DNA General – Page 52 – Hartley DNA & Genealogy

April 4, 2016April 13, 2017

Mapping My DNA To My Four Grandparents

I was thinking of calling this Blog “Kathy Meet Kitty“. Kathy is Kathy Johnston who taught me how to map my ancestral segments by comparing my DNA to two of my siblings’ DNA results and determining our crossover points. The crossover points can then be used to map out which grandparent you got your DNA from without having to physically test those grandparents. This is quite convenient as all my grandparents have been gone for quite a while. Kitty is Kitty Munson who has developed a Chromosome Mapper here. I have not seen a blog using Kitty’s Chromosome Mapper to map ancestral DNA segments via Kathy Johnston’s method, so I thought that I would write one. Kathy’s method is posted here.

Two Types of Segments

There are two types of segments, thus at least two types of segment mapping. This concept is best explained at the Segmentology Blog in an article appropriately called, What is a Segment?

ancestral segments

That Segmentology article first mentions ancestral segments. These are the segments that Kathy Johnston knows how to map. I have written many blogs about mapping my ancestral segments using her method. Ancestral Segments are the segments that you actually get from your ancestors. They fill up all your DNA. Here is an example of the ancestral segments that I have mapped to my four grandparents.

Look at Chromosomes 1, 5, 6 and 7 for starters. This shows all my DNA filled in. The 2 paternal grandparents are on the top half of the chromosomes in blue and grean and the maternal two grandparents are on the bottom in red and peach color. The DNA I received alternates between one grandparent and another and fills in all the area. In fact, that is the process of recombination and can be seen in the Ancestral Segment Maps.

shared segments

These are segments that you find at gedmatch.com for example. These are our DNA matches. These matches may have a proposed relationship based on how much DNA you and your match share. Here is an example of some of my matches using Kitty’s Chromosome Mapper.

The best way to fill in a map like this is by testing as many relatives as possible. Now look at chromosome 1, 5, 6, and 7 on the shared segment map compared to the ancestral segment map above. The ancestral segment map on Chromosome 1, for example, shows how much DNA I actually got from my Hartley grandfather. The blue in the Shared Segment Map shows how much I matched my father’s cousin. Next look at the maternal (bottom) part of Chromosome 1. Here the Rathfelder and Lentz matches on the right hand side are filled in on the Ancestral Segment Map. However, there is an additional section of Lentz on the left hand side of the Ancestral Segment Map where I don’t even have a match. I can tell I got my DNA there from my Lentz maternal grandmother. That is due to the crossover points I have and the fact that the DNA you get from your grandparents alternates between grandparent. On the maternal side, the alternation is between Rathfelder and Lentz.

If you find any inconsistencies between my Ancestral Segment Map and my Shared Segment Map, that means I messed up somehow.

More Ancestral Segment Mapping: Sister Heidi

In order to map my ancestral segments, I needed two siblings, so I used my two sisters, Heidi and Sharon. Here is Heidi’s ancestral DNA mapped out:

A few observations:

The areas of pale blue are where I had trouble figuring out how to map the ancestral segments, so nothing is mapped in these areas. I may have mapped out some of the segments, but then had difficulty telling whether they were maternal or paternal due to lack of known cousins that had tested. So I left these areas blank
The maternal areas shown as MG1 and MG2 – For these areas, I knew I had two maternal grandparents but I wasn’t sure which was which. Again based on lack of known cousins that had tested. I could perhaps guess, based on actual matches I had in these segments or where those matches were from, but I noted where the crossovers were and left these grandparents un-named.
These unknown grandparents are consistent within each chromosome and each sibling within each chromosome, but they are not consistent between chromosomes. So the unknown MG2 in Chromosome 8 may not be the same MG2 in Chromosome 11.
In my (Joel’s) Ancestral Segment Map, I don’t show any DNA on my paternal side for the X Chromosome. That is because males don’t get an X Chromosome from their father.
Heidi shows that she got her paternal X from her dad’s mom – a Frazer. Further, that chromosome did not appear to recombine. That means that she got that whole chunk from one of her great grandparents on the Frazer side.

How Do You Know What You Are Finding If You Don’t Know Where To Look?

These maps are very helpful in showing you where to look for DNA. Many people have matches that have ancestral names that are common to us but are not related. For example, my mother has matches with people that have Fraser or Frazer ancestors. I am related to Frazer on my father’s side. That means that I can forget about following up on maternal Frazer matches.

If I do want to look for Frazers, I need to look in my green areas (or my sister’s green areas) which is on her paternal side.
My sister Heidi is in an important Frazer Triangulation Group on her Chromosome 1 on the right hand side. She triangulates with others in a Frazer DNA Project I am working on. I am not in that group. Look at my Chromosome 1. It is nearly all covered by Hartley DNA. That explains why I don’t match these other Frazers at standard thresholds.
What if we were to want to look for Lentz ancestors of Heidi? We need to look at the red areas. Chromosomes 1, 6, 9. 14, 20, and 22 would be a good place to look. Fortunately, I also have Heidi’s matches on a spreadsheet. They are mostly divided by maternal and paternal matches. My mother has been tested for DNA. Based on that, I have Heidi’s phased maternal and paternal results and her matches to each of those results using Gedmatch.com.

Finally Sharon

My sister Sharon completes the Ancestral Segment Mapping:

The autosomal DNA that is missing on Sharon’s Map is the same for her 2 siblings. This is because Kathy Johnson’s ancestral segment mapping technique compares the siblings to each other using the Gedmatch.com chromosome browser.
Sharon has a lot of Frazer DNA match potential at Chromosomes 1, 8-12, 15, and 22.
However, Sharon is also not in the Frazer Triangulation Group in Chromosome 1 on the right hand side. In that particular section, she got her DNA from her Hartley paternal side.
The above point shows why it is important to test siblings.
Heidi and Sharon both have a large match (50+ cM) with someone on their X Chromosome. This person also has autosomal matches with my sisters and others in the Frazer DNA project.

Summary and Observations:

Ancestral Segment Mapping can be useful in determining which grandparent your matches match.
I know already whether my matches are on my maternal or paternal side. However, this goes back one more generation and further sorts my matches to grandparents. This cuts down the guessing by another half.
The maps also point out the areas where you can’t be as sure as to which grandparent your matches match as those areas are not mapped yet.
Ancestral Segments should line up with Triangulation Groups
Ancestral Segment Mapping can show matches that are Identical by Chance (IBC) or false matches.

February 21, 2016February 21, 2016

Mapping All My Frazer DNA

Thanks to a technique pioneered by Kathy Johnston, I have been able to map my DNA to my 4 grandparents. In the process of doing this, I can see where my 2 sisters got their DNA from also. One of those 4 grandparents is my father’s mother who was a Frazer. Both her parents were born in Ireland, so that helps in finding matches. I thought that it would be interesting to look at each of the Frazer DNA Project member’s matches to my family to see where they are on my family’s DNA maps.

The larger Chromosomes are the most difficult to map, as there are more potential segments and crossovers. The segments are the chunks of DNA we got from each grandparent. The crossovers are the vertical lines between the segments where the DNA we got crosses over from one grandparent to another.

Chromosome 1

I’ll spend a little more time on Chromosome 1 as it is the first.

The colors will not be consistent to a name between chromosomes. Also the position of the my and my sister’s chromosomes may not be the same
S and H are my sisters Sharon and Heidi. My bar is in the middle here (J)
The orange in this Chromosome is Frazer and represents my Frazer grandmother.
The numbers in the bars represent reference people. For Frazer, my reference is usually Paul, my 2nd cousin, once removed. However, I also used Jane above in this example
Note that if I had not tested my sisters, my chances for matching other Frazers would be very low for Chromosome 1. I couldn’t match a Frazer for most of this Chromosome. I would only be able to match another Frazer at either end.
When the 3 orange Frazer segments in my family are put together, we can potentially match a Frazer for the whole length of the Chromosome – except between 186 and 205.

The Triangulation Group (TG) in Chromosome 1

I’ve pointed this out before. The TG is to the right of the Chromosome and only my sister Heidi is in this TG.

Note that the first match in the TG above between MFA and Jane goes beyond where my sister Heidi could match a Frazer (198-205). This is fine as MFA and Jane have their own crossover points that are different than those in my family.

Chromosome 2

Here I’ll start with my spreadsheet matches.

What might I expect here? Note that the matches are only with my 2 sisters. My guess is that I won’t have Frazer mapped on my Chromosome in these 2 areas (196-222). Also note a match with Jonathan who is on the more distant James Line of the Frazer Project. In addition, my sister’s matches with PF overlap by a small amount her match with Jonathan. This could be significant if this forms a Triangulation Group.

