An Update on an Irish Butler’s Big Y

Not too long ago I wrote about my Butler father in law’s Big Y results here. I found it a bit frustratinng that FTDNA changed their matching criteria. Richared is I2 on the YDNA nomenclature and his terminal SNP is now I-A427. Here are the matches shown at FTDNA:

However, there was a catch to the matching. Now Richard has a match if:

A person is considered a match if they have 30 or fewer differences in SNPs with you, and their haplogroup is downstream from your haplogroup or downstream from your four closest parent haplogroups.

Since my last Blog, I uploaded Richard’s VCF file to YFull.

I made sure to show that his ancestor was from Ireland, as I didn’t see any other Irish Flags. Now Richard is in an I-A427 group with no further branching along with two other YFull people. I’m hoping that once the next Y Tree comes out, that Richard will be on a new branch of the Y Tree. But back to the matching. If I count the id’s above, I get 17 other than Richard that are positive for I-A427. Yet Richard has no A427 matches by the FTDNA criteria. And that holds true for the four branches above A427 even though there are likely many more people that are positive for those SNPs.

Once Richard was on YFull, I joined him to the I-M223 Group. That way, group adminsters can see his results there and do any needed analysis.

FTDNA’s SNP Tree

I was unable to get FTDNA’s SNP tree working for my last blog. Here is how it looks for Richard:

I have a little trouble reading the FTDNA tree. I went two levels above A427 to P78. It looks like the two branches under P78 are the larger S25733 and the smaller Y7219. Under S25733 there is A427 and PH2670.  This leads me to modify the tree I had drawn in my previous Blog:

This was drawn to show that FTDNA may be ahead of YFull in some aspects and YFull may be ahead of FTDNA in others. The yellow level and down don’t  apply to the Butler/Whitson I-M223 Branches. Peter from the Project and Richard have both tested negative for S23612. That means that they are awaiting to be put in a  new branch below A427 that is parallel to S23612.

Here is where I expect the new branch to be:

Eventually, there should be additional branching below this yellow level. I would expect there to be more than just Butlers and Whitsons in this branch as this branch could still be over 4,000 years old. Note that probabably due to planned family testing, the Y24488 Branch got down to as recent as 150 years ago for their common ancestor.

VCF and BAM files

The two files that are generated when your Big Y results come in are the VCF and BAM files. FTDNA has not been generating the BAM files due to their conversion from HG19 to HG38. Due to a better understanding of YDNA a new standard was needed as new locations were found on the Y Chromosome. Thus the new HG38. For example, here is a list of some of Richard’s Novel SNPs:

YFull shows the HG19 position and the HG38 position.

The BAM Files are much larger than the VCF files. Other than that I don’t know a lot about them. YFull used to only accept the BAM files, but now that BAM files are held up, they wisely decided to accept VCF files. They get their money ($49) and we get most of the analysis. The rest of the analysis is done for free once the BAM file is available. Here is YFull’s ad:

Note they state that they only get about 50-70% of what they need from the VCF file. Also note that no age estimation is done without the BAM file. That is one of the most popular features of YFull. So I will definitely send YFull my BAM link once it is available.

Any Shared SNPs at YFull?

Again, no. YFull doesn’t do SNP sharing on old SNPs. Isn’t that age discimination? This is from the YFull site:

Q: What is YFull’s “SNP matches” methodology?

A: The methodology is reflected in the SNP matches table, which provides information about Shared SNPs and Assumed Shared SNPs of compared samples. The table is limited to SNPs having an estimated age of 3500 ybp or younger (using TMRCA from the YTree), with a maximum of 100 lines of information.

I-A427 has a TMRCA of 4700 years before present. That is ancient. Richard is only off by 1200 years.

Are the Novel SNPs At YFull the Same As the Unnamed Variants At FTDNA?

I think so. From my last Blog, FTDNA showed that Richard had 33 Unnamed Variants of High Quality. YFull shows 18 Novel SNPs of best quality and 11 of acceptable quality. That adds up to 29 which is two off from FTDNA’s 33 Novel SNPs and Unnamed Variants appear to be the same thing. However, based on differing interpretations different Novel SNPs were reported at different reported qualities:

This is a partial listing of all of Richard’s Variants. YFull is on the left and Big Y is on the right. I lined everthing up by the position numbers. YFull reports two Novel SNPs as ‘Ambiguous Quality’ that FTDNA reports as High Quality. Then FTDNA has 7 Novel SNPs rated at High that YFull does not even report. Again, it’s good to have a second opinion.

