Category: DNA General

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Don’s Frazer DNA

I recently had an email from Ros introducing me to her 3rd cousin Don. Don is a Frazer descendant and genealogist who had recently taken an autosomal DNA test. Both Ros and Don are from Australia. I am happy to write a Blog about Don and his DNA. Unfortunately, due to a storm here in Massachusetts, our power is out. No problem, I can use my laptop. However, I had to figure out to connect to the internet through my cell phone. Now I know how to do that.

Before the electricity went out, I checked Gedmatch and Don matches my sister Lori.

This is quite interesting as I have mapped out the DNA for myself and 4 of my siblings. Lori is the only one out of 5 tested siblings that has Frazer DNA in that area of Chromosome 13. The map shows how we got the DNA from our four grandparents. Our grandparent of interest to this group is Frazer.

The others siblings have mostly or all Hartley DNA on their paternal sides. Also Lori was the last sibling that was tested. This points out the importance of testing siblings.

Here is the line that Don is on:

As Don is a 3rd cousin to Ros, that means that he descends from John Parker Frazer and Honora White on the left purple line. My sister Lori isn’t even on this line. She descends from a Frazer one layer up making her a 6th cousin to Don. That is quite a way back for DNA to be working, so that’s pretty good. Put another way, Lori and Don’s common Frazer ancestor is 7 generations away.

Don’s Frazer/Stinson Line DNA Matches

Don’s closest relative on the Frazer/Stinson DNA chart above is Vivien. She is a second cousin once removed to Don. Vivien is also Don’s top match on his ‘One to Many’ list at Gedmatch.

Don and Vivien’s common ancestors John Parker Frazer and Honora White are actually 3.5 generations away. That is, 3 generations from Vivien and 4 from Don average out to 3.5 generations. Gedmatch shows that the common ancestor by DNA is 3.4 generations away. That means that Don and Vivien share a slightly less amount of DNA than average. I would expect that about half of the DNA they share would be Frazer DNA and half would be Frazer DNA.  One odd thing was that I didn’t see Vivien’s daughter Jean on Don’s list of DNA matches.

don and ros

The next person on Don’s ‘One to Many’ list is Ros. By that list, it looks like they share 28 cM of DNA/ However when I choose the actual match, it shows that they share much less DNA than that for some reason:

An average amount of DNA shared between 3rd cousins is 74 cM, so that raises some questions. Did Ros just get a lot less than average (which is possible) or perhaps there was a second marriage for one the ancestors in common or other explanation.

don and michael

Based on the chart above, Don and Michael are 4th cousins, once removed.

Note that Don and Michael share a segment on Chromosome 7. This is the same segment that Don and Vivien shared. That would mean that Don and Michael would have gotten this DNA from either Archibald Frazer, b. 1778 or Ann Stinson. That is pretty old DNA.

The New and Improved Frazer Autosomal Matrix

I made some changes to the Frazer Autosomal DNA Matrix

I tried to put the Matrix more in line with what I think the genealogy is.

  • Heidi through Gladys descend from Violet and James Frazer. Violet is the daughter of Richard. James father is unknown, but I have put him as a son of Philip Frazer as a likely candidate.
  • Patricia, Susan, Bill and Gladys under that scenario descend from all three sons in the Archibald Line: Philip, Richard and Archibald (who married Ann Stinson).
  • I have Michael and Jane descending from Richard and Archibald
  • Cathy through Don descend only from the Archibald that married Ann Stinson.

Don’s Triangulation Group (TG) Matrix

Here I have added Don to the existing Frazer DNA TG Matrix.

Don is in two Triangulation Groups. The first one I already had with Michael, Vivien and Janet.

I took Michael from the Richard Line as I don’t know if the match is with him there or in the Archibald/Stinson Line. I don’t know for sure that the common ancestor that the DNA is identifying is the original Frazer couple in Ireland or someone else. A good candidate for the ‘someone else’ would be anywhere there is an unnamed spouse in the direct ancestry.

The second TG is new and is with Pat and Susan.

This seems more straightforward than the previous TG. However, this TG could represent a common ancestor a generation earlier as the yellow family above also descends from the Richard Frazer line (brother of the Archibald above). However, that would be less likely than the above scenario.

Don’s YDNA

Don hasn’t tested for YDNA, but as a direct Frazer descendant, he would be a good candidate for it. So far, three Irish Frazers from our DNA study roup have taken the YDNA STR test. Two have been from the Archibald Line and one from the James Line. These lines go back to the early 1700’s in Ireland. The most recent STR tree that I drew for the Irish Frazers is here:

That STR tree reflects this genealogical tree:

Right now the STRs 391=11 and CDYa = 45-50 define the Archibald Frazer born about 1715 Line. The STR 444 = 13 that Rick has defines the Richard Patterson Frazer b. 1830 Line. The STR 576 = 19 defines the George Frazer b. 1838 Line. If Don were to test his YDNA STRs, that would define the line of Archibald Frazer b. about 1778 who married Ann Stinson Line.

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Fitting Barry into the Dicks Genealogy by DNA

My wife’s mom and 1/2 great Aunt Esther seem to be getting some good Dicks descendant matches at Gedmatch recently. One of the newest ones is Barry. Barry is match #5 on Esther’s ‘One to Many’ list at Gedmatch. Barry is match #8 for my mother in law Joan. #8 out of 2,000 matches is not bad.

The Genealogy

Barry tested at Ancestry. He hasn’t linked his tree to his DNA test, but I have found a little tree that Barry put together:

I quickly started off by recreating the tree. However, I headed in the wrong direction. There was a Harbour Buffett marriage on-line for a William Dicks and Edith Hann which I assumed was the right one. Apparently there were two William Dicks/Edith Hann married couples. One was in Harbour Buffett and the other in Little Harbour East. Here’s a map posted at the Newfoundland Gedmatch Facebook Page that I high-lighted:

Little Harbour East apparently is adjacent to Little Harbour.

Barry’s tree connects to Hayley’s tree.

My previous Blog was on Hayley’s DNA. According to Barry, this branch of Dicks moved from Harbour Buffett to Little Harbour East in the 1860’s. Hayley helped me out by sending along the Little Harbour East Censuses for 1921 and 1935:

I was unable to find Bertram on my own, probably due to a Census misspelling. Here is a photo of the twice-married William Dicks sent to me by Hayley:

Barry’s DNA

Hayley is Barry’s first match on his ‘One to Many’ list at Gedmatch:

They have all sorts of DNA shared. A common ancestor of 2.5 usually means a 1st cousin, once removed. That is what we have here:

Esther is a 2nd cousin once removed to Barry based on the chart above. By DNA, on average, their common ancestor should be 3.5 generations away. Here is what the DNA match between Esther and Barry shows:

This shows that either Barry and Esther share more than the average DNA for a 2nd cousin once removed or that they have extra ancestors in common. Based on Newfoundland genealogy, I would guess the latter. By DNA, Barry and Esther look to be more like 2nd cousins.

Joan and Barry should be 3rd cousins by their common ancestor, Christopher Dicks. At Gedmatch, that would be on average 4.0 generations to a common ancestor. Here is what Gedmatch shows for the DNA match between Barry and Joan:

The difference isn’t as pronounced with Joan. Perhaps because her ancestry is one quarter Newfoundland and Esther’s is 100% Newfoundland.

The Autosomal Matrix

I like to look at the matches in Gedmatch’s Autosomal Matrix as the different lines of descent sometimes become apparent.

If I look at Barry going across, his largest non-close family match is with Esther. This tells me that compared to all these other Dicks descendants, he fits in the Christopher Dicks group.