Here’s my family’s Chromosome 2

I had a little problem with this one, but it’s mostly right. Here the colors are switched, so Frazer is now green.

Notice that my 2 sisters, S and H have Frazer segments from at least half way through their Chromosomes to the end. This is where the matches are (195-221).
Notice that between me and my sisters, we should have good coverage for Frazer ancestor matches.
I (J row) cannot match any Frazer where my sisters matched as I have orange Hartley DNA in the area of 195-221.

Here is Jonathan’s family mapped out. He is on the horizontal line 1. Only Jonathan can match my 2 sisters from 142 to 221. His 2 sisters are on rows 2 and 3.

Any Triangulation Group?

It would be interesting if there was a triangulation group between these 2 distant lines. So far, we have not had much luck in finding one for Jonathan’s James Line. Perhaps we have one here. This is what Gedmatch shows for Sharon’s match with Jonathan in yellow and Paul in blue:

In numbers, Gedmatch also shows where the small overlap is with these 2 segments:

The overlap is shown in the last column. The yellow (Sharon’s match with Jonathan) and blue (Sharon’s match with Paul overlap from 205 to 207. Let’s see what Heidi’s matches show:

Here the overlap is pretty much the same, but is a bit shorter for Heidi.

So for a Triangulation Group, Jonathan would also have to match Paul. I would expect this to be a small match, so I bring down the gedmatch numbers. This is a bit controversial, by the way, but I think I’m on fairly solid footing here. I took the limits way down to 3 cM. Here are all the results of the match between Jonathan and Paul, but I’m really interested in Chromosome 2:

To me, it is more than mere coincidence that Jonathan and Paul match at the exact place where they have an overlap in my 2 sisters’ matches. In all 3 cases, the match is between 205 and 207 on Chromosome 2.

Is This the First James Line Triangulation Group (TG)?

Yes and no. What I mean is that this is not strictly a James line TG but a TG between the James Line and the Archibald Line of the Frazer DNA Project. We have what we need for a Triangulation group. Paul matches Sharon and Heidi. Jonathan matches Sharon and Heidi, and Paul matches Jonathan on the small segment where he needs to match him in order for there to be a TG.

A triangulation group should represent a common ancestor. But who is the common ancestor? I can think of 3 possibilities:

The common ancestor of the Archibald and James Lines. This is based on the known genealogies. This common ancestor probably goes back to the late 1600’s.
A more recent unknown James Line ancestor. I have an additional line of Frazers that I haven’t placed that may be part of the James Line. This would be a good candidate.
A common collateral family. That is, a common family that married into both of our families with a common ancestor. This would be the least known option.

Chromosome 3

Chromosome 3 should be simpler. There is one Frazer match with my family. That is between Heidi and Cathy. Cathy is a a descendant of Archibald Frazer b. 1802 and Catherine Parker.

This is a small single match, so possibly not even a valid match. Let’s look to see if this match is in a spot where Heidi got Frazer DNA from her grandmother:

It looks like this match is in the about the only area where Heidi (row H) could’ve gotten any Frazer DNA match. Recall the match is from 15-21. But shouldn’t Sharon in the S Row also match Cathy in her purple Frazer segment? Actually, she does. I’m working from 2 spreadsheets and only had Sharon’s match on one of the 2 spreadsheets.

See, the DNA corrected my oversight!

Chromosome 5

There weren’t any Frazer Project matches to my family on Chromosome 4 that I had recorded. Here is the match between my sister Heidi and our 2nd cousin once removed Paul. He also matches my sister Sharon at the same spots.

My prediction is that the map should look like the one for Chromosome 3 in the first part of the Chromosome. Chromosome 5 is another Chromosome that I found difficult to map:

Note that I didn’t get a lot of Frazer in my Chromosome 5 (last row J). There is also a section from 107 to 173 where there would be no Frazer matches with me or my sisters. Perhaps if I tested another sibling….?

Chromosome 7

Here I see a smattering of matches. I included my fairly close Frazer relative Paul as a reference even though he doesn’t match my family on this Chromosome.

Here, none of these matches come together. What does the Chromosome map show?

As with many of my maps, I have different version as I have tried to perfect them. But something looks wrong here. Either the map is wrong or my matches above are wrong. Sharon should have a Frazer match with Jane at 99 to 107, but that is showing as blue which in this case is my non-Frazer Hartley side. I had one other case where one of the Frazers matched on my mother’s side. After lowering the thresholds a bit, I got this match between my non-Frazer mother and Jane:

That means that Jane either matches one of my mother’s ancestors way back or is identical by state or by chance in this area. But what about the match between my sister Heidi and MFA of the Frazer DNA Project? I lowered the thresholds a bit again at Gedmatch and checked to see if MFA also matched my mother.

Oh, my. It seems like everyone is related to everyone! Welcome to the family. Actually, if MFA and Jane were to be related to my mom, it would make more sense on her orange Lentz side (which is where they do indeed match). That is the side where my mom has a grandmother from Sheffield, England. The green side would make less sense at that is primarily German and specifically Germans that lived for many years in a colony in Latvia. Well, at least I don’t have to revise my Chromosome 7 map.

Chromosome 9

I see one lone match between my sister Sharon and my cousin Paul.

That makes sense. Sharon is the only one with Chromosome 9 Frazer DNA in my family. As no other Frazers in the Project appear to match here, I can assume that this match is on my McMaster side. Paul and Sharon share a Frazer ancestor that married a McMaster, so half our shared DNA could be on the McMaster side coming down through our respective Frazer lines.

Chromosome 10

Out of curiosity, I checked to see if my sister Sharon would match Paul on the first bar (S) if I lowered the Thresholds. She did between 6 and 9 (top left green segment). Again, this could be McMaster DNA.

Chromosome 12

This Chromosome has been discussed before as it is part of a TG.

Here are few more [probably McMaster] segments that are matches between cousin Paul and my family:

Chromosome 14

My sister Heidi has a small match with Charlotte of the James Line.

I don’t know if it is a valid match, but it falls in the right area of Heidi’s chromosome.

Chromosome 17

Here I have a lone match with MFA

Looks like I’m the only hope for Frazer matches in this Chromosome. As the chromosomes get higher in number, they get shorter. The shorter chromosomes have fewer segments and are simpler than the longer lowered numbered chromosomes.

Chromosome 20

Here I am again with Bonnie from the James Line:

I wrote a whole blog on this Chromosome on January 12, 2016.

I have a bit to finish on this Chromosome. Note that Bonnie’s match with me on the bottom bar fits in from 47 to 54. It seemed like Sharon should match Bonnie also. I looked more closely at my spreadsheet and she was there. Here is what gedmatch shows.

Chromosome 21

My sister Heidi matches Cathy. These 2 also matched at Chromosome 3 above.

Here I have a problem.

I have some nice colors but no grandparents named. I don’t have enough cousins that match me on this short Chromosome to identify which grandparent is which. But maybe that’s OK. When I check to see if Cathy matches with Heidi’s paternally phased DNA (that is, her Frazer side) there is no match. Cathy matches Heidi’s maternal, non-Frazer side (or is Identical by Chance).

So either way, this is not a good match for the Frazer project. However, this is a good thing to know. This does not invalidate the match Cathy did have with Heidi at Chromosome 3.

Chromosome 22 (Last One)

There are just a few small matches in our family with cousin Paul left. They are small, and likely to represent the McMaster side of our ancestors. These McMasters apparently lived parallel lives to the Frazers in bordering County Sligo. Perhaps they came to their particular area of Ireland for the same reasons as the Frazers and stayed or left for the same reasons.

Finally, the last map.

Summary

I have listed every known Frazer match to myself and my 2 sisters in the Frazer DNA Project
These matches were checked against my Chromosome maps to make sure they mapped to the correct Frazer grandparent
In some cases, the Frazer matches were found not be Frazer matches at all because they matched my non-Frazer mother
One pleasant surprise was finding an additional Triangulation Group at Chromosome 2. This TG was between the 2 main Frazer Lines in the DNA Project: The Archibald and James Lines.

February 16, 2016December 30, 2022

All My Mother’s DNA

A lot of my writing has been on the Frazer DNA Project. That Project involves DNA on my Father’s side. I’d like to focus on my mother’s DNA in this Blog.

Mitochondrial DNA

I have had my mitochondrial DNA tested in myself, so it would be the same as my mother’s. mtDNA is interesting as one can trace the mutations down from genetic Eve. My haplotype (and my mom’s) is H5’36. I like the fact that there is a prime [‘] in the designation. I think this is because they ran out of room in the place where it belonged among the other haplotypes. I have 2 exact mtDNA matches. Both of their ancestries trace to Ireland. This is interesting as I have not traced my mother’s maternal line back to Ireland. As far as I know, her maternal line went back to the Sheffield, ENG area or just outside of it. However, the focus of this blog is not mitochondrial DNA.