Any Shared Novel SNPs at YFull?

I think so. I copied all the Noved SNPs into Excel and filtererd all the ones that said ‘shared’ on them:

Here is what I gather:

  • Even though these 14 Novel SNPs are shared, I can’t tell who they are shared with
  • There are an equal amount of low quality Novel SNPs shared as well as Best Quality Novel SNPs
  • One Novel SNP is new as there was no HG19 Position given
  • All these Novel SNPs have been named except for two. The YF designation is a YFull numbering system, but as far as I know, not a SNP naming designation.
  • I expect these Best quality and acceptable quality shared Nove SNPs to form a new branch or branches.

Summary and Conclusions

  • The Big Y Results have gotten tbe ball rolling for the I-M223 Group of the Whitson/Butler YDNA Project
  • Once the BAM file is available from FTDNA it will be uploaded to YFull
  • Richard’s Big Y VCF file has been uploaded to YFull. I expect new branching once a new Y Tree comes out. These seem to come out about every two months. The last one came out at the beginning of January.
  • FTDNA’s I-M223 administrators will also be looking at the Big Y results and the Y Full results for Richard, to see if further branching of A427 is warranted.
  • One or two others from the Witson/Buter I-M223 Branch have expressed interest in taking the Big Y test. These tests could get to how the Butlers and Witsons are related. This may also give some geographic information on common ancestors. The Butlers were known to be in Ireland? Were the Whitsons also there? If so, when?

 

My Father In Law’s Big Y Butler Results

I ordered a Big Y test for my Butler father in law last Summer and got the results right before the start of the New Year. Unfortunately my father in law passed away last Spring, but Family Tree DNA had kept his DNA sample from a previous Family Finder test.

Recap of Butler YDNA

My wife’s father’s family is in the I2 Haplogroup. He is also in a Whitson Project which I administer. Here is a summary of the Whitson Project which includes Butlers, Whitsons, Whetstones and others:

The group has grown from 12 to 15 since I last wrote about it. My father in law’s ancestor was Michael Butler. Here is a general idea of where I2 – M223 can be found:

Richard shares I-A427 Haplogroup with another Butler. These Butlers believe that their ancestors were origninally from the SE of Ireland. It is likely that all the Whitsons and Butlers in the I-M223 Group above are also I-A427

From I-M223 to I-A427

 

This tree is a bit over a year old. A427 is at the bottom right of the tree. Somehow these Germanic Butler ancestors made it to Ireland. Of course, they had thousands of years to make it there.

A427 and Children at YFull

The normal strategy is to upload Big Y results to YFull. YFull takes a look at the results and likely puts you in a downstream group to A427. YFull has a YTree. This is the A427 portion of the tree:

  • I am quite amazed at the span of years in this tree.  The Time to Most Recent Common Ancestor (TMRCA) for A427 is 4700 YBP (Years before present). The TMRCA for I-Y24488 is 150 ybp. That is a span of about 4700 years for this branch!
  • The other observation is that it appears that a family group at the bottom of the tree got together for some planned Big Y testing.
  • Not all kits have flags, but I don’t see any Irish Flags for the kits that do have flags.

The FTDNA I-M223 Project

This project has the results from about 3500 men who have had YDNA tests. Here are the results of those put in the A427 group:

There are others below this group that have been put into branches below A427. Among this group are 3 Butlers and 3 Whitsons. I have written before about signature STRs. The signature STRs are highlighted for Butlers and Whitsons:

The mode of the STRs are at the top of the list. Deviations from that mode are in pink or purple. The areas where the STRs are in a colored block or similar within the Whtison/Butler Group are the signature STRs for Whitson/Butler.