  • Barry has a good match with Ken in the Crann group, but not with others in that group. This could indicate a non-Dicks match between Barry and Ken.
  • Ken has large DNA matches with many of the Dicks descendants on the Matrix.
  • I had forgotten that Ken has a Dicks ancestor on the Burton line also. The matrix seems to show he is more closely matched to that line than the Cran Line. I had forgotten about Ken’s Dicks/Burton ancestors, so the Matrix didn’t highlight that.
  • Esther and Nelson match others more as they are one generation closer to their common ancestors than others.
  • Esther has an additional Dicks line that I haven’t figured out yet.
  • Others will have other relationships with families outside the Dicks family which would cause interference.

Triangulation Groups: A Better Way

A Triangulation Group (TG) is a group of three or more people. All their DNA matches each other in every combination. When this happens, the group should have a common ancestor. In a group of all Dicks descendants, the common ancestor is more likely to be a Dicks ancestor (or spouse). The problem with creating a large Dicks TG Matrix is that it takes a while to look at all the possible matches.

The goal when I have done all the Dicks triangulation is to put all the results into another matrix. I had done that before with the Henry line which is a brother line to Christopher Dicks, b. about 1784. I took out the Henry Line for simplicity below:

Looks like I am missing at least Ken, Sandi, Hayley and Barry. I should also add in Clayton, as there is some question as to which line he is in. The pink TGs indicate that the DNA could be coming from the spouse of a Dicks. For example, an all Adams line TG, could be DNA coming just from Adams and not Dicks. Marilyn aka Molly and Howie are siblings. If two siblings plus another match, this is not usually considered a TG as the siblings have the same parents. Esther and Joan are in many TGs, but as they were the only two at the time from the Christopher b. about 1813 Line, those TGs go outside that line (or are from the unknown wife of Christopher).

When I do this comparison of Dicks DNA, I get 1620 lines of matches. However, each combination is repeated, so it is only 810 lines really. When I make the new TG Matrix, there is good news and bad news. The good news is that Ken and Barry especially have created a lot of new TGs. The bad news is that it makes the TG Matrix show up very small:

I made a slight adjustment in the TG Matrix. I put Molly and Howie in just one row, but that row is for Joyce and Crann. A few other observations:

  • Barry appears to be in TGs 7 times with the Christopher Line. That appears to place him solidly in the Christopher (born about 1813) line
  • Barry appears to be in TGs 3 times with Nelson of the Adams line. This could be partially because Nelson is one generation closer to common ancestors.
  • Ken’s results are confusing to read. He seems to be in TGs outside the Cran group more than in it.

Ken’s results

Ken’s closest relationship in his Dicks/Cran line is 3rd cousin, once removed. That is with the common ancestor of Robert Dicks and Jane Cran.

However Ken is also 3rd cousin once removed with Esther and Nelson with the common ancestor of Christopher Dicks, the father of Robert Dicks born about 1784. It may also be that Ken is in many non-Dicks TGs with Dicks descendants as he may be more closely related on those lines than the Dicks lines. For example, I know that Ken has an Upshall ancestor. The TG that he has with Esther and Joan could be a Dicks TG, an Upshall TG or some other name where we have a missing ancestor. Compare the Christopher Line to the Cran Line:

Barry is only 2nd cousin once removed to Esther and 3rd cousin to Joan. This makes a big difference in the DNA comparisons compared to Ken’s Cran relative results. Another thing that I forgot was that Ken has ancestors in the Dicks/Burton line also:

Let’s say that Ken’s case is advanced DNA analysis and I don’t have to figure out all his matches right away.

Summary and Conclusions

  • Barry and Hayley appear to be linked closely by DNA to Esther and Joan. The interpretation is that they are linked in the same Christopher Dicks Line.
  • Without Barry’s results, it would have been difficult to interpret Hayley’s results by the TGs. However, as we know that Hayley is closely related to Barry, his results apply to Hayley’s
  • Ken’s results aren’t easy to interpret just within the context of the Dicks DNA study. I left my previous Blog on Ken thinking there was more to be discovered about all his matches and I still feel that way.

 

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A New Harbour Buffet DNA Match

My wife’s great Aunt Esther is Ms. DNA for Harbour Buffet. She likely matches anyone else by DNA who has Harbour Buffet ancestors. Both Esther’s mom and dad were from Harbour Buffet:

I noticed recently that Esther has a new match at Gedmatch named Doug. Doug is Esther’s fourth match on her ‘One to Many’ list at Gedmatch. Her first is my mother in law. The second is my wife. The third is Ken who I blogged about here.  I have a feeling that Ken and Doug will match by DNA.

Here is Doug’s tree:

A lot of Douglas’ ancestors were from Harbour Buffet. Douglas has two Samuel Kirby’s in his ancestry. Also an Upshall which is great. Notably missing from Douglas’ ancestry is the Dicks name. I have written many blogs about the Dicks family.

Here is Doug’s match to Esther by DNA at Gedmatch:

Remember that I thought that Doug would have a big match with Ken above? Well I checked and didn’t see Ken on Doug’s ‘One to Many’ match list at Gedmatch. This is a little surprising as they appear to share at least two surnames.

Doug and My Mother in Law, Joan

My mother in law, Joan is related to her 1/2 Aunt Esther on the Upshall line, but not the Kirby line. Here is how Joan matches Doug by DNA:

When I add in Esther to the mix, here is a simplified view of their combined ancestry:

  • It is simplified to show common ancestors and potential common ancestors
  • Further it is missing two of Douglas’ Kirby lines
  • It is meant to show that Joan does not descend from the Kirby family
  • It is possible that Henry and Jane Upshall could have been siblings.
  • Note that the two potential Upshall siblings Henry and Jane are shown in different generations.

DNA Triangulation – Upshall?

Triangulation as implied by the name requires the DNA matching between three people. The potential for this happens at Chromosome 2. Esther and Douglas match between about 209 and 243M. Douglas and Joan and Esther and Joan match between about 238 and 243M. When this happens, it is likely that the three people share a common ancestor. In this case, an Upshall common ancestor would be possible based on the genealogy. That is, possible, until I consider Molly.

Molly is in the Dicks DNA Project that I have been working on for some time. She also matches Douglas on Chromosome 2. Here is how Douglas matches Esther (1) Molly’s brother Howie (2), Molly (3) and Joan (4):

This shows that Molly and her brother Howie are in a Triangulation Group (TG) with Douglas and Esther. Then Douglas, Esther and Joan are in a TG. How can this be?

A Possible Crann Explanation for Douglas, Esther, Molly, Howie and Joan

The problem above is that Molly has no known Upshall ancestry but has Crann and Dicks ancestry. Douglas has no known Dicks ancestry but has Upshall ancestry. In a previous Blog, I had theorized that either an Upshall or a Dicks had married a Crann:

This was based on Crann lines in green above with no Newfoundland ancestry. What if the father of Henry Upshall above married a Crann? Supposing that Crann was also the mother of Jane Upshall? This is perhaps a house of cards, but an interesting theory that would explain the DNA matches. Under this scenario, the TG for Molly, Howie, Esther and Douglas would represent Crann DNA. The TG for Douglas, Esther and Joan could either be Upshall or Crann DNA.

a few arguments against my theory

The theory above is not without its problems. One is that Douglas doesn’t match any of the non-Newfoundland people with Crann ancestry. The other problem is that I notice Douglas has a tree on Ancestry with different ancestors for Jane Upshall:

This would also be confusing, if true, as Esther has Burton ancestors on her maternal side.

Well, as they say, Rome was not built in a day.