Autosomal DNA Testers

Unlike mtDNA, which goes up the mother’s mother’s mother’s line, atDNA can go in any and all directions up the ancestral ladder. It is much less focused. Sort of like Attention Deficit Disorder (ADD). In analyzing atDNA, it is best to have known testers that can be used as a reference point to sort the scattered matches into the right families. The testers I have with known genealogies are:

Catherine – She is the lone 1st cousin once removed representing my mother’s father’s Rathfelder/Gangnus side.
Judy – She is also a 1st cousin once removed representing my mother’s mother’s ancestral grandparents: Jacob Lentz and Annie Nicholson. Judy is my 2nd cousin. She tested at 23andme and matches me there but has not uploaded to Gedmatch yet for more comparisons.
Joan – She tested at Ancestry and is my mother’s second cousin once removed. Her common ancestors with my mom are William Nicholson b. 1836 and Martha Ellis b. 1835. Joan is also 3rd cousin with me and my 2 sisters which I have had tested. She is 3rd cousin to Judy through the Nicholson line but not the Lentz line as she has no Lentz ancestors.

Here is how the relationships look in a chart:

Here are 3 of my mom’s grandparents: Maria Gangnus; Jacob Lentz and Annie Nicholson. The last is her great grandfather, William Nicholson.

Ancestor Chromosome Mapper – Kitty Cooper

Kitty Cooper has developed a popular Chromosome Mapper. We should be able to map my mom’s paternal side from her DNA matches with Catherine and her maternal side from her matches with Judy and Joan. Judy has not uploaded to gedmatch, so I just used her match results with me at 23andme to represent her DNA matches with my mom. The actual DNA Judy shares with my mom is much more than shown for Jacob Lentz and Annie Nicholson.

Some observations:

There are 8 autosomal chromosomes with no matches from these 3 cousins
The map phases the results into paternal (top part of the bar shown in blue) and maternal results (bottom part of the bar shown in red and peach)
Chromosome 9 – On the maternal (bottom) side the 2 close segments indicate where my mom, Gladys, has a crossover point. the color goes from red (the DNA she got from her Nicholson grandmother) to peach (the DNA she got from her Lentz grandfather)
Chromosome 9 and 14 – Here we see results stacked up on top of each other. Without our testers, we would not know which side the results my mom’s matches came from. In these areas, at least, we will know for sure whether the matches are on the paternal or maternal side
All other matches – We will know if the matches between mom and anyone in these areas are maternal or paternal.
If anyone matches my mom in the red areas (and also matches Joan), we will know it is not with an ancestor of the Nicholson family.
Anyone who doesn’t match the people mapped out above in the area where they should match probably represent a match from the other side. For example, a large match along the area of Chromosome 18 that doesn’t match Catherine (who is on the paternal side) would likely be a maternal side match. The only other option would be a false match (Identical by State IBS or Identical by Chance IBC).
In the areas where there are no matches, it is a guess as to whether those are paternal or maternal matches. If someone has a tree showing that all their ancestors have been in Germany, that would be a hint that the match should be on my mother’s father’s side. He was German and born in Europe.

More on Joan and the Nicholson Matches

I have already written about Rathfelder matches in a previous blog. I haven’t yet addressed Joan’s Nicholson matches. I’d like to do that now. One way to look at how my mom and Joan match is through Gedmatch. They have a utility that will show the people that match 2 other people. I ran that and came up with myself and my 3 sisters as well as several others. One spot that looks like a Triangulation Group is found on Chromosome 5:

#1 is Joan. I didn’t include myself and my 2 sisters, but I know they match Joan here. In fact, here is Joan’s match with me, my younger sister, my mother and my older sister on the same Chromosome:

Now, back to the previous image. In order for my mother’s green matches above to be in a triangulation group (TG), they have to match Joan and each other. I’ll check:

Joan matches green #2 above at around 11 cM
Green #2 matches green #3 at about 10
Green #3 matches green #4 at about 15 cM
For comparison Joan and my mom match each other at about 30 cM

I didn’t do all the comparisons, but did enough to suppose that this is a TG. Technically, I’m supposed to do every comparison. I didn’t check the pink match as it was small and didn’t line up with the other matches.

What Do the Green TG Matches Mean?

A TG should indicate a common ancestors. Likely this common ancestor will be one of the ancestors of Annie Nicholson:

All I have to do now is write to the 3 green matches. Then hope that the common ancestor isn’t too far back and that they have good family trees. Hey, it could happen.

January 28, 2016April 13, 2017

Butler YDNA

This blog is not about all Butler YDNA, but about my father in law Richard’s YDNA. His results came in this week, so I thought I’d write a little about them. As he had 10 children, I thought that they might be interested.

Butler Genealogy

The Butlers are Irish. They are believed to come from the Kilkenny area. However, the documentation for that is not the best. Michael Butler was b. in Ireland around 1810. His son, Edward was b. in the 1830’s and made his way to the New World. He likely arrived in St. John, New Brunswick where he married Mary Crowley in 1855. I mention more details in my Blog on the Butler Brick Wall.

Deep Roots of the Butlers and Family Lore

My wife says that Butler is a Norman French name. She says the Butler name came from the fact that they were wine tasters. According to Ancestry.com:

Butler Name Meaning

English and Irish: from a word that originally denoted a wine steward, usually the chief servant of a medieval household, from Norman French butuiller (Old French bouteillier, Latin buticularius, from buticula ‘bottle’). In the large households of royalty and the most powerful nobility, the title came to denote an officer of high rank and responsibility, only nominally concerned with the supply of wine, if at all.

I had been a little skeptical about the family lore and figured that the Butler YDNA would be typically Irish which is R1b. According to Family Tree DNA:

R1b, which originated in western Europe, is the most common Y-DNA haplogroup among Irish men, at a frequency of about 81.5%. I1 is the second most common with 6%, followed by I2b at 5%, R1a at 2.5%, and E1b1b at 2%. G2a is found in only about 1%. Also rare are I2a (1%) and J2 (1%).

So What Did the Results Show?

I was wrong. According to FTDNA my father in law is I-M223. According to FTDNA:

I-M223 was known as I2b1 and is now known as I2a2a by ISOGG

ISOGG is the International Society of Genetic Genealogists. I’m not sure if that means that our Butler is in the 5% or 1% group in Ireland. However, they are either quite rare or very rare there. So I signed up my father in law for the Butler YDNA project and also the I-M223 Project at FTDNA. At the I-M223 project, they put him in the group with others that are fairly close matches. Three have the name Butler and one has the name Whitson. That makes me feel like we are on the right track. It is not unusual to have other surnames match on the YDNA line. However, it is better to not be in the minority. The FTDNA group further put my father in law Richard into this curious category:

1.2.1.2.1.1.1.1- M223>…>L701>P78>S25733>A427: test I-M223 SNP Pack or I-M223 SNP Pack or S23612

This is a group with a lot of numbers. These first numbers probably went back to when someone could tell there was a certain signature in the YDNA results, but all the SNP tests weren’t developed yet. The second numbers are the SNP tests that the administrator thinks Richard would pass if he were to take them all. That is good, because it puts him several steps down the SNP tree. The last part is what the administrator wants the tester to do. One is to take a test that will test several SNPs. The other is to test for a specific SNP. In this case, the SNP is S23612.

Origins of the I-M223 Haplogroup

The I-M223 Haplogroup came into existence about around 17,600 years before present (ybp). Give or take a few thousand. The A427 branch is much more recent at 5,200 ybp. According to one YDNA Butler match to Richard, he feels that the origin of this branch of Butler that didn’t test positive for S23612 was in England and before that Germany. Some information from the Eupedia website also mentions that the L701 branch may have arisen from the Goths. I can imagine a stimulating dinner conversation with the Butler family: “So, I hear that the Butlers are descended from the Goths.” “What…???? I thought that we were descended from the Normans”. Who knows, maybe the Goths moved into France at some point and mixed with the Normans. Or they could’ve moved from Germany to England where the Normans were and then made their way to Ireland. I’m sure that there are many possible scenarios.

More Recent Connections

Two of the more recent Butler YDNA matches to Richard had roots in Ireland, so that makes sense. One had his earliest known Butler ancestor from the border of Laois and Kilkenny County. That is shown by a blue balloon below. That match had a GD or Genetic Distance of 4. The other was from Wexford and had a GD of 2 with Richard.

