maternal nor paternal grandparent.

Here is the 2nd part of the TG at Chromosome 2:

tg2marilynhowie

The appearance of Marilyn and Howie in this TG is clear: 201M. I just found out recently that there is a way to expand matches to great detail as shown in the Gedmatch Chromosome Broswer. Here is Marilyn and Howie expanded at around 201M:

marilynhowiechr2-201

This is difficult to see. The number in the middle is 200M. That is one tick mark away from 201 where Marilyn and Howie enter the TG. Another interesting thing is that Marilyn (Molly) above gets out of the TG at 208 and Howie gets out between 212 and 218.  What does all this mean?

  • Based on the expanded view, Marilyn and Howie are FIR from a little after 195M. They jump into the TG at 201. FIR means that Marilyn and Howie share the same 2 grandparents – one maternal and one paternal. However, without the comparison of another sibling, this is difficult to see. I am assuming that from 195 to 201M, Marilyn and Howie share the same 2 grandparents, but not necessarily the same two as after 201M. At 201M, Marilyn and Howie both get their DNA from their paternal grandmother Sarah Priscilla. Sarah is the one with Dicks DNA.
  • At 208M, Marilyn drops out of the TG before Howie.

Here is an expanded view of an already expanded view of Marilyn and Howie at 208M:

chr2-210

Every little tick mark [^] is 1M. So 2 ^’s before 210M is 208M. That is where Marilyn and Howie go from FIR to HIR. An HIR is a Half Identical Region. That means that Marilyn and Howie match one grandparent (on the maternal or paternal side) and they don’t match the other grandparent (on the opposite of the maternal or paternal side where they do match). This is easier to show by mapping it out:

chr2map

It is clear that from 201 to 208, that Marilyn and Howie are in a TG. They are also FIR. That means that they have 2 grandparents the same (one paternal and one maternal, here represented by blue and yellow). The TG identifies the paternal grandparent as Sarah. She is the one that descends from the Dicks family. We don’t know which Maternal grandparent that Marilyn and Howie got their DNA from. We just know that it is the same grandparent.

At 208M, two things happen. Marilyn exits the TG and is now in an HIR with her brother Howie. HIR means that Marilyn gets her DNA from one grandparent (on the maternal or paternal side). On the other side from where she gets her DNA, she doesn’t get her DNA from the other. In this case, that means that she continues to match the same maternal grandparent and switches the paternal grandparent that she gets her DNA from from Sarah to Jesse.

All this is to say that it is helpful to have a sibling or more tested.

Chromosome 12

Like the TG at Chromosome 2, the TG that Howie is in at Chromosome 12 is not new. It has been described previously. Here is what it looks like in a spreadsheet:

tg12howie

The difference is that there is a Joyce Line TG within an apparent Dicks TG (in gold). Also within the gold TG there are single matches of people from the Henry Dicks Line. That could mean a few things:

  • The green matches are in non-Dicks lines
  • The green matches are with Dicks lines. If that is true, that would mean that the gold TG must point back to the wife of Christopher Dicks who I have as Margaret b. 1789.

In TG2, I had missed Denise in part of the TG. Previously I had missed Pauline in this one. Part of the reason I may have missed Denise in TG2 is that her match with Marilyn was less than 7 cM so didn’t show up at Gedmatch at threshold levels. In this case Marilyn doesn’t match Pauline, because she drops out of the TG right around the spot where Pauline joins in the TG (127M).

Here is Joan compared with Esther, Howie, Marilyn and Pauline:

joanchr12

In the above browser image, Joan’s maternal grandparent mapping would likely go Upshall, Daly, Upshall. One can see where Howie and Marilyn jump into the TG in the 2 yellow bars. You can also see how Marilyn (#3) jumps out of the TG on the right and Pauline (#4) jumps in (green bar).

For comparison, I will show the same matches from Esther’s point of view:

estherchr12

Esther’s view has to be exactly the same for #1 as they are comparing the same 2 people (Joan and Esther). Esther’s view gives a crisper indication of Marilyn’s crossover.

Chromosome 12 is shorter than Chromosome 2, so it should be simpler. Here are Marilyn and Howie compared at Chromosome 12:

mhchr12

Marilyn and Howie have 3 HIR’s, one FIR and one area where they don’t match either of their grandparents. In that area where they don’t match, if Marilyn got her DNA from her her maternal grandmother and paternal grandfather, for example, it would mean that Howie would have to get his DNA from his maternal grandfather and paternal grandmother.