Summary and Conclusions:

  • Douglas and Esther have a large DNA match
  • Douglas and Joan (who doesn’t have Kirby ancestry) match to a lesser extent
  • I assume that most of Douglas and Esther’s DNA matching has to do with their common Kirby and Emberley ancestors. However, as these names are not in my wife’s and mother in law’s ancestry, I have not been following these names.
  • Douglas, Joan, and Esther share the ancestral Upshall name which appears to be somewhat rare.
  • Some of the DNA shared between Douglas and Joan appears to be from a common Upshall ancestor
  • A Triangulation group between Molly, Howie, Douglas and Esther could be from a Crann line. However, this is a theory at this time. As part of that theory, a Crann would have married an Upshall.
  • I was expecting Douglas to match Ken who I had looked at before. Ken also has an Upshall in his ancestry. However, I could not find a DNA match between Douglas and Ken.
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Blaine’s X Chromosome Challenge

Recently, Blaine Bettinger challenged people on his Genetic Genealogy Tips & Techniques page:

Who is your closest X match at GEDmatch, that you didn’t target test? 

Blaine’s previous challenge challenge produced some interesting results and I was running out of ideas, so I thought that I’d try it. Technically, my closest X match is fourth on my Gedmatch list below. That match is my maternal 1st cousin Rusty at 120 cM, but I think that Blaine meant to look for the first match that we didn’t know.

The top six matches are my mom, four siblings and a maternal 1st cousin. I have four matches at the bottom of the list. They all have the same email address, so I assume they are closely related. These are my highest X Chromosome matches where I don’t know how we are related. A good surprise is that the top match Alice has a family tree indicated by a GED hyperlink.

I quickly checked the GED link looking for maternal matches. My mom’s matches are usually German on her dad’s side, or from Sheffield, England. I was disappointed to not see any of those places on the list. I did however see a Pennsylvania name of Faunce. My mom is from Pennsylvania and has a Faunce ancestor.

Here is Alice’s tree as posted at Gedmatch :

Here is my mom’s tree:

If Alice’s tree had a Jacob Faunce, then I would have had a match and Catherine and Elizabeth Faunce could have been sisters. However, it is not that easy.

Back to the DNA

Here is the detailed match I have with Alice:

Here is the results of mapping the X Chromosome to myself and 4 siblings:

My match with Alice was in my Lentz area which leads back to Faunce. I have the bar starting with J. It looks like Sharon and Jonathan should also match Alice on the X. Here is the path that the X Chromosome inheritance could have taken for my mom:

Alice also has a clear sailing path for her X Chromosome. It goes from her mom Rosalie, to her grandmother Alice, then her great grandmother Ida, 2nd great grandfather Anson Hale and finally to Alice’s 3rd great grandmother Elizabeth Faunce. Now that I’ve established a route where there could be an X Chromosome match, I need to get back to the genealogy.

Catherine Faunce and Her Daughter Mary A Baker

It took me a long time to figure out who was the wife of my 2nd great grandfather George Washington Lentz b. 1840. I was determined to find out who she was. The 1910 Census George’s son Jacob Lentz gave me a hint.

Here on Earl Street there were three generations of Lentz. My grandmother, Emma, her dad Jacob Lentz and his mother Mary Lentz. Of particular interest was the fact that an Aunt, Sohpia Kemble was living with them. She was 72 at the time. Next, I go back 10 years to 1900:

Mary Lentz is living with her two sisters in Palmyra, NJ. One of Mary’s sisters is single – Elizabeth Baker. That gives me the maiden name of Mary Lentz. The Findagrave.com has an article on Mary Baker Lentz’s mom who was Catherine Faunce:

Here is the marriage record for Catherine Faunce in 1824:

The record reader interpreted Faunce as Fanner.

Elizabeth Faunce

Alice has her ancestor Elizabeth Faunce as the mother of Anson Hale on her tree. Here is Anson and mother Elizabeth in 1860 along with the rest of the family with them at that time:

Here Elizabeth was born in Pennsylvania. I had a lot of trouble finding information on Elizabeth outside of Ancestry Trees. This makes me suspicious that the trees are copying each other. The 1880 Census tells us that Elizabeth’s parents were also born in Pennsylvania. I was able to find a tree Alice put on FamilySearch:

Above, I’m not sure the jump from Pennsylvania to Plymouth, MA is warranted. My understanding is that the Philadelphia Faunce family was originally the German Fans which got anglicized to Faunce.  The Plymouth, MA Faunce was probably always the English Faunce. Another point is that in the 1880 Census, Elizabeth [Faunce] Hale lists both her parents as being born in Pennsylvania.

William Hale and Elizabeth are in Howell in 1850:

Joseph appears to be their eldest. He was born around 1832, so let’s say William and Elizabeth married in 1831. It turns out that may have been a good guess as I find this at Ancestry:

I at least feel better finding a record outside of a Family Tree. Now I feel justified in adding the Faunce surname to Elizabeth. However, note that these two were married in Philadelphia where my mom’s Faunce ancestors lived. From my tree, I have a Jacob Faunce living in Kensington, Philadelphia in 1820. At this time, Elizabeth would have been between 7 and 12 depending on whether she was born in 1809 or 1813.

There were eight people living in Jacob’s house in 1820. Let’s say there were two parents and six children. Of the six children, four were girls. One was under 10, two were 10-15 and one was at least 16. It could be that Elizabeth Faunce was one of these four girls.

Summary and Conclusion

  • My closest non-identified X match is on my Lentz line
  • That X inheritance line could follow back to my ancestor Catherine Faunce in Philadelphia
  • My closest match Alice’s X inheritance line could follow back to her ancestor Elizabeth Faunce who married William Hale in Philadelphia in 1831
  • Alice has a father for Elizabeth who was from Plymouth Massachusetts
  • Based on the DNA and genealogy I believe this Plymouth father may not be correct for Elizabeth Faunce.
  • I am suggesting that Elizabeth Faunce is linked with a Philadelphia Faunce family based on DNA and genealogy.
  • Although I have shown that it is possible for Elizabeth’s father to be my Ancestor Jacob Faunce, I have not been able to prove that by the DNA and genealogy.

 

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Cousin Mike Joins the Fray

I was presently surprised when looking over my AncestryDNA matches recently. I saw my second cousin Mike. Now due to the fact that I have many second cousins descending from James Hartley and Annie Snell, I don’t happen to know them all personally. Fortunately, I do know Mike and if I met him somewhere would surely say hi.

Mike at AncestryDNA

At AncestryDNA there is a button to push called Shared Matches. When I look for Shared Matches between me and Mike, I get a lot of people. I first get my 4 tested siblings. Then I get 11 second cousins. These are actually 2nd cousins by DNA. In other words, Ancestry looks at the amount of DNA shared and guesses that these should be in the 2nd cousin range. So Ancestry has the first four of my list of shared second cousins in the 1st to 2nd cousin range. The rest on the list are in the 2nd to 3rd cousin range. However, these are all actual second cousins that Mike and I share. These would be descendants of the 13 children that my great grandparents James Hartley and Annie Snell had. Actually, first on his list of 2nd cousins is Joyce. She is a first cousin once removed. I had her tested at the last family reunion. I wrote a Blog about her results here, and about Mike’s sister Holly here. Down in the Third Cousin Shared Matches there may be 2nd cousins once removed. There is also one non-Hartley Snell relative listed there.

Mike at Gedmatch

I asked Mike to upload his DNA results to Gedmatch. That is where you can find out more about your DNA. For example, here is how Mike matches his sister Holly on Chromosome 15:

I bring up this example, because full siblings match each other in a different way than any other relationship.