This shows some likelihood of having a common ancestor within a certain number of generations when your match has a GD of 4:

Here is a match with a GD of 2. Note the differences in Percentages.

Kilkenny or Wexford?

The 2 GD match who had a mariner Butler ancestor in Wexford is interesting for 2 reasons. When Edward H Butler, the son of Edward Butler, the immigrant ancestor died in 1925, he listed his father as being born in County Wexford, Ireland. The second reason is that the photo we have of the immigrant Edward Butler shows him in a sailor outfit.

Compare the above with the image of sailors our helpful YDNA Butler relative sent:

Perhaps Edward Butler had mariner background in Ireland or perhaps he was in the Navy in the American Civil War.

Two Death Certificates

Here is Edward Butler’s Death Certificate from 1915 showing that he and his two parents were born in Kilkenny

Ten years later in 1925, his son, Edward H Butler died and recorded that his father was born in County Wexford, Ireland. Why had his birthplace changed in 10 years?

So although the YDNA results don’t clarify the death certificates, they are consistent with where the death certificates say the Butlers were from!

January 25, 2016February 11, 2016

Beware the False DNA Match

In this blog, I’ll write about false DNA matches: what they are; how to find them; examples – some from the Frazer DNA Project I am working on.

What Are False Autosomal DNA Matches?

False DNA matches are those that are not Identical By Descent (IBD). Perhaps you have heard the term. It basically means that the match is not from a person that is your ancestor. That sounds like defining something by what it is already. And it kind of is. A false match is also called Identical By State (IBS) or Identical By Chance (IBC). These are two different names for pretty much the same thing. It basically means that when the computer generated your match it wasn’t from an ancestor. ISOGG has a good article on the subject.

How Can I Tell If I Have a False Match?

There are several ways. I’ll list a few. I will give examples later in the Blog. The first list is more sure fire, but involves additional testing of parents or other relatives.

FINDING FALSE MATCHES BASED ON ADDITIONAL DNA TESTING

If a person matches you but doesn’t match your mother or father’s DNA results, that is a false match. As you got all your DNA from your parents, this has to be a false match.
Conversely, if you match someone else but don’t match their mother or father’s results, you have a false match.
This is similar to the above. There is a way to phase your own results if you have had one or both of your parents tested. If you do not match on the phased (that is maternal or paternal) portion of your results, then it is most likely a false match.
The last method has to do with chromosome mapping. I have written some about this in the past. If you have mapped your DNA to one grandparent, and the match is in the same area of your chromosome, from a different grandparent, then that has to be a false match. I’ll give an example later. There are 2 ways to do this mapping. One way is to test a lot of relatives and map their results to a common ancestor. Another way is if you have 2 siblings tested in addition to yourself, it is possible to figure out from which of your 4 grandparents your DNA came from. This method has been pioneered by Kathy Johnston.

WHAT IF I DON’T HAVE PARENTS OR OTHER RELATIVES TESTED?

Testing parents is the best way. Then it is good to test other relatives. If that is not possible, then one may look at statistics. Many of the statistics are at the ISOGG article I mentioned above
15 cM or greater match – these are considered to be all good matches
less than 5 cM – very few at this level will be considered true matches. ISOGG reports that about 85% of matches at this level are false. So it’s better not to go there.
Triangulation – this is a way to determine true matches (or IBD). I have read that any match 5 cM or greater that triangulates will likely be a true match. In my experience only the larger cM matches tend to triangulate, so for me, this is a self-fulfilling prophecy. I won’t get into the triangulation aspect much in this blog.

My False Match With Deb

Deb was one of the first false matches that I was in touch with. I had thought that perhaps we had colonial ancestry. We shared many colonial ancestors including some of the Pilgrims from Plymouth, Massachusetts. She mentioned that she had her parents tested also. This would have been helpful to find out which side we were related on. However, I matched neither her mother’s nor father’s results. So it had to be a false match. Here is how we show to match at Ancestry:

It looks legit. It even says that Deb and I have a Shared Ancestor Hint. But in this case it is a bad hint. Another clue that this might be a false match is that the match is fairly low. At Ancestry, they use a filter and the match was only 6.0 cM. Here she is on my spreadsheet.

The matches in my spreadsheet are above the thresholds for FTDNA and Gedmatch. The lower number is phased to my father’s side, so one would think that the match would be good. However, my paternal phasing is based on a test with my mother. These phasings are not 100% accurate apparently. Deb also matches with my 2 sisters. In addition, she matches my two sisters on the X Chromosome. Apparently, these are all false matches. I have also read that many female X Chromosome matches are false. I suppose these are two examples. The bottom line is that I don’t match Deb’s parents and my sisters don’t. So these cannot be real matches.

Another False Ancestry Match

I have another example that I just thought of. I have another Shared Ancestor Hint. This one is on my mother’s side. It is based on an AncestryDNA match between Kay and myself. Kay also matches my sister Heidi but not my sister Sharon. So Heidi shows this same False Shared Ancestor Hint.

This match is down to 5.4 cM at Ancestry with their fancy filtering methodology. Unfortunately, Ancestry apparently doesn’t have the technology to check that even though my mother tested with AncestryDNA, my mother doesn’t also match Kay – at least not by DNA. However, Ancestry clearly shows that Kay and my hint’s line to me is through my mother. So this is a false match. Ancestry is wrong again. However, they do have a lot more money than I do.

Frazer False Matches

I have perhaps more experience with the Frazer side of my DNA than other DNA having worked on the Frazer DNA Project for a while. There are also false matches within that project. Here are a few false matches on Chromosome 7 between my two sisters and Frazer DNA Project Members. My sisters are SH and HHM.

HERE’S HOW I FIGURED OUT HOW THESE 2 FRAZER MATCHES WERE FALSE

Jane and MFA are in the Frazer DNA Project. In fact they have great matches elsewhere and even triangulate. So why am I calling these matches false? The main reason is the Chromosome Mapping I have done. This was done by a method I have described in previous posts. Three siblings are compared (my 2 sisters and me). Crossover points are determined. Here is what my Chromosome 7 looks like.

I have a cousin on my mom’s side who tested (in green). Her match at 56-75 with my 2 sisters and me ensures that the maternal side is on the top of the 3 DNA bars. This is because at that location (56-75), there is only one color that all the siblings share (green). That means blue and purple represent DNA from my paternal side. Blue is from our Hartley grandfather and purple in this case represents my Frazer grandmother. The numbers represent matches with relatives who I have had tested that are related to two of my four grandparents. In this case, the relatives matched my mother’s father (green) and my father’s father (blue).

SHARON’S FALSE FRAZER MATCH

My sister Sharon’s DNA is represented by the first horizontal bar. She has blue Hartley DNA from the beginning to point 129,000,000 (or 129 for short). At that point from 129 to the right end, the DNA from Sharon’s Frazer grandmother takes over. 129 is the crossover between where she gets her Hartley DNA to where she gets her Frazer DNA on Chromosome 7.

I have that Sharon matched Jane from the Frazer DNA Project from 98 to 107 for 7.6 cM. However, this cannot be a Frazer match as Sharon got all her DNA from the beginning of her paternal side to point 129 from her Hartley (non-Frazer) grandfather.

HEIDI’S FALSE FRAZER MATCH

Likewise, my sister’s match with MFA of the Frazer DNA Project is also false. Her bottom bar is all blue which means she has all [non-Frazer] Hartley DNA. There is no room for her to match MFA from the Frazer DNA Project from 130 to 135. In fact, Heidi has a match with her reference Hartley relative from 134 to 139. What the map shows above is that you cannot get DNA from 2 different paternal (or maternal) grandparents at the same location. It has to be either one or the other.

Interestingly, these false matches happened in the places where they could not have happened. If they were to have been real matches, they could’ve happened with me (Joel) as I have more purple area on my bar above. Or MFA could’ve had a true match with Sharon where she had some purple room, rather than with Heidi – which is a false match.

So Are False Matches Good Or Bad?

They are neither good nor bad. However, if you have a match that is false and you think it is true, then that could be bad. That would lead to wrong conclusions. Notice that in the above example, both the matches were just above the Gedmatch 7.0 cM cutoff. Just because a match is above the cutoff, doesn’t mean it is a real match. That level was chosen because there are probably more true matches than false matches at that level, but there are still a lot of false matches around 7 cM. Gedmatch and testing companies don’t generally like to filter out matches that could be true.