We have more detail on the positions from the TG:

tgpauline

Howie and Molly jump into the TG at 114M. Molly jumps out at 126M and Howie jumps out at 132M. Actually, he had to as that is the end of the Chromosome!

Looking at Marilyn and Howie’s expanded view of Chromosome 12, their FIR starts at 101M. That switches to an HIR at about 126.5M. That corresponds where Marilyn gets out of the TG. It also corresponds where the green goes to yellow in the Gedmatch Chromosome browser in the image above.

mh12map

This looks similar to the Chromosome 2 map of Marilyn and Howie. This time I was a bit more brave due to my experience with Chromosome 2 and mapped their DNA to the beginning of their HIR rather than just to the beginning of where they jumped into the TG (113M). The reason for this is for there to be a change at 113M would require a double crossover for these two which is unlikely. Another note is that the yellow grandparent in this example may not be the same as the yellow one in Chromosome 2. It is just meant to represent one of the maternal grandparents in each case.

One More Question On Crossovers

I’m learning this as I go along. I had determined a crossover above at 126.5M above where one sibling left the TG and the other stayed in. However, I did not have a crossover at 114M where both siblings entered the TG. Why is that? I had a crossover at 126.5 because the chromosome browser verified that the siblings were switching from a FIR to an HIR at 126.5. To me, this verified the crossover in conjunction with the change in TG at the same location. At 114M, there was no change:

chr12pos114m

Above is the close-up view of Marilyn’s match to Howie on Chromosome 12 between positions 110 and 120M. The whole area on either side of 114M is FIR. That likely indicates no crossover at Marilyn’s and Howie’s grandparent level. However, it was Marilyn’s great grandmother Bertha Joyce that had her grandparents’ Dicks and Joyce DNA recombining into a crossover. It is likely that this TG represents the DNA that Bertha Joyce received from her grandparents probably sometime around the American Civil War. I note that the TG that I looked at above at Chromosome 2 followed the same pattern. The crossover was where one sibling left the TG and the other remained. Where the two siblings started in the TG, there was no change in the FIR region to an HIR.

So the answer is that there was a crossover at some point at position 114M, but quite a while before the time period that we are looking at here. So it is hidden in my map above.

Dicks TG Matrix Update

dicksmatrixupdate

  • Here I took out Eric as his father Claude (who is believed to be the one descended from the Dicks family) was not found to be in a TG. Eric was in a TG with Joan and Esther, but that must have been on his maternal (non-Dicks) side.
  • I didn’t add 2 extra columns for Howie, but put him in the appropriate boxes where the existing TGs for his sister Marilyn were.
  • I added Denise to TG2E and Pauline to TG12B. That was an important addition for Marilyn and Howie as it seem to indicate that their Dicks DNA comes from the Joyce rather than the Cran Line in this case. Recall that in TG2E, I was suggesting that this might represent the Cran line for Marilyn and Howie.

The All-Dicks Comparison

autosomalmatrix

The top left box are the Christopher Line descendants. The bottom right box is the Henry Dicks Line descendants. This now includes Claude and Howie. For an interesting comparison, run down the two columns of Molly and Howie and see how the total cMs of their matches differ.

Summary and Conclusions

  • I didn’t add any new TGs by the addition of Marilyn’s brother Howie and Eric’s father Claude.
  • Marilyn and Howie are the first known Dicks descendant siblings to have their DNA tested. So I took advantage of that to explain how crossovers work and how they are important in mapping DNA.
  • The combination of the sibling comparisons and TGs made it possible to partially map two of Marilyn’s and Howie’s paternal grandparents on portions of Chromosomes 2 and 12.
  • I also showed a likely scenario for Joan’s crossover point within a TG which would lead to mapping segments that she received from her maternal grandparents
  • I clarified a few issues and refined the Dicks Triangulation Group Matrix

 

 

DNA Phasing of Raw DNA When One Sibling is Missing: Part 10

In this Blog, I would like to portray my phasing results in an Excel Bar Chart if possible. This has been one of the most difficult parts a phasing my DNA for me.