  • We all get a chromosome from our mom and one from our dad. They in turn got one from their mom and one from their dad. That means there are four ways that we can get DNA from our parents. Those four ways are from our four grandparents
  • The blue bar on the bottom shows where Mike and Holly match by DNA.
  • The yellow bar above the blue means that Mike and Holly share the DNA from one parent only. And they get their DNA from only one parent of that parent. However, we don’t know which one right now.
  • The green bar above the blue bar means that Mike and Holly share DNA from both their mother and father. Not only that, they share the DNA from one of the mother’s parents and one of the father’s parents. However, we don’t know which one yet.
  • The red area is where Holly and Mike share no DNA from either parent. That is the opposite of the green area. That means Mike may get his DNA from a maternal grandfather and Holly from a paternal grandmother in that area. I’ll give some examples below.

Here are Mike and Holly’s grandparents:

Here is how Mike and Holly match each other on Chromosome 7:

Below the first green bar (which is called a Fully Identical Region or FIR), I have split this out for Mike and Holly. This is split to identify Mike and Holly’s maternal and paternal sides (but we don’t know which yet). Mike and Holly have two of the same colors. That means that they got the DNA from the same two grandparents. One of those grandparents is paternal and one is maternal. We don’t know which is which yet, but we can easily figure out the paternal grandmother. We can do that because all of Mike and Holly’s second cousin DNA matches on the Hartley side that I mentioned above.

The first match is Mike’s 1st cousin once removed Joyce. Then there are my 4 siblings. #6 and 7 are two other Hartley-descended 2nd cousins. That means that all this DNA maps to Mike’s grandmother Grace May Hartley. Put together, these matches go from 15.6M to 95.6M for Mike.

Here I assigned blue as Mike and Holly’s paternal grandmother. In the green area, Holly had to have the same DNA from the same Hartley grandmother. In the red area, Holly had to have the DNA from her Gifford grandfather because neither grandparent matches in a red area. Now let’s look at Holly’s 2nd cousin matches.

Above, Holly matches Joyce from 6-42M.

Because Holly gets her DNA from her Hartley grandmother before about the 16M mark, that must mean Mike gets his paternal DNA in that area on his Gifford side. Otherwise, he would have matched at least one of his Hartley cousins there.  Then I moved some of the orange DNA to the left. This would be maternal DNA which is from either Jenney or Murray. This also meets the requirement of the first yellow area. That area is called an HIR or Half Identical Region. It is where Mike and Holly share the DNA from one grandparent but not the other. In order to know which grandparent that DNA is from, we would need to have a match to a Murray or Jenney. In order to do this right we would also need another color for the 2nd maternal grandparent.

This is also a lot easier when there are three siblings to compare because then we could find out where the crossovers are. An example of a crossover is on Mike’s DNA where the DNA he got on the paternal side goes from Gifford to Hartley.

Me and Mike and Our DNA

When I look at my DNA matches at Gedmatch, my match with Mike is the highest level shared between any of my second cousins – at least the cousins that have uploaded to Gedmatch. Mike’s sister Holly had the record before that. Here is what the specifics look like between Mike and myself:

At the bottom of the list is a number of 2.7 generations. That is how far back it looks like our common ancestors are based on the DNA match. They are actually 3.0 generations away. That means that we share more than the average DNA for 2nd cousins. Some of my second cousins will share more than average amounts and some will share less than average amounts of DNA. If I look at Mike’s match list, he shares more DNA with two of my sisters and another 2nd cousin than he does with me.

Mapping My DNA By Cousins

I showed one way to map DNA from your grandparents comparing siblings’ DNA. Another way is to directly map your cousins’ matches to a chart. Kitty Munson has developed some software to do this. Right now my map looks like this:

The darker blue maps to James Hartley and Annie Snell. That would be via my 1st cousins once removed and my 2nd cousins with the same ancestors. Mike’s DNA fills in a few blanks in my map:

I guess the changes are subtle. The Hartley side should only ever fill up about one half of my paternal chromosomes. The other half for me would be for Frazer and Frazer ancestors.

Mike’s X Chromosome Matches: No Hartleys There

Mike’s biggest X Chromosome match is with his sister Holly:

Mike, like me, won’t match any Hartley relatives on the X Chromosome. That is because a father never passes an X Chromosome down to a son – only a Y Chromosome. The big match between Mike and Holly is from their mom. She got her X Chromosome from some combination of Jenney and Murray.

Mike’s Lancashire DNA Match

These matches above represent Lee’s DNA matches on Chromosome 13 with 5 siblings in my family, our two 1st cousins once removed and Mike in the green.

I have mentioned in a previous Blog about Joyce, that Hartley descendants have a match with Lee at AncestryDNA and Gedmatch. Lee shows all his ancestors as being from England.

In this match, Lee’s ancestors are in orange and mine are in blue. When I zoom in to Trawden, where the Hartleys were from, I see Lee has ancestors in this area:

At the time our ancestors were in Trawden, they had to go to Colne for baptisms, weddings and funerals as there was no Church of England Church in Trawden. Colne is represented by the orange to the NW of Trawden.

The Snells came to this country in the 1600’s and the Hartleys in the 1800’s. That means that Lee’s matches would be on the Hartley side vs. the Snell side. Lee has two interesting people in his ancestry. One is Margaret Hartley b. 1836 and another is Mary Baldwin b. 1836.

  • Although these two women were both born in 1836, they are in different generations from Lee
  • Margaret Hartley is on Lee’s paternal side and Mary Baldwin is on Lee’s maternal side. If Lee were to ever test his mom, we would know on which side the Hartleys match.
  • Lee doesn’t show any parents for Margaret Hartley or Mary Baldwin

I have our Trawden born ancestor Greenwood Hartley with a Baldwin grandmother:

This is really on the edge of my knowledge. I chose Betty Baldwin and James Hartley as the most likely parents for Robert Hartley out of many potential candidates.

Lee had a dead end for his Margaret Hartley ancestor. Here are some potential parents I found for Margaret:

This was the same issue I had for finding parents for Robert. Was Margaret the daughter of John and Susan Hartley, John and Hannah Hartley or John and Margaret Hartley? Or perhaps even someone else? At least one of the Margarets died young.

Greenwood is staring at me from the past and saying, “You can’t figure out who my are grandparents are? They are _______ and _______”

a look at Mary Baldwin b. 1836

Due to a problem finding Margaret Hartley’s parents, I’ll take a look at a less common surname in Mary Baldwin. Based on this scrawly writing, she was baptized a Wesleyan in Colne:

This baptism was outside the Church of England.  A Wesleyan, perhaps what we would consider Methodist was considered a non-conformist church. Here is some information on Mary’s dad Eli:

And here is a brother of Eli:

I still need to get back a ways to get to our potential ancestor, Betty Baldwin who was born perhaps around 1780. Any potential shared ancestor would likely be Betty’s parents or before. We’ll say that Jane Baldwin was actually Jenney Spencer:

Again, we get a multiple choice for the father of this James Baldwin. Here is a batch of them from around 1790:

Here I will choose the James from Barrowford for a few reasons. One is that his dad was Elias and two, he was from Barrowford. Here is the 1851 Census showing that this James Baldwin was born in Barrowford.

This also shows James son David b. in 1812. That gets us back to the old-timers: Elias and Peggy Baldwin. Unfortunately, it looks like Elias didn’t do too well:

He died of decline at age 35. Betty could have been his daughter, but it would have made for some tight time frames. She would have had to have been born perhaps late 1783. Then she would have been only about 17 at the time of her marriage. So the genealogy is the difficult part of the genetic genealogy.