Summary

It is good to be aware of (and wary of) false matches
Just because a match is above a threshold doesn’t mean that it is a true match
Matches below a threshold could be true also, but the odds are against that
False matches do not triangulate
False matches do not match either of your parents’ DNA
Neither do they match either of your matches’ parents’ DNA
False matches may match a phased kit of your own DNA as phasing a parent based on another parent’s testing is not 100% accurate
If a match doesn’t match your paternally or maternally phased kit, it can be considered false
A low match level means high likelihood of false matches; a high match level means a high likelihood of true matches
At about 15 cM there should be no false matches
Don’t blindly accept AncestryDNA Shared Ancestor Hints.

January 14, 2016November 28, 2016

Analyzing Chromosome 15 of a James Frazer Line Family

This is part of the Frazer DNA Project. For those descending from 2 brothers who were in North Roscommon in the early 1700’s. The younger brother was James and the older was Archibald. Joanna has 2 of her siblings tested for autosomal DNA. That means we should be able to figure from which of her 4 grandparents most or all of her family’s DNA comes from. This is using a methodology developed by Kathy Johnston. I previously looked at Joanna’s family’s Chromosome 22 in How a Maternal DNA Match May Shed Light On a Paternal Match. These Chromosomes were chosen for 2 reasons:

They are Chromosomes where Joanna recently got a known relative’s matches on one of her non-Frazer grandparent’s side.
They are Chromosomes where there were already matches in the Frazer DNA Project to at least one known Frazer relaive.

Rather than do this analysis and email the results to Joanna, I thought that I would do the analysis in a blog.

Joanna’s Chromosome 15: Three Siblings Compared

First, I go to gedmatch and compare Joanna’s three siblings to each other: Jonathan (1), Janet (2) and Joanna (3).

Here green is a Fully Identical Region (HIR), red is no match, and yellow is a Half Identical Region (HIR). Janet and Joanna match as a HIR for the whole length of Chromosome 15 That means they will share one granparent’s DNA for the whole Chromosome 15. Next I add the crossover points for all 3 and assign one person to each. This is the person that appears in 2 out of 3 of the crossovers. Well, here is something I haven’t run into before. All the crossovers belong to Jonathan (1):

There are 3 crossover points. They are between Jonathan and Janet and Jonathan and Joanna. The one in common with those crossover comparisons is Jonathan. That is complementary to the fact that there are no crossovers in the comparison between Janet and Joanna. Next we change this comparison into a Chromosome 15 map where we will look at the 4 grandparents that contributed DNA to this family. The 1, 2, and 3 below on the left stand for Jonathan, Janet, and Joanna. Jonathan and Janet have an FIR in the first segment. That means that they both got the same DNA from the same 2 grandparents – one on each side of the maternal/paternal split. That split is represented by the horizontal line between the 2 colors. So for Jonathan’s Line 1 and Janet’s Line 2 we add two colors representing these same 2 grandparents’ DNA that Jonathan and Janet inherited:

Jonathan has all the crossovers here. Janet and Joanna don’t have any. The crossovers are where the grandparents change. As Janet has no change (crossover), we’ll say she got her DNA from the same 2 grandparents along her whole Chromosome 15. Then I added numbers at the bottom. These are where the matches start and stop (rounded to the nearest million) between the 3 siblings as shown in the gedmatch comparisons above:

Joanna (3) will be feeling left out by now, so let’s see what we can do. Janet and Joanna have that HIR that we talked about. That means they will match on one grandparent and not the other. Let’s pick one for them to match. It doesn’t matter whether it is the green or blue grandparent at this point, because the colors are only relative now and not locked in. I pick green as their match and purple will be the grandparent that Joanna has that doesn’t match Janet’s blue DNA-contributing grandparent. All these decisions!

Now we can try to fill Jonathan in. This should be easy:

Jonathan and Joanna have no match in segment 2 and 4
Jonathan and Janet have no match in segment 3

Joanna and Janet both have green grandparents the whole way. For Jonathan to not match them in all those places, there has to be a different color. I have been using orange for the 4th color representing the 4th grandparent’s DNA.

Next, I said that Jonathan and Joanna (1 & 3) have no match in the second and fourth segments. The non-purple in the lower half is blue. Jonathan and Janet are non-blue in the 3rd segment as they don’t match, so that is purple.

And that was probably the easiest chromosome I’ve ever looked at! Now to add real life actual grandparents. The new matches that Joanna’s family got in were with their maternal grandmother – Miriam Williams. Jonathan matched her, but Joanna and Janet did not. This match rounded in millions is between 90 and 97. I like how gedmatch has the commas; it makes life easier.

This is on the right side of the Chromosome 15 segment map. I will say that Grandmother Williams is orange, as that is the one that is different from the 2 sisters on the right. Next we will look at Frazer DNA Project matches that Joanna’s family has. I have good matches and sketchy ones that are small.

We decided above that Williams (Maternal Grandmother) should be orange on the top of the maternal/paternal split. That means that Frazer (Paternal side) will be below that maternal/paternal split line. Janet and Joanna have a large Frazer match on the right hand region, so that would be – uh oh, it looks like I made a mistake. Note in the above spreadsheet that Joanna and Janet both have large matches with BZ. BZ is a Frazer (paternal grandfather) relative. The only places that Joanna and Janet (2 & 3) can have the same grandparent (color) on the right hand side last segment is at the green location. That boots Granny Williams down to blue.

Where Did I Go Wrong?

I went wrong above when I assigned Miriam to orange. This was based on Jonathan having a match with a Miriam relative and Janet (2) having no match with that same relative. I did have a little qualm about doing this but reasoned thusly: “If Jonathan had a match and Janet didn’t, then it had to be orange.” Also why wouldn’t Janet have a Williams relative match? She has all that blue area to match. So I’ll have to take note not to make that assumption again. I suppose it’s one of those situations where absence of proof is not proof of absence. Fortunately, the Frazer matches bailed me out of my bad assumption.

Adding the Other Grandparents

One More Correction

After coming back to look at this after many months, I see a mistake I made. It was Joanna (3) that had a match with a Williams relative not Jonathan. This version is done in Powerpoint which is easier to use. I now have Joanna at the top and Jonathan at the bottom.

This has to be right. Purple is Joanna’s only unique color in the 90-97 area. And only Joanna had a Williams relative match. Likewise, Joanna and Janet had Frazer matches from 67-92. Green is the only color those two sister have in common in that area.

Summary and Conclusions

Powerpoint is a better software for visual phasing
It is best to use names for identification, not numbers
With just one maternal grandparent and one paternal grandparent, I was able to fill in the missing grandparents.

January 12, 2016April 13, 2017

My Big Fat Chromosome 20

I never would have guessed 10 years ago that I would be blogging about my Chromosome 20. 10 Years ago I was definitely interested in genealogy, but knew virtually nothing about DNA. Even if I did know anything about DNA I would not have guessed that it would have anything to do with genealogy.

My Chromosome 20

My Chromosome 20 actually isn’t that big and fat. Actually it is one of my smallest chromosomes. However, I have more matches there than on any other chromosome. In fact, over 1,000 – more than a quarter of my matches – are on Chromosome 20. This is pretty amazing considering I have 23 chromosomes counting my X Chromosome. If my matches were spread out evenly over these 23 chromosomes, I would expect each chromosome to have about 4% of my matches. This representation shows the ridiculous number of matches I have on Chromosome 20. They are on the bottom of the image in light blue.

This particular representation is for just my FTDNA Family Finder matches. I believe the threshold was set relatively high and this was done a while ago. However, at the time and threshold, it appears that more than half of all my matches were at Chromosome 20.

How To Explain All the Matches? Colonial Massachusetts?

I had a difficult time explaining all the matches I had on Chromosome 20. Most were on my paternal side as that is where most of my matches are. I had guessed that these may have been due to a colonial effect as that had been suggested in various places. My great grandmother’s mother was a Bradford and was descended from the Mayflower Bradfords. A lot of those early Pilgrims married other related Pilgrims. In fact, some of my Chromosome 20 matches were descended from a Brewster who was one of the Pilgrims that I am also descended from. Then there were a few who seemed to be related on my Irish Frazer side. Finally I had a match with Bonnie from the Frazer DNA Project I am working on. She matched on Chromosome 20 but was outside my large triangulation groups.

Chromosome 20 Triangulation Groups

I also have Triangulation Groups (TGs) for Chromosome 20 – very large ones. In fact, gedmatch would overload when I tried to run an analysis I had so many. I have 2 paternal TGs and one maternal TG. There also may be sub-TGs within those. I have roughly 650 matches in these combined TGs. So now, based on testing my mother, I knew if my matches were maternal or paternal and if they were in TGs, but I still didn’t know much about where the common ancestors could be other than a vague guess about colonial Massachusetts. What I did was ignore Chromosome 20. I gave up even adding matches to my spreadsheet because I had so many. These matches tended to be around 13 cM with some higher and some lower.