Big Y Results

The Big Y Results so far have been dissapointing. I had thought that the results would bring the Butlers into a more recent SNP than A427. Apparently that will have to await YFull analysis or analysis by the M223 administrators. Here are my father in law’s Big Y Matches:

 

At first, I thought this was a mistake, so I wrote to the M223 Activity Feed. There answer was that there is a new matching definition:

A person is considered a match if they have 30 or fewer differences in SNPs with you, and their haplogroup is downstream from your haplogroup or downstream from your four closest parent haplogroups.

To me, this seems like a backwards way of matching. However, I’m sure FTDNA have their reasons. According to YFull, the TMRCA for A427 is 4700 years ago. YFull uses an average SNP rate of 144.41 years. That would mean that there would be about 32.5 SNPs in that time. I assume that there would be many more SNPs due to branching.

More Snooping Around and Problem Solved

I finally downloaded the SNPs for Richard, my late father in law. At the top of the list was this:

Note that S23612 tested negative. Under Test is also S23612. That tells me that FTDNA did a special test for S23612 in addition to the Big Y as they also questioned the results. That means that Richard’s Big Y results are actually stuck back in antiquity – for now.

Help: The Butlers/Whitsons Stuck at 4700 Years Ago!

 

YFull named the only branch under A427 for Y4884. Notice that I underlined in red the equivalent level SNP S23612. For whatever reason, FTDNA decided that should be the name of the branch. There are two others that have had a Big Y or equivalent test and uploaded their results to YFull that are stuck at A427. It is possible that Richard will form a new branch with one of those.

I combined the YFull Tree and the ISOGG Tree and came up with this:

Now What?

What is needed now is someone in the I-M223 Group of the Whitson/Butler Group to take the Big Y test. This would bring the SNPs up to a more reasonable time frame. I suspect a new Whitson/Butler SNP branch will come down at the level of the yellow box above.

Richard’s Butler “Variants”

Remember that I estimated that in 4700 years there should be 32.5 SNPs? Well guess what. Richard has a total of 33 Unnamed Variants according to his Big Y test. What are Unnamed Variants? Unnamed Variants can be not-yet SNPs. These 33 Unnamed Variants are waiting for matches. Once there is a match, it is possible for these Unnamed Variants to become named SNPs that would form their own branches. So say that someone from the I-M223 branch of the Whitson/Butler Project were to take the Big Y test. It would be likely that there would be a match on 30 or so of those Unnamed Variants and that 3 may remain as Variants, sometimes called Private SNPs.

Here is what the Unnamed Variants look like for Richard:

To the right of the list, there is a Reference Letter and a Genotype Letter. These letters are A, G, C, or T. Then there is a confidence level. This is set to High by default. Each unnamed Variant is a Position Number. According to FTDNA:

The Position column displays the position (location) of the unnamed variant on the Y-chromosome with respect to the GRCh38 human reference genome, which is maintained by the Genome Reference Consortium.

YBrowse

It is possible to go to ISOGG’s YBrowse page to look up these positions I suppose this would take a while to look up 33. Here is the first Unnamed Variant 10005112:

This shows where the ‘Variant’ is on the Y Chromosome. If there were any named SNP or other information, it would appear below the Browser.

Unnamed Variants with SNP Names

Believe it or not, I went through every one of Richard’s Unnamed Variants in the YBrowser. Come to find out, some of them did have names – just not with FTDNA. Here are the six out of 33 that did:

This was interesting, but probably not any of these SNPs are on a tree right now.

Summary and Conclusions

  • Right now, Richard’s Big Y results have not shown him in a more recent Haplogroup than I-A427. That goes back to at least 4700 years before present or about 2700 B.C.
  • FTDNA tested Richard for the only presently known SNP below A427 which is S23612. This is equivalent to YFull’s Y4884. FTDNA found that Richard did not have this SNP.
  • I will upload Richard’s Big Y results to YFull for analysis once they are released by FTDNA. This may result in further branching below A427 other than S23612 (or Y4884).
  • A Big Y test by an additional Butler or Whitson in the I-M223 Branch of the Whitson project would result in many new matches of Variants which would become named SNPs and likely form new branches. This matching would give an approximate date of the Butler and/or Whitson’s common ancestor.

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.

Kilkenny Wexford

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

4 GD Butler

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

2 GD Butler

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.

edwardh

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

Sailor Outfit

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

Edward Butler Death 1915

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?

Edward H Death 1925

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