I have looked at Stacked Bar Charts in Excel as they seem to be the closest to what I am looking for. Today I looked at a method for producing Gantt Charts at ablebits.com which seems to hold some promise of application for DNA mapping:

bar-chart-excel

I had my Maternal Patterns’ Starts and Stops from my last blog. I took those and converted them to Build 36 and put them in a spreadsheet:

momcrossoverstable

Start is the ID# I was using. Start36 is the Chromosome position of the Start of the pattern in Build 36. App ID is the approximate position of the Crossover. Then I have that same location in Build 37 and Build 36. Following the logic in the Ablebits.com tutorial, I have the first Maternal Crossovers for Chromosome 7 in my simplified Chart:

matfirstxover7

I got this by choosing the Build 36 column and choosing Insert Stacked Bar. I suppose a better Title would have been Chromosome 7 Maternal Crossover rather than Build 36. This was taken from my Column Header. The goal is to get a 2 color bar above. However, I already see a problem. The bar needs to be different colors for different people. Well, I have to start somewhere.

Next, I put in the next crossover location for each person. I took this position and subtracted from it the first Crossover to get a length.

step2crossexcel

You may note that the Bar Chart inverts the original order. It gives Sharon a 4 which is now on top. Here is my visual phasing of Chromosome 7 that I am trying to replicate:

chr7visphase

My Excel Bar Chart order is Sharon, Jon, Joel, Heidi. My visual phasing order is Sharon, Joel, Heidi, Jon. The 2 maternal colors I have above are green and orange representing Lentz and Rathfelder. If I keep orange as Rathfelder, that means I want to change bar 2 and 3 (Joel and Jon) on the Excel Bar Chart. One way to do this is to move over the first Crossovers for Joel and Jon in my spreadsheet:

modchart

However, that made the 2 male siblings’ first maternal grandparent match too long. I needed to move the start over 2 places in my spreadsheet:

mat7revised

Now the Chr7 Maternal Crossover column can be called Lentz and the 2length column can be called Rathfelder.

Next, I added another column for the next Lentz portion of DNA:

chr73rdxover

I was hoping that if I named the next column Lentz, that Excel would give me the same blue as the first Lentz. I was able to right click on the gray and change it to blue. I then added another Rathfelder segment. For this to work in Excel, a Rathfelder length is added rather than a start and stop location.

chr7xover3

Again, I had to reformat the Excel-chosen color to be consistent with what I had for Rathfelder. I chose the last position for Heidi and Sharon as the highest that I had as this was their last segment. After a bit of wrangling with Excel, I was able to get this:

chr7

So that is the presentation. However, I notice that on my visual phasing, I had 5 segments for Jon and only 4 here. I missed his last Rathfelder segment. I had ended Jon’s Chromosome too early. Here is the correction:

chr7corrected

It still looks like one of Jon’s crossovers in the middle of the Chromosome may be off, but I’ll have to figure that out later.

Paternal Bar Chart

Now that I have something that looks like a maternal Chromosome Map, I need the paternal side to go along with it. It looks like if I add 4 more rows to my spreadsheet, I may have it.

I did this and I added Hartley and Frazer (my paternal side grandparents) to the right of the maternal side grandparents. I had to make a new chart that came out like this:

chr7matpat

Here #4 is my Paternal DNA. I found it a bit disconcerting that my paternal side was longer than the maternal. Here I’ve added a bit of formatting and made the colors consistent (one color per grandparent):

chr7patmatmap

Well, I guess I’ll just leave this imperfect. It will give me something to work on later. I did change the scale from millions to M’s to be easier to read.  The above shows that Jon and Heidi share their paternal grandfather’s Hartley DNA un-recombined on Chromosome 7.

Summary and Conclusions

  • Learning how to phase my raw DNA has been interesting and time consuming
  • Delving into the A’s, G’s, T’s and C’s promotes understanding of one’s DNA
  • I owe a lot to M MacNeill and Whit Athey in learning how to do this phasing
  • Due to the data intensive nature of phasing, I would recommend the use of MS Access or some other database software.
  • An understanding of Excel or similar spreadsheet software is also important.
  • I had tested my brother Jon as an afterthought. It turned out that his test results were important in determining the phasing of the 4 siblings.
  • I have the overall skeleton of the phasing with crossovers. There is still a lot of work to complete the individual Chromosomes and trouble shoot problem areas.
  • Further, I have not worked on the X Chromosome due to the different nature of that Chromosome. My brother and I are already phased. My sisters are not.
  • Once these maps are done they will be a reference to all matches to my 3 siblings and myself.