Sticky Segments Or Pileup Areas?

While looking for a Chromosome 20 explanation, I read about sticky segments and pileup areas. Sticky segments are those that came down intact for many generations. They don’t want to go away. However, a few sticky segments wouldn’t explain over 1,000 matches. It seemed like I had a pileup, so I looked into those. Pileup areas are areas are described by Jim Bartlett in his comment on one of his blogs:

I do find that each person tends to have two kinds of pileup areas: 1) are fairly narrow, are widespread, and are outlined in this ISOGG article: http://isogg.org/wiki/IBD#Excess_IBD_sharing; and 2) are also fairly compact (7-9cM) and are unique to each person. I believe these are caused by a unique set of markers in our personal DNA that makes it easy to form matches with others in that region. These are characterized by many segments in a narrow range, which do not generally Triangulate, and the Matches don’t see this as a pile-up area, only you do.

However, my case didn’t seem to match some of the explanations of sticky segments or pileup areas. My matches were larger and did triangulate. Furthermore, they were not in areas of the chromosomes described in the ISOGG article above.

Enter Kathy Johnston and Her Crossover/Segment Analysis

At the beginning of 2015, Kathy posted her instructions on an FTDNA Forum for analyzing DNA based on the 3 siblings. She showed how to determine the 4 grandparents’ contributing DNA for each of these siblings. I discovered her post at the end of 2015. Could this help me figure out my Chromosome 20? I tried Kathy’s method and got some surprising results.

Finding Chromosome 20 Crossover Points

Finding crossover points in Chromosome 20 was not as easy as it has been in other chromosomes. According to Kathy, usually there will be one owner of a crossover point. This owner will appear in 2 out of the 3 comparisons at a crossover point. In this one, I found only one clear owner. That was my sister Heidi at position 47. For the other ambiguous crossover points, I gave a double initial separated by a slash.

Below, the gedmatch comparison is transformed into a maternal/paternal Chromosome 20 map. The green area means that Heidi matches Joel on the 3rd segment. This match is a Fully Identical Region (FIR). This means they match the same maternal grandparent and the same paternal grandparent. For Joel, I move those grandparent to the right as I have no crossovers until the last crossover point.

Sharon has no match with her 2 siblings in the same area, so that will mean she shares the complementary grandparent on her maternal and paternal DNA. This will be represented by 2 different colors. I again extend that double segment to Sharon’s crossover points.

Looking at the earlier gedmatch comparison, in the 2 segments to the right of Heidi’s existing mapped segment, there is a Half Identical Region (HIR). That means a grandparent matches on one chromosome and doesn’t match on the other. This will be shown as 2 different colors in this area when comparing Heidi to Joel. This first HIR choice is chosen randomly as no names or side (maternal/paternal) have yet been assigned to the grandparents.

Next, we have an illogical situation.

In the next to last segment, the smaller one, Sharon is no match with Heidi or Joel and Heidi and Joel have a half match. That is illogical because if Sharon doesn’t match with Joel, that is the same orange/purple scheme continued in the small segment for Sharon. Then if Sharon and Heidi are opposites, it goes back to green/blue for Heidi in that small segment. Those are the same colors that Joel already has, so that means that Heidi and Joel can’t be HIR which means they should have one matching color and one non-matching color. However, look at that small segment again in the first two rows. The red is strong in the first row. In the second row, I hardly see any red – with red indicating no match at gedmatch. Therefor, I’m going with the first comparison of Heidi and Sharon. Plus this goes with the matches that I will mention soon that Sharon has. I make Sharon and Heidi opposite in Sharon’s little segment and extend that segment to the end.

I filled in some of the no matches and FIRs on the right. On the left, I was left with 2 illogical no matches again, so I chose the redder of the 2. This left me with having to guess a HIR on the left. I am only allowed one guess, so I left this blank for now.

Adding Real Grandparents

It would be nice to add actual grandparents here and not just speak of my orange grandparent, for example. I can do this using two of Sharon’s matches.

These 2 important matches Sharon has are both on the paternal side. James is related to my grandfather and Bonnie is in the Frazer DNA Project on my Frazer grandmother’s side. Coincidentally, the orange match above goes with the orange on my chromosome map. That would make my paternal grandfather Hartley orange and paternal grandmother Frazer green.

Joel’s Matches

Here’s my Frazer match with Bonnie. 47 to 54 is in my green Frazer region on my map. So that is a relief.

Below is my only maternal match. It is with a cousin on my maternal grandmother’s line. She matches only with me because she tested at 23andme and hasn’t uploaded to gedmatch yet.

However, Judy gets me unstuck on my maternal side. Her match is telling me that from zero to 8, I can identify my grandparent. I already have blue from 6 to 8 (from using my brighter red logic). So I just need to extend the blue all the way to the left on my maternal segment line. That gives me a solid blue on Chromosome 20 on my maternal side.

This is as far as I can figure out now without further guessing. Perhaps when cousin Judy gets her DNA uploaded to Gedmatch, I will know more. So what does this tell me about my 1,000 plus Chromosome 20 matches and 600 plus matches that appear to be in Triangulation Groups?

Mystery Solved?

I think it is. These matches correspond to the area on the map above between 16 and 49. By the above mapping these massive amount of matches are solidly in Frazer territory for me. Instead of my huge block of matches being in colonial Massachusetts, I see that they are on my Frazer line. That came as quite a surprise. These ancestors were in Ireland mostly. I assume that many of these ancestors got out of Ireland. Perhaps they moved to the United States and married people who were descended from colonial Americans. That would explain some of the other colonial matches.

Summary, Application and Conclusions

When you are looking for DNA matches, it helps to know where you are looking
While I was looking at my largest group of matches, I was looking in the wrong place even though I had some reasonable assumptions
Kathy Johnston’s method cuts through bad assumptions and replaces them with sound logic
Phasing by parents cuts the looking in half but didn’t help me with identifying a huge block of Chromosome 20 matches. However, Kathy Johnston’s method is twice as good as phasing as it separates all matches to areas of 4 grandparents.
This method needs 3 siblings and some known tested relatives.
If I have this mapped correctly, any maternal match after 6 million for Sharon will be on the Rathfelder line and any maternal match for me will be on the Lentz line.
Interestingly, I have only about 42 matches for my sister Sharon on this Chromosome. Given that the makeup of her Chromosome 20 is mostly opposite of her 2 sibling, this makes a lot of sense.
I forgot to mention that my sister Heidi has almost as many matches as I do on Chromosome 20. Her shorter Frazer segment compared to mine would explain the slightly fewer matches.
The fact that all these matches are on my Frazer line doesn’t necessarily mean that they are Frazer matches. They could be McMaster, Clarke, Spratt or any other known or unknown ancestor of my Frazer grandmother.

January 12, 2016November 22, 2016

How a Maternal DNA Match May Shed Light On a Paternal Match

Uh oh, this sounds like a boring topic. I have been blogging about Frazer Segments and Crossovers, and this is a continuation on the subject.

How To Find Frazer DNA Using Non-Frazer DNA

I suppose this is another way to say it. Joanna has just gotten in a match from her non-Frazer maternal side. How could this possibly give information on her Paternal Frazer side?

My Understanding of the DNA Facts of Life

When your (or my) parents procreated you, those 2 parent’s DNA combined to form your 2 sets of 22 Chromosomes. [We’ll leave the X and Y out of it for now.] But remember, your parents already had 2 sets of chromosome from their parents – your grandparents. When the DNA combined it was really the four grandparent’s DNA that was twisting and combining in different ways to form you and give your your maternal and paternal pair of chromosomes. When the twisting and recombining sorted itself out there were alternating segments of your 2 maternal grandparents on your maternal chromosome and alternating segments of your 2 paternal grandparents on the other paternal chromosome. The places where the segments changed from the DNA of one grandparent to the other is called the crossover point. This can be seen when the DNA of 3 siblings are compared.

The Gedmatch.com Comparison – One to One

Let’s take a peek at Joanna’s family’s Chromosome 22. This is the shortest of the chromosomes, so theoretically, it will have the fewest amount of segments and crossovers. Here we have 3 comparisons from gedmatch.com of Joanna’s family. The comparisons are stacked up on top of each other.

Now we need to know how Joanna’s grandparents’ DNA combined in her and her 2 sibs. The matches are in dark blue, but we want to know more than that. Let’s start with the comparison of Jonathan to Janet in the first row. From about 14 or 15 million to 36 million there is a half match also called a Half Identical Region (HIR). Then there is no match. After that there is a full match – technically called a Fully Identical Region. Now look at Jonathan compared to Joanna. Those two match the whole length. But there are still crossover points. From about 14 to 16 there is an HIR. Then there is an FIR in solid green. At the point where the HIR changes to a FIR is called a crossover point. That is where there is a change from one grandparent to the other.