Summary

Well I looked at some aspects of Mike’s DNA:

  • How Mike and Holly have Fully Identical Regions (FIRs) in their matches with each other. Normally, these FIRs only occur between full siblings.
  • I looked at how to use the matches between Mike, Holly and their cousins to map out which grandparent they got their DNA from on certain parts of their chromosomes.
  • I looked at another way of mapping DNA developed by Kitty Munson.
  • I looked at a DNA match Mike shares with some other Hartley cousins. This DNA match is from an English man with Lancashire ancestors and probably represents deep Hartley ancestors that haven’t been identified yet.
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Tracking Down DNA from Colne, Lancashire or Part One of the Hartley Brick Wall Series

So far, I have done pretty well at finding out from which grandparent I get my DNA. However, figuring out where the split is for my great grandparents is a bit more difficult. Due to a brick wall problem with the Hartley genealogy, I would like to know which of my DNA is Hartley and which is Snell. There are different ways to do this. One way is to find matches with UK, NZ or AU at the end of their emails. These matches would also match where I got DNA from my Hartley grandfather who was the son of a Hartley and a Snell. My Hartley ancestors came from England in the late 1800’s. My Snell ancestors were in England also, but going back to the 1600’s which should be too far back for the DNA to track in most cases.

One match I found was Linda. She has a UK address to her email. She is on Ancestry and Gedmatch and has trees at both places. Here is her match with my siblings, Heidi and Jonathan:

Linda also has a smaller match with my father’s cousin Joyce on Chromosome 10.

Linda and the Colne Connection

Linda has a large tree with over 16,000 people. I am interested in some of her ancestors in the Colne area. My ancestors lived in Colne, but the church where they were baptized and wed was in Colne.

This is the Ancestry map enlarged to the max. My dot is blue in Trawden. Linda had more than one ancestor in Colne and lists one in Winewall and one in Wycoller. Wycoller is now a park which explains the green area. It would be a short walk from Trawden to Winewall. All the places may be walked to with not too much difficulty. Linda’s ancestral surnames in the area are:

  • Jowett, b. 1878 Colne: too recent for what I am looking for
  • Three male Waddingtons, born in Colne: 1710; 1737; and 1805. The last male Waddington would be too recent my purposes.
  • Thomas Rycroft b. 1684; Matilda Rycroft b. 1772, both in Colne
  • Female Crook, b. 1711, Colne
  • Hannah Foulds, b. 1720, and a male Foulds, b. 1692 both in Colne. I recognize the Foulds name as a prominent local name from my previous research in the area.
  • Allison Blackburn, b. 1688, Winewall
  • Robert Waddington, b. 1770, Wycoller

Of course, there is a possibility that none of these names are associated with Hartley. However, as there is a DNA match and a place match, there is a possibility that there is a match on one of these lines.

Linda’s Colne area tree

I feel like I’m exploring in someone’s house when I look at their tree. Here is the part of the tree that I am interested in:

Coghill didn’t show up on the Colne area map as her birthplace is listed as Lancashire. There should be a sweet spot in the tree above assuming that we are related. I am looking for a connection to my tree, so connecting person cannot be too recent. If we go back too far, it becomes improbably that there is an autosomal DNA match. Here is my Trawden Tree:

Going down the middle row, I am not certain about James Hartley and Betty Baldwin. I am quite sure about Greenwood Pilling and Nancy Shackleton. That means that my first choice would be to connect Robert Hartley to Linda’s tree somehow. In Linda’s Waddington line, the William Waddington or Foulds Rycroft family could have had a daughter that married a Hartley that had Robert. That daughter would have come about following a Hartley/Waddington or Hartley/Rycroft wedding.

Hartley and Waddington

When I search the online Colne Parish records for Hartley/Waddington, I get these two records:

I was looking for a female Waddington that married a Hartley. We see that in the second listing above. Also of note in attendance was John Crook. Crook is a surname in Linda’s line. There is a Mary Waddington born in 1752, but she is the daughter of John possibly a generation earlier:

Here are some of the children of William and Mary Hartley in the time frame that I am interested in. There were very likely more than one William and Mary Hartley family. At least the family at Noyna-end and Aldershead seem to be different based on the closeness of baptisms. This is also assuming that the baptisms were close to the birth dates. In fact, three baptisms in 1773 could indicate three different families:

Baptism: 21 Mar 1773 St Bartholomew, Colne, Lancashire, England
William Hartley – son of Wm Hartley & Mary
Abode: Noyna-end
Register: Baptisms 1756 – 1774, Page 92, Entry 16
Source: LDS Film 1471023

Baptism: 12 Aug 1773 St Bartholomew, Colne, Lancashire, England
Jonathan Hartley – son of Wm Hartley & Mary
Abode: Aldershead
Register: Baptisms 1756 – 1774, Page 94, Entry 6
Source: LDS Film 1471023

Baptism: 17 Oct 1773 St Bartholomew, Colne, Lancashire, England
Robert Hartley – son of Wm Hartley & Mary
Abode: Greenfield
Register: Baptisms 1756 – 1774, Page 95, Entry 7
Source: LDS Film 1471023

Baptism: 25 Dec 1775 St Bartholomew, Colne, Lancashire, England
Robert Hartley – son of William Hartley & Mary
Abode: Wycoller
Register: Baptisms 1774 – 1789, Page 11, Entry 12
Source: LDS Film 1471023

Baptism: 22 Dec 1777 St Bartholomew, Colne, Lancashire, England
Ellin Hartley – daughter of William Hartley & Mary
Abode: Wycoller
Register: Baptisms 1774 – 1789, Page 25, Entry 24
Source: LDS Film 1471023

Baptism: 7 Oct 1781 St Bartholomew, Colne, Lancashire, England
Peter Hartley – son of William Hartley & Mary
Abode: Green-field
Register: Baptisms 1774 – 1789, Page 61, Entry 2
Source: LDS Film 1471023

Baptism: 2 Feb 1783 St Bartholomew, Colne, Lancashire, England
Richard Hartley – son of William Hartley & Mary
Abode: Two Laws
Register: Baptisms 1774 – 1789, Page 71, Entry 4
Source: LDS Film 1471023

I recognize the name of Aldershead where Jonathan was born. This was not far from Seghole where the Pillings lived. However, Jonathan appeared to have died young:

Burial: 16 Aug 1776 St Bartholomew, Colne, Lancashire, England
Jonathan Hartley –
Age: infant
Abode: Aldershead
Register: Burials 1774 – 1789, Page 7, Entry 12
Source: LDS Film 1471023

Robert would seem to be a good choice for the father of my Robert, but I see no Robert, son of Robert being born around 1803 when I believe my Robert was born based on his burial record:

Baptism: 8 Jan 1792 St Bartholomew, Colne, Lancashire, England
Robert Hartley – Son of Robert Hartley & Mary
Born: 8 Jul 1791
Abode: Edge
Occupation: Weaver
Register: Baptisms 1790 – 1812, Page 23, Entry 22
Source: LDS Film 1471024

Baptism: 22 Jan 1809 St Bartholomew, Colne, Lancashire, England
Robert Hartley – Son of Robert Hartley & Susan
Born: 26 Nov 1808
Abode: Lanshaw Bridge
Occupation: Innkeeper
Register: Baptisms 1790 – 1812, Page 254, Entry 13
Source: LDS Film 1471024

I have the same problem with Robert son of William:

Baptism: 7 Oct 1792 St Bartholomew, Colne, Lancashire, England
Robert Hartley – Son of William Hartley & Margaret
Born: 5 Jul 1790
Abode: Boughgap
Occupation: Weaver
Notes: [Robert & Henry bracketed together]
Register: Baptisms 1790 – 1812, Page 33, Entry 254
Source: LDS Film 1471024

Baptism: 20 May 1810 St Bartholomew, Colne, Lancashire, England
Robert Hartley – Son of Wm Hartley & Mary
Born: 6 Jan 1810
Abode: Spouthouses
Occupation: Weaver
Register: Baptisms 1790 – 1812, Page 279, Entry 158
Source: LDS Film 1471024

There was only one Robert born of a Peter Hartley in 1809. There was also only one Robert born of Richard in 1796. That seems to rule out those possibilities.