Adding Crossover Points as Lines

Now I put in the crossover points as vertical lines. The person who has 2 crossovers in a line gets to own that crossover point. So along the first vertical line, there is a change from Jonathan to Joanna and from Janet to Joanna. Joanna is the one I see most often there, so she owns the first crossover. Here, I assign Jonathan a 1, Janet a 2 and Joanna 3 as having 3 J’s would be too confusing.

Maternal and Paternal Split In Joanna’s Family

Next we take what is shown above, and make it look more like a chromosome browser, except one that shows both maternal and paternal sides. It will look like a chromosome map. Let’s look at Jonathan compared to Joanna above. There is a FIR for segment 2-4. That means Jonathan and Joanna match on both their maternal and paternal side. That further means that they share the same maternal and paternal grandparent’s DNA at those locations. Seeing as we may not know which grandparents they are at this time, we give them a color. In this case, we’ll say that those matching grandparents are green and blue. Blue will be either a maternal or paternal grandparent and green will be the opposite. We don’t know this yet either. The green on Jonathan’s chromosome matches Joanna’s green and his blue matches Joanna’s blue on the other chromosome:

Above is the DNA from Jonathan’s and Joanna’s grandparents. One maternal and one paternal. Next according to Kathy Johnston, we can move 1 (Jonathan’s) grandparents to the left and 3 (Joanna’s) to the left. That is because there is no crossover point blocking them.

Note that from my first image above from gedmatch, Jonathan and Janet have no match in the third segment. This means Janet has to have the opposite 2 grandparents at this segment.

Unfortunately Janet’s segment (i.e. grandparent’s DNA) is trapped between her two (#2) vertical crossover points, so we can’t expand those segments. Next, we need to add the HIRs. But should we go the right, or to the left? Here is where I’m tempted to cheat a little. Joanna and family have Frazer cousin matches here:

So in what we are doing, that would be the paternal grandfather’s side.

On the maternal grandmother’s side there are 3 new matches.

As we don’t have anything for Janet in this area (15-25), I’ll choose to go that way, to see if it helps us at all. Jonathan and Janet are HIR for the 1st two segments, so on Janet’s bar (#2), we will extend one segment (randomly orange) to the left and change the other (from purple to green). Now you can see between bar #1 and #2 on the first 2 segments, they match on the top and not on the bottom. That is a HIR or half match. This meets what our gedmatch comparison was telling us was happening between this 2 siblings.

Then Janet and Joanna had no match in the lower left, so I made the Joanna (3) opposite to Janet (2). Choosing Janet’s half identical region sets a few things in motion. Recall that Joanna and her siblings each had a match to a maternal grandmother relative on this Chromosome 22. They were all around 15 or 16 to 25. Looking up and down to the right of the #3 crossover, the only color in common in that area is green. This gives us 3 important new pieces of information:

Green has to represent Joanna’s family’s maternal grandmother.
That also sets purple as the maternal grandfather (Henry Dickins)
blue and orange now have to be Joanna’s family’s paternal grandparents.

Now we have gone from relative grandparents to actual maternal grandparents. But there is still more to fill in. We know from the Frazer DNA Project that Joanna’s family has 3 paternal grandfather (Frazer) matches here:

Too bad I don’t have them in the same order as the segment chart above. I think that the Frazer will be blue. Let’s guess that the last vertical crossover line is at position 45. From the area of 42-45, there are 3 of Joanna’s family who have matches with a Frazer. We already have 2 out of 3 blues available for these Frazer matches, so Frazer has to be blue. The last blue can be added on Janet’s row #3 in the small segment area of 42-45. We know from our first gedmatch comparison that Janet and Joanna have HIRs for the last 2 segments. I made Janet (2) have her paternal side blue so it matched with the other 2 Frazer matches. Then I made sure that between Janet and Joanna (2 and 3) their last segments didn’t match maternally on both sides. They had to match only one side. That was the Frazer side. Then the maternal side had to be purple for it to be a half match. Here is where Joanna’s family got their DNA from each grandparent. This was the beginning of Joanna and her siblings for Chromosome #22. It is pretty interesting that we can find out their grandparents’ contributing DNA considering these grandparents were all born in the 1800’s.

Now back to the original comparison:

I think everything holds together. Note that Joanna had only one crossover near the beginning. Janet has 2 in the middle and Jonathan has one at the end. This is portrayed in our Chromosome map in 4 colors also.

I had mentioned how some of my earlier analyses were using the longest and most difficult chromosomes. This should be a more simple and clearer example.

One Side Helps the Other

These 4 grandparents were determined using just 2 known matches to Joanna and her 2 siblings. One match was on the maternal side and one was on the paternal side. Once the maternal side was set, that made it easier to determine where the paternal match went. This process works because: 1) Joanna and her 2 siblings all tested their DNA and they can compare to each other using gedmatch.com; 2) There are known matches to Joanna and her siblings – one on the maternal side and one on the paternal side. These act as a reference to set where the 4 grandparents fit in for this analysis. It also helped that these matches matched all three siblings.

Applications

Jonathan and Joanna cannot have any matches on their Seymour Line on Chromosome 22.
Likewise, Janet cannot have a Seymour match above the region of about 42 million.
Joanna will probably not have any meaningful matches with her Dickins Line on Chromosome 22.
The family does not have parents available for DNA testing, so a match at any point for each of these siblings will still have to be checked to determine whether it is on the maternal or paternal side.
Triangulation Groups will also follow the segment lines for each sibling
Each of these 4 grandparent segments are made up of other smaller segments from their ancestors.

January 8, 2016August 8, 2016

More Fun With Segments and Crossovers: Part 4

In this blog, I plan to look at the previous analysis I had done on my Chromosome 1 based on comparing my DNA to my 2 sisters. That was done in atDNA Under the Hood: Segments and Crossovers. I will break that down further using phased results. I have had my mother tested for her autosomal DNA. As a result on gedmatch.com, I have been able to produce 2 kits for each person. Those kits split out the results into the DNA I got from my mom and the DNA I got from my dad.

Recap On My Chromosome 1

Before I wrote my blog, I tried using a technique proposed by Kathy Johnston to show where all my segments had come from. Gedmatch is used to compare 3 siblings. Vertical crossover lines are established and DNA segments from contributing grandparents are established. This was my preblog placement of crossover lines and who they were assigned to using initials.

Note all the close crossover lines on the right side. This was a bit confusing. Here is my first try at assigning those segments to my two sisters and me.

In my blog, I simplified the crossovers a bit.

I came up with these segments.

However, in at least one way, I noted on my Chromosome (J), there was a mistake. I had a large known match with someone that was likely on my Hartley (green) line that went through the short orange segment I had. So I knew that had to be wrong.

Assigning Segments With Phased Results – Paternal Side

As mentioned above, I have 3 phased paternal kits for my 2 sisters and myself. These are based on the testing of my mother. A computer program essentially subtracts out the DNA I got from my mother and assigns the rest of my DNA to my father. I took the 3 paternally phased kits and compared them. So this will represent the precursor to the paternal orange and green segments that I developed (shown above).

See how much simpler this is than comparing the whole DNA with the maternal and paternal side. This shows just the paternal side where the siblings do and do not match each other. Plus this clearly shows that these crossover points are specifically paternal crossover points. Sharon, Heidi and Joel each have 2 of them. This also points out mistakes I made in my previous analysis on the paternal side. Notice the 2 J’s at position 23 and 237. I take this to mean that I have a very large segment from one paternal grandparent in the middle and 2 short ones on the end. I’ll take the results from my previous blog and adjust that accordingly – taking out that tiny segment I already knew was wrong. I also added a ‘P’ after these 2 J’s at the top of these 2 vertical lines to show that they were my paternal crossover points.

Aah, much better. Heidi is matching me between 77 and 205, so I got that right. Remember, I’m just looking at the top half/paternal part of the chromosome at this point. Also I had it right that Sharon and Joel match from 190 to 237. Except I had it as 186. That difference may be from the effect of phasing. Between 19 and 23 all three siblings match. So Sharon’s orange Frazer segment gets moved a little to the left there. Also in the 1st segment, we shouldn’t all match. I had guessed wrong there. Heidi and Joel match, but not Sharon.

Note the following:

On each paternal line (green and orange) there are 2 paternal cutoff points producing 3 segments
The original full comparison (maternal and paternal) had 12 crossover points vs. the 6 paternal ones here
These segments alternate between my 2 paternal grandparents.
Between the 3 siblings we could match a descendant of my grandmother Frazer’s ancestor at any point except between 186 and 205. Looking up and down at that point, there will be no orange representing Frazer
On the 3 spreadsheets of matches for these siblings, I can assign with confidence, Frazer ancestor or Hartley ancestor to each of the paternal matches in the regions indicated above. This is a huge step forward in DNA analysis.