Let’s try Rycroft

I haven’t eliminated the Waddington line for the mother of Robert – only for the father of Robert. And I have only eliminated Waddington assuming that the baptisms took place at Colne. I am also not looking for the mother of Robert as that would be a more complicated search. For example, what if a Waddington married and her husband died. She then married a Hartley. Likely the wedding record would show the married and not the birth name.

There were not a lot of Hartley/Rycroft weddings that I could find. Here is a fairly early one.

I did find a Susanna:

Baptism: 16 Oct 1714 St Bartholomew, Colne, Lancashire, England
Susanna Rycroft – filia Johannis Rycroft
Abode: Winewall
Register: Baptisms 1697 – 1734, Page 155, Entry 16
Source: LDS Film 1471023

However, Linda doesn’t have a John Rycroft in her ancestry after 1640, so I’ll rule that out for now due to the fact that a DNA match may not make it that far back.

I found this entry interesting:

Here we have the names Hartley, Rycroft, Foulds and Waddington. This Hartley Rycroft was the daughter of Betty Rycroft:

Baptism: 2 Sep 1798 St Bartholomew, Colne, Lancashire, England
Hartley Rycroft – Son of Betty Rycroft, Spinster
Born: 25 Jun 1798
Abode: Lane Head
Register: Baptisms 1790 – 1812, Page 99, Entry 200
Source: LDS Film 1471024

Here we are getting complicated as the Hartley is only the first name. Was the mother trying to name the father? This Betty was likely the daughter of Foulds:

Baptism: 6 Nov 1774 St Bartholomew, Colne, Lancashire, England
Betty Rycroft – daugr of Foulds Rycroft & Mary
Abode: Trauden
Register: Baptisms 1774 – 1789, Page 4, Entry 3
Source: LDS Film 1471023

Any Hartley/Crook Connections?

In looking through my Blog, I see that I didn’t look at the Crook surname. I use the Lancashire online search when I look for my Colne records. Linda has a Thomasin Crook born in 1711, so that goes back quite a way. I see two Hartley/Crook weddings in the early 1600’s which would likely be too early for a DNA match. Here is a later Crook/Hartley wedding, but I am not sure how John Crook is related. Also Mary Hartley is from Otterburn in Yorkshire. Otterburn looks to be about 20 Km North of Colne.

So this is all very interesting, and I have learned more about Linda’s ancestors, but not so much about mine. However, I do feel that breaking down the brick wall could come from these kind of back door methods in conjunction with DNA matches.

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Snell Autosomal DNA

I don’t think I’ve written specifically about Snell Autosomal DNA. This DNA has been difficult to separate out. I have lots of 2nd cousins that lead back to our common great grandparents: James Hartley and Annie Snell. But it is difficult to separate out the DNA from those two. The best way to do this is to find someone who goes back before Annie Snell. Here is one apparent match before Annie:

This is actually a match to my sister Sharon. I asked the administrator for M.M. to upload to Gedmatch. I’m pretty sure this is the match:

About One Eighth of My DNA is Snell DNA

I get exactly one half of my DNA from my dad and one half from my mom. I get on average 25% of my DNA from each of my grandparents. It is that point that the numbers start to vary. I get on average 12.5% of my DNA from each of my great grandparents. At this level the 12.5% number varies even more. Here is how I have mapped me and four of my siblings on Chromosome 5 where the match is to MM:

The above maps my four grandparents to my DNA. Stated another way it shows how much DNA I got from my 4 grandparents and where I got that DNA on each of my chromosome. About half of each grandparent color should be split up into two great grandparent colors. The bottom part was done by Martin MacNeill. I created the top part with visual phasing. I assumed that the bottom part was correct. There are some discrepancies of where the crossovers occur due to scale. My crossover from Hartley to Frazer is at 172.6. That explains why I don’t match M.M. If I take Gedmatch way down, I actually do match M.M. here:

If I was mapping this tiny segment, I could say that it came from either Anthony Snell or Betsey Luther. If I wanted to limit it to one person, I could say that this is my Otis Snell DNA [Anthony and Betsey’s son].

It is difficult to see, but there is now some new light blue at the end of my Chromosome 5 for Otis Snell. For my siblings, they would have longer patches of blue. Actually, this would be true for all my siblings except for Lori. She doesn’t match M.M. This means I made a mistake on my Chromosome Sibling Map. It should look like this:

Matches are a good way to check your work. Lori’s last crossover from Hartley to Frazer (Yellow) is at about position 167.5M.

What About Other Snell DNA?

One way to find other related Snells is through a Gedmatch utility. This utility finds people that are matched to both you and your match. Here are a few that match my brother Jonathan on Chromosome 5 :

Unfortunately, I either couldn’t find these people with overlapping DNA matches easily or they had a tree that didn’t go back far enough.

Snells at Ancestrydna

Here is a match that is perfect at AncestryDNA. Our common ancestors are the parents of Annie Snell [Isiah Hatch Snell and Hannah Thomas Bradford]:

I have gone to his mother on the chart above. However, he hasn’t uploaded to Gedmatch.com for comparison. And there is the problem for genetic genealogists. AncestryDNA has good information but no chromosome browser and tools. Gedmatch has good tools but not as many people and the trees aren’t as good.

So for now, I will be content with my little bit of DNA that I got from Otis Snell’s parents on my Chromosome 5.

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Three New People in the Newfoundland Dicks DNA Project

I was happy to find out that Katherine and her two Aunts, Grace and Dorothy have tested their DNA. They are all descended from the Dicks Family of Newfoundland. Here is the Elisabeth Dicks Adams Line:

Here Dorothy, Grace and Katherine are shown on the lower left. If I compare the DNA of Dorothy, Grace and Katherine, it would show the DNA they have in common. That would be the DNA from Edna Slade and the husband of Edna Slade. If I then compare Katherine’s family to Cheryl, Sandra and Nelson, the matches eliminate the non-Dicks DNA of Edna’s husband. However, at that point, we would expect about half the DNA to be from the Elizabeth Dicks common ancestor and half from the Adams side. In order to eliminate the Adams DNA, I compare the Dicks/Adams DNA to the larger Dicks project. This comparison removes the Adams DNA.

Katherine’s family is still on the lower left. There are five Dicks siblings in the tree which make up the major lines. They are: Elisabeth; Frances; Christopher; Rachel; and Robert. The tree only represents Dicks descendants that have had their DNA tested and uploaded to gedmatch. One exception is Kenneth Albert who is only at FTDNA right now.

Comparing Dicks Descendants’ DNA

My next step is to compare the 18 Dicks above to see how their DNA matches with each other. If three people match each other on the same segment of the same chromosome, that indicates a common ancestor. That common ancestor should be Christopher Dicks or his wife Margaret. Here is how all the Dicks descendants match each other in general (without the specific segment information).

This compares Dicks descendants to Dicks descendants, however, as this is Newfoundland, there are other matches. The descendants of Elisabeth Dicks match each other in the top left box. The descendants of Frances Dicks match each other in the bottom right box. Normally, there would be higher matches within the boxes than outside. But note that for the Frances descendants, there are some higher matches outside the box. This means that are surname matches outside the Dicks family. One example of that is in the next Section.

Charles matches with Kathy, Deborah and grace

As I was looking at the triangulation between Dicks descendants, I noticed that Charles was triangulating with Kathy, Deborah, and Grace. Now Charles is from the Frances Line and K, D and G are from the Elisabeth Line. So finding Charles in a Triangulation Group with Kathy’s family was unexpected. Remember that triangulation means that those in the Triangulation Group (TG) have at least one most recent common ancestor. I was about to ask Kathy about this when I noticed this in one of her emails:

“I was also quite interested in Charles ______ as one of his biological grandmother’s a few generations back was a Ruth Slade.”

Notice above that Kathy has Slades in her ancestry. The good news was that I was able to tell something was going on out of the ordinary just by the DNA.

Here is a summary of Charles’ matches of the Dicks descendants:

The four notes in the TG column are areas where Charles could match Kathy and her family on the Slade line.

Triangulation Groups

I should say that all Triangulation Groups are not created equal. Based on the location of the Triangulation Group (TG) there are hints as to the results. For example, many of the TGs are within the Elisabeth Dicks/Thomas Adams Line. As a result, the TG could be pointing to Dicks or Adams. In addition, there is some consensus that siblings should not be used for TGs. I differ a little on that, however. I would say, why not? If we can use cousins, or Aunts, why can’t we use two Aunts as two parts of the triangle? However, again, the results of the triangle may be limited.

Adams TGs?

Here are the TGs that could point to an Adams ancestor:

I say this because there are only Dicks/Adams descendants in these TGs. I am running out of room in my TG Matrix, or I would add these possible Adams TG. I will add the one on Chromosome 12. This is because it looks like there is already a Dicks TG in this spot:

Note that it looks like there is a Dicks TG already on Chromosome 12 from position 114 to 127. As these are two separate TGs, that would indicate that this TG represents the DNA that came down from the Adams side. That was my same reasoning for having a James Joyce TG on the right side of the chart in this position.

a confusing Chromosome 4

There is a lot going on at Chromosome 4:

This is what is referred to as a rolling TG. Howie appears to be in the beginning of it, but drops out. Then later Pauline joins in. So this could be looked at as a rolling TG, or two TGs. To save room on my chart, I’ll call  it one TG located from (41-72).

Note that there is a non-triangulation between Joan and Nelson. This is important as it happens right in the middle of a triangulation between Pauline, Dorothy and Grace. This tells me that Joan and Nelson likely share a non-Dicks ancestor. The other possibility is that Dorothy, Grace and Pauline could share a non-Dicks ancestor. I don’t know all the genealogy to check. However, the two groups are showing different shared ancestors.

A head scratchin’ Chromosome 9

Here Esther shows up in a TG with Dorothy and Grace. However, she was already in a TG with Sandra, Nelson and Kenneth (whose DNA results no longer show up in Gedmatch). This means that Esther is related to these two groups of people in two different ways. Esther being related to two groups of people is not unusual given the intermarriage in Newfoundland. Also recall that many genetic genealogist wouldn’t consider this a TG as due to Dorothy and Grace being sisters.

Updated Dicks TG Matrix

Here is what I get for the updated Dicks TG Matrix based on the three newly DNA tested Dicks descendants:

Summary and Conclusions

  • Although the study is geared toward Dicks DNA, other DNA does show up. The Slade name was one example in this Blog.
  • Kathy, Dorothy and Grace have added to our knowledge of the Dicks family.
  • The dark green in the matrix above was for matches with a brother of Christopher Dicks who was born about 1784. However, I didn’t update that information for this Blog.
  • Where DNA overlaps and there are two groups of matches, that should point to two groups of ancestors. This gives a good pointer on where to search for additional common family ancestors.
  • The work I do here is similar to the Circles shown at AncestryDNA. My wife’s great Aunt Esther shows up in a Margaret Circle with 11 other people. Margaret was the wife of Christopher Dicks b. about 1789. However, Triangulation Groups are more detailed. What AncestryDNA does is a mechanized version. They just show people that match each other by DNA and match each other by family tree regardless of where they match on which Chromosome.
  • Here is AncestryDNA’s cookie cutter bio on Margaret: “Margaret was born in 1789. She married Christopher Dicks and they had four children together. She then married Christopher Dicks and they had 14 children together. She also had one son and one daughter from another relationship. She died on February 28, 1867, in Harbour Buffett, Newfoundland and Labrador, Canada, having lived a long life of 78 years, and was buried there.“
  • One person in the AncestryDNA “Margaret” circle is not in this group and matches Esther at an ‘extremely high’ level of DNA. It would be worthwhile to get in touch with this person.

 

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Part 7 – Raw DNA From 5 Siblings and a Mother – DNA From Mom

I’ve spent my last 6 Blogs on this topic finding out which alleles came from my dad. In this Blog, I would like to work on finding my siblings’ and my alleles that come from mom.

The Ironic Step of Phasing – Mom Alleles from Dad Alleles

I call this ironic step in that it was my mom that was tested for DNA. Based on her results we found out a lot of the alleles that her children got from our dad who passed away quite a while ago. Now, we use those alleles we got from dad to figure out which alleles we got from mom. From the Whit Athey Paper referenced at the ISOGG Web Page on Phasing:

If a child is heterozygous at a particular SNP, and if it is possible to determine which parent contributed one of the bases, then the other parent necessarily contributed the other (or alternate) base.

 

First I copy my FillinOne Table to a MomfromDadOne Table. Then I’ll do a query on that.

This says where I am heterozygous, and I have an allele from dad, I want to see where I’m missing one from mom.

I have over 50,000 of these which will be easy to update. I will want to put Joelallele2 in the blank where JoelfromDad = Joelallele1. Then I will want Joelallele1 in the JoelfromMom space when my allele from Dad is Joelallele2.

I ran this query twice for each sibling, so 10 times. This updated 50-60,000 alleles per sibling, so about a quarter of a million alleles altogether.

Finding Mom Patterns

Now that I have filled in more alleles from Mom, it should be easier to find Mom Patterns. Here is a Query to find Min and Max for the AAAAB Pattern:

Results in:

This saves a lot of time and gives me the start and stop positions of all the AAAAB Mom Patterns. In my previous look which I now see as premature, I only found 2 AAAAB Patterns. Now thanks to my MomfromDad update above, I have at least 17 AAAAB Patterns. The only drawback is that if there is more than one AAAAB Pattern within a Chromosome, it will not show that. However, if I run all the Mom Patterns, and find overlapping Patterns, that can be reconciled later. In fact, I see an overlap already:

The first AAAAB Pattern I found was 162-233M which I did see as large. I already had found an AAABA Pattern from 192-249M. This could mean that AAAAB goes from 162-192 and that the 233M AAAAB pattern was just an outlying singleton.

I also recall that I want ID’s, so I’ll add that to my query:

Because I have so much new information, I’ll put this into a new spreadsheet:

AAABA Mom Pattern

I just have to change the Query slightly to get the AAABA Mom Pattern:

The results of this Query go into the new spreadsheet. This spreadsheet will be sorted by Chromosome later.

I added a column for IDEnd minus IDStart:

Where this is zero, it would indicate a single Pattern.

I went through all the Mom Patterns and got a spreadsheet of 194 rows that need to be reconciled. Here are Chromosomes 1 and 2 sorted:

Reconciling Chromosome 1

I have added in a column for possible assignment of a crossover to a sibling. Note that up to about 20M everything looks OK. There are discrete Patterns. ABBBA to AABBA is a change in the second position which belongs to Sharon. The change from AABBA to AABBB goes to Lori. Then the AABBB is the same as BBAAA which goes to ABAAA. That would be my crossover [Joel].