At this point, I could go back to the original full comparison and adjust the maternal segments or look at the maternally phased sibling comparisons. I’ll do the latter, to complete the picture.

Assigning Segments With Phased Results – Maternal Side

Here we have 10 maternal crossovers Vs. the 6 previous paternal ones. This is the complicated side. I had trouble assigning crossover points. These should be assigned to people who have 2 changing areas along the vertical line. For example, Sharon gets an ‘S’ for the first vertical line (crossover point) because of the defined segment she has in the comparison between her and Heidi in the first row and her and Joel in the second row. At the first question mark crossover point, there is one change shared by only Heidi and Sharon. Also there is a weird region between 204 and 206. I’ll ignore that section for now. I would like to start on the right, because I have a match with a known Lentz relative there (my maternal mother’s line). The very last segment doesn’t make sense because it shows that Sharon matches Joel and Heidi matches Joel but Sharon doesn’t match Heidi. We’ll ignore that and keep my segments the way they are as they make sense by the original gedmatch full comparison. Moving from the right to the left, the next segment in makes sense. On the third segment from the end, all 3 siblings should have the same maternal grandparent. I’ll have to change that to Lentz for Heidi. So I’ll put a purple section in the middle of my blue Rathfelder grandfather on the bottom right:

As I have mentioned previously, Chromosome 1 should be the hardest to analyze, as it is the longest. If I can get this one right, all the others should be a walk in the park. 160 to 204 is all the same maternally, so that makes sense. What doesn’t make sense is segment 77-160. Again the maternally phased comparison has Sharon matching Joel and Heidi matching Joel but Sharon and Heidi not matching. However, in the original full comparison Heidi and Sharon are opposites and the other matches are half matches, so we’ll stay with what we have. I note this non-sensical sequence 6 times on the maternal side. Not good. Also notice that Heidi has a maternal crossover at 77. Some crossovers for Heidi and others are both maternal and paternal. This appears to be one of them. That means there should be a change from Lentz to Rathfelder here. But when I check the original full comparison, I see that Heidi Vs. Joel should be opposite, so I’m tempted to leave it the way it is here. Hopefully, this will get easier.

Segment 23-40: Here, I need a paternal correction as it shows the same paternal match for all three siblings. In my paternal phased gedmatch comparison, it shows that Sharon and Heidi match from 23-77, but I don’t match either of my sisters paternally. This is fixed by moving my green Hartley segment to the left (J Row).

This gives me even more Hartley segment in green. Next I notice in the 5th segment (40-77) that Heidi to Joel was supposed to be opposite in the full comparison. I can fix this by moving Heidi’s Lentz segment to the left. Talk about tedious.

At any rate, that’s a bit more aesthetically pleasing. Now there’s another problem at 23-40. The original full gedmatch comparison has Sharon to Joel as opposites which is now right, but Sharon to Heidi and Heidi to Joel as half matches and I have them as full. I don’t want to mess with the Sharon-Joel opposite match here, so I’ll skootch the Lentz a little more to the left.

Segment 19-23 – Only 3 more segments to go (hopefully). The full comparison has Sharon and Joel as full matches (FIRs) and the other 2 as half matches. That looks good.

8-19: Sharon to Heidi are opposites and the others are half matches. Giving Sharon a bit more purple will fix that. Plus Sharon has a maternal crossover there, so it makes sense.

Home Stretch. Sharon to Joel needs to be opposite in the first segment. No correction needed here. This is as good as I can get Chromosome 1 right now.

The Frazer DNA Project Connection

Here is where the Richard Frazer Triangulation Group is:

Here was my earlier attempt at chromosome 1 without phased DNA. This was from last week when I was younger and more foolish. It’s off, but not totally.

Summary

It was a long blog, but who wants short blogs with wrong answers?
Using phased DNA (paternal and maternal) made the answer more clear, but the process was no easier.
My paternally phased comparison behaved better than the maternal. However, if you knew my mom, you would understand why.
It took a combination of the full sibling comparison plus the phased paternal and maternal comparisons plus known relative matches to complete the diagram
For anyone that matches me or my siblings on Chromosome 1, I should now be able to tell which grandparent they match
This blog has been approved by the FDA as a cure for insomnia

January 8, 2016August 8, 2016

More James Line Segments

In the last 2 blogs, I wrote about segments and crossovers. In this one I am continuing on with James Line Segments. The James Line is from James Frazer b. in the early 1700’s from North Roscommon, Ireland. I am looking at Chromosome 14, because there seems to be a lot going on there. Here are some of the Frazer matches from my master list of matches from testers in the Frazer DNA Project:

Not all of these matches will come into play, because we are looking at the family of Jonathan, Janet and Joanna. Here Jonathan matches JFS on the Michael Frazer Line b. 1764 (a branch of the James Line). Janet matches the same person at 2 different places. Janet and Jonathan match BZ their 2nd cousin at differing levels. Also Jonathan matches BR from the Archibald line (brother of James Frazer) at a smaller amount. This may or may not hold up.

Remember, we can do this analysis because siblings have what are called Fully Identical Regions (FIRs). This means that they match their same paternal and maternal grandparents (but we don’t know which initially). Then by comparing the Half Identical Regions (HIRs) and places they don’t match, it is possible to map out all 4 grandparents. With matches to known people, it is possible to fill in which grandparent is which.

Chromosome 14 appears to be more simpler than my earlier examples:

Here, there are only 5 crossover points. The crossover is where the DNA recombines. Janet has only one crossover point and Jonathan and Joanna each have 2. Note above that Jonathan (1) and Joanna (3) have a FIR in the first segment indicated by the green bar in the middle row. That means they have the same Paternal and Maternal grandparents. I’ll give those grandparents a green and blue color for both Jonathan’s (1) and Joanna’s (3) DNA segment below.

The crossover point is where something is going to change due to DNA that got recombined from Joanna’s family’s grandparents via their parents. I suppose you might say we are recreating how this family was formed by the different combinations of their grandparents’ DNA. I can’t extend Jonathan’s grandparents at this point (at crossover 1). I can extend Joanna’s as her crossover point doesn’t occur until line 3 (which is her crossover or recombination point).

Now note in the gedmatch browser comparison above that Janet and Joanna have no match in the first 2 segments. That means that Janet will have the opposite grandparents in those segments shown as being orange and purple.

Next, I see that in the 3rd segment, Joanna matches Janet perfectly (FIR). We will note that and extend Janet’s segments to the right hand side as she only has one crossover point.

Next I filled in some opposite regions between Janet and Joanna and Jonathan to Janet.

However, note that in the comparison between Jonathan and Janet, there is something odd.

In the third segment, there is no match as shown by a grey underneath (no blue). However, on the top there are no red marks. I though that it was too easy. Next, I will add an HIR from Jonathan to Janet in the last 2 segments.

Next Jonathan and Joanna have a no match on the last chromosome, so they are opposites. There seems to be no easy solution for the middle part of Jonathan’s Chromosome 14 – or rather there could be more than one solution, so I’ll just pick one for now and see how it fits with the matches.

And there you have my version 1 of Jonathan and his sisters’ Chromosome 14. It doesn’t look that great. Janet’s chromosome looks too symmetrical. Also Jonathan has one of his crossovers on Joanna’s crossover point (3).

Now for the Frazer DNA Project matches to Jonathan and family.

Here’s where the puzzle begins. We don’t know which of the 4 colors that the Frazer could be. That could be either

Janet has matches from 32-50; 59-100; and 92-101. This means I drew Janet wrong. I have her with a break in the middle of these. That is, unless, the match with JFS is a false match.

Jonathan has matches from 80-99; 92-101; and 99-102. That could either be green or purple, but his first match at 80 would make it look like the green. I’ll give it another try with Janet having her green be the Frazer for the whole length. This is what I came up with:

Joanna and Family Version 2 Chromosome 14

That looks better. Now Janet’s segments are not so symmetrical and Jonathan’s crossovers are at his own crossover points. Joanna has a crossover on Janet’s crossover point, so maybe she should have solid orange, but that would cause other inconsistencies.

Now I’ll add the Frazer to the green areas and Seymour grandparents in orange showing where some of our Frazer DNA testers match.

I know that Joanna is looking for other relatives to test on her mother’s side. So once those DNA results are in, that will further confirm which maternal grandparents the blue and purple segments belong to.

This was not as easy as I thought it would be.