I did a Query showing where all the alleles were filled in for the Mom Patterns:

This shows where my Crossover is at ID # 8984. I have added a few more columns to my Mom Pattern Spreadsheet to add the more refined cut points:

Next I’ll look at 77M.

As best I can tell, there are two single AABAB’s in the middle of an AABBB Pattern. Next I will want to find the start of that AABBB Pattern. To find that I do a query to look for the AABBB Pattern in Chromosome 1. That Query results in more AABBB Patterns.

A Problem

I have a problem in that it appears that the Mom Patterns of AABBB and AABAB appear to overlap each other on Chromosome 1. I assume that means that I did something wrong.

refilling the dad patterns

That means that I should go back and fill the Dad Pattern back in:

First I recreate a Fill-in Table using the old Three Principles Table. Then I do update queries on that. Hopefully these numbers will work:

Back to Mom Patterns From Dad Patterns

Just so I’m not going backwards, I’ll redo this step. I copied my revised fill-in Table to a revised Mom from Dad Table. This time I’ll keep track of the alleles for fun:

So in retrospect, I don’t know if I made a mistake with the Dad fill-in’s or in the Mom fill-in from the Dad Pattern. Hopefully, there were no mistakes this time.

 

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Part 6 – Raw DNA From 5 Siblings and a Mother – Filling In Paternal Blanks

In my last Blog, I said that I would work on the Maternal Patterns and then fill in blanks. However, my Maternal Pattern Table is not very filled. After some thought and re-reading the Whit Athey Paper on Phasing, on which I base this work, I decided to:

  1. Fill in the Paternal Blanks
  2. Use the Paternal Data to fill in the Maternal alleles
  3. Fill out the Maternal Pattern Table
  4. Fill in the Maternal blanks based on the Maternal Pattern Table

Filling In Paternal Blanks

I might as well start filling in the AAAAA Patterns. On my Dad Pattern Excel Spreadsheet, I can filter for that pattern:

However, I now need a formula for Excel including all the ID positions above. This was the point of my starting this project over – to get those IDs. The formula will be in the form of “Between A And B OR Between C And D OR…” So first I need a formula in Excel to create the formula in Access. That formula is called Concatenate. According to a Google search, concatenate means to “link (things) together in a chain or series”. The symbol in Excel for concatenate is simply the ampersand (&).

Here is my formula and the outcome:

However, I have another idea. I can concatenate the concatenation. First, I add an extra space on the end of my “Or”. Then I drag down the formula to fill in the other chromosomes. Then I take off the last “Or”.

That gives me this helpful string of AAAAA Positions:

This will save me a lot of cutting and pasting in Access.

Back to Access

First I copied my old Table to a new one called tblFillInOne. I will create an Update Query for that Table.

I am only updating Dad alleles from other Dad alleles, so I import those 5 alleles plus the location ID. Then I use the expression builder, to paste in the location of the AAAAA Patterns in all 22 chromosomes. So now I have the Pattern and the location, but I need some more criteria. I would like the criteria to say if there is any allele in any of the five columns and any blanks in those columns, then replace the blank space with one of the existing alleles.

Here is a simple Update Query:

This says, that if my allele is null and Sharon’s isn’t, then replace mine with Sharon’s. The problem is that this would take four separate Update Queries. With 5 siblings, that would be 20 queries.

Another risky Update Query would use this form:

Here I am saying if any allele is not null (other than mine) replace that in my slot where I have a blank. The thing I don’t know if the Update To: field can have a variable criteria. I’ll try it. When I run this as a Select Query, it puts a bit of a strain on my computer. Eventually, it gives me 18,385 rows. When I run the View function on the Update Query, I get the same number of rows, so I’ll hit the Run button and hope for the best.

If I run this Select Query again, I should get no results if everything updated.  I did get no results, so I assume that it worked. I want to save this Update Query and use it for the other four siblings.

Filling in Sharon’s missing alleles from the AAAAA Paternal pattern

I used the same logic for Sharon:

Now she has all the Is Null values and I don’t. I moved the Update To: criteria over to Sharon. I took out Sharon’s allele and added mine in her place. Again, this gives my old computer a workout. I get 18,315 rows again which seems suspicious. I see the problem. I appears that Access updated my results with a (-1) rather than with an allele.

That means that I just have to do 20 Queries. However, they should go quickly.

Back to the Simple AAAAA Query

Due to all the Update Queries, I’ll make a Spreadsheet to keep track of each Update Query I do:

It turns out that it is easier to run this Update Query sorted by ‘From’:

That way, I can just move Sharon’s allele from Dad and the Is Null along the Update Query:

With these fast 20 Update Queries, I updated over 100,000 alleles:

AAAAB Fill-in

This could be a little easier. For this one, we don’t want to touch the last ‘B’. The last B represents Lori, so we will only be filling in to and with the other four siblings.

And then we need the fill-in locations.

AAABA and AAABB Fill-in

AAABA is about the same as AAAAB except the B in the AAABA corresponds to Jonathan. He is all alone as a B so he gives no alleles and takes no alleles. The other siblings share their AAAA’s in this Pattern.

In an AAABB Pattern, the three A’s will share with each other and the two B’s will share with each other. This happens to break down along V1 and V2 lines, so I expect there will not be as much sharing as between AncestryDNA versions.  The sharing of A’s and B’s looks like this in my Fill-in Tracker:

I have darkened out the areas where an A cannot share their A with a B and a B cannot share their B with an A. As I predicted, the AAABB filled-in alleles were less:

All the other patterns filled in

All the other patterns will be of the same type. There is one AAAAA which is all the same. The other combinations are four of one type and one of the other or three of one type and two of the other.

There are 20 fill-in’s for AAAAA. As a quality check, there are 12 fill-in’s for a 4-1 Pattern and there are eight fill-in’s for a 3-2 Pattern. I would recommend using a fill-in tracker to make sure all the combinations are being covered. The specific numbers of alleles being filled in for each combination of each Pattern are not all that important, but they are interesting.

Fixing an abbab mistake

When I was filling in the ABBAB Pattern, I noticed a mistake I made. I filled in 3754 rows of Joel alleles into Heidi blank spots. In an ABBAB Pattern, I am only supposed to be filling in my alleles into Jon’s blanks. Here is the mistake:

That means in those positions, I’ll have an ABAAB Pattern where I should have an ABBAB Pattern. Oh no. So how do I fix that? I need a fix query. Under Pos ID, I’ll put in all the locations that are supposed to be ABBAB. Then I’ll make sure the first position isn’t the same as the second:

That results in only 103 rows.

If I update those 103 rows to Null, that should be a start:

Next I set the first position to be different than the last in this ABBAB Pattern:

That fixes another 212 rows. That may be all the rows to fix. I looked for more JoelfromDad = Heidi from dad where JoelfromDad <> LorifromDad and where JonfromDad <> LorifromDad, but didn’t see anything. The other updates must have been in areas with AAAAA by chance areas. In the meantime, I copied the first two columns on the left to the right, so I don’t lose my place when I am scanning across the spreadsheet.

Dad Pattern Fill-in First Round

The dark blue areas are the ones where there should not be any filling in based on the Pattern.

Summary

  • The Fill-in Step is a major part of phasing. In this step I filled in over 1 million paternal alleles in my DNA and in my 4 siblings’ DNA.
  • I noticed a mistake I made along the way, but figured out a way to fix it.
  • I figured out a shortcut to describe the different patterns by way of ID’s. The shortcut involved using a concatenation of a concatenation.
  • I haven’t yet filled in the random AAAAA Patterns that are within the other patterns. I imagine that would be important to do at some point. I know that David Pike has a utility to find Runs of Homozygosity. I suppose that would be useful for filling in alleles.