Waiting for the Frazier BigY Manual Review and Frazer Y-HAP-Backbone Test

A lot has been happening with Frazer YDNA recently. In January, Rick’s new BigY 700 came in. Rodney upgraded his BigY 500 to a BigY 700. This came in at about the same time as Rick’s results. At the beginning of February, the new Frazier BigY 700 results started to come in. However, there are still a few loose ends.

  • I assume that there will be a manual review of the Frazier results by FTDNA
  • Rodney and Jonathan from the James Frazer Line both have pending Y-HAP-Backbone tests ordered by FTDNA. These were apparently ordered to fill in gaps from their BigY testing.

What Gaps Do Rodney and Jonathan Have in Their BigY Testing?

This was discussed some in my Blog: Frazer YDNA Loose Ends and Private Variants. In that Blog, I looked at Private Variants. The conclusion of my review was that I thought that FT420438 and FT420010 should be added here:

Let’s see if that still makes sense now that the Frazier results are in. In my last Blog on the Frazier results, I came to the conclusion that these SNPs should be added:

FT420010

The good news is that in both my analyses, I had FT420010 in the R-YP6489 Block. The bad news is that in my first Blog, I had FT20438 in that Block and not FT426078. In my more recent Blog, I had FT426078 in the R-YP6489 Block and not FT20438. Confusing, isn’t it? My assumption is that FT420010 does indeed belong with R-YP6489. I will just check Frazier to make sure:

Position #5987829 is the position for the SNP FT420010:

Here is a chart I just made to compare the testing results between the five testers:

This shows that for FT420010, the three people who had the BigY 700 tested positive. Jonathan and Paul had the BigY 500 and their tests were inconclusive. That means that there were not enough reads or not enough positive reads. All this to say that FT420010 checks out. What I don’t know is if it belongs even further upstream – say to where the Stuarts are on the Block Tree:

FT426078

This is a SNP that I suggested should go in the area of YP6489. Here is the position number:

Did Frazier test positive for this SNP? Here are the six Private Variants for Frazier:

Frazier did have Position number 4056256.

Paul’s results were inconclusive for this position number on his YDNA test:

This is where my comparison chart should come in handy:

Next, I fill in the other boxes:

The unfortunate part about this is that Rick’s BigY 700 which should have had more covereage than the BigY 500 tests, did not test for Position #4056256. However, based on Rodney and the Frazier tester  testing positive, I think that FT426078 will be added to the Frazer/Frazier group of R-YP6489.

FT420438

Prior to the Frazier BigY test results, I had suggested that FT420438 be added to the area of R-YP6489. Let’s see if that still makes sense.

Here is a summary of what I had for my earlier Blog:

At that time Frazier was not yet tested. What are the Frazier results for this position? Again, these are the six Private Frazier Variants:

I see nothing in that list starting with 118… Next, I’ll look at Frazier’s csv file:

It was worthwhile downloading the large Frazier csv file, because the results are interesting. This shows that Frazier has no mutation at this reference. If the Reference and Genotype are the same, that means that there was no mutation –  unlike Rodney and Rick:

In testing YDNA, a negative result is as important as a positive one. That means that FT420438 is a defining SNP for the Roscommon Frazer group along with the three others they already have.

A Predicted Frazer/Frazier Block Tree

Here is what this appears to show:

This view is from the perspective of the new Frazier tester who would be in the right column. Two of his six Frazier Private Variants will go up to R-YP6489 reducing the Frazier Private Variants to four. Rodney will have a reduction of four in his Private Variants. That will likely reduce the average Private Variants of Rodney and Jonathan from 4 to two. Rick will have a reduction of two Private Variants. That should reduce Rick and Paul’s Group from three Private Variants to two.

More on the Frazer/Frazier Block Tree

It seems like this area of the Tree where the red arrow is pointing is important:

This must be the are where the two Frazer/Frazier branches divided from each other. However when was this date? From the Rodney/Jonathan Line there should be 8 SNPs below the point where I show the arrow. On the Rick/Paul Line there should be 9 SNPs. On the Frazier Branch there should be a mere 4 SNPs if my analysis is correct. The average Frazer Line is 8.5 SNPs long. I’ll average that with the Frazier Branch that has 4 Private Variants to get 6-1/4 SNPs. I’ve seen various number of years to apply to these SNPs. I’ll try 84. 84 times 6.25 is 525 years. That brings us back to about the year 1495. That is a little earlier than my previous guess of 1600. If I apply the 84 years to the remaining 5 SNPs that I have in R-YP6489 that is another 420 years. That brings us back to the year 1075 when we are bumping up against the Stuarts and possibly Grant. That would make sense as it would help if this date was around the time (or before) of the adoption of surnames.

So where I have the arrow pointed should be about 1075. The next break in the blocks should be around 1495. The next break in the blocks on the left two Frazer lines should be around 1690 which is the date we are guessing that Archibald Frazer, the father of the James and Archibald Lines was born. The number of 84 per SNP breaks down between 1495 and 1690 as there would be four SNPs during this period. This is a little less than 50 years per SNP. As the 84 years should be an average, it could be that there were a lot of SNPs forming during this period of time on the Frazer Line. It seems like the Frazier Line was helpful here as this line perhaps had fewer SNPs forming between 1495 and the present. At an estimated 4 Private Variants over about 525 years, that is one SNP about every 131 years. The same effect can be seen in the Stuart and Grant Lines, though this could be partly due to the Stuarts taking the BigY 700 and Grant taking the BigY 500 test.

Rodney and Jonathan’s Y-HAP-Backbone Tests

I’m still not sure why FTDNA ordered Y-HAP-Backbone Tests for Rodney and Jonathan.

Jonathan was missing some information on these three positions. However, Jonathan had good result for these three positions. It could be that there were some discrepancies between Frazer/Frazier and Stuart/Grant with other SNPs that I don’t know about that FTDNA wanted to clear up.

Summary and Conclusions

  • In my previous two Blogs, I came to some conclusions as to where some of the Private Variants should end up for the five Frazer/Frazier testers. However, in this Blog I put that information together to give a fuller picture.
  • In order for there to be a new SNP that is unique to the Frazers of Roscommon, it has to be positive for that group, but also negative for the Frazier tester. That was the case for FT420438. That would also be true for the existing three SNPs in the Roscommon Ireland Frazerr Block of FT421618. I didn’t check FTDNA’s work for the existing three SNPs in the Block, but I assume that they were right.
  • I showed where I think that Frazer/Frazier Block Tree will end up once FTDNA has finished its manual review. I also did some guesswork as to the dates at some important junctures in the Block Tree.
  • The Stuarts and Frazers seem to go their separate ways around the year 1075
  • The Frazer and Frazier lines seem to separate around 1495.
  • I’m still curious as to why FTDNA ordered Y-HAP-Backbone tests for Rodney and Jonathan.

 

The First Frasher/Frazier BigY Results

The long-awaited Frasher/Frazer BigY results are starting to come in. This test was ordered around the time Rick from the Roscommon Frazer group ordered his test last August. However, the Frasher/Frazier test was delayed due to quality issues.

The Status of the Frazer BigY Project

Prior to the Frasher/Frazier test results, there were four Frazer BigY testers. They all had pretty well-defined relationships based on genealogy:

Rick was the one who ordered a new BigY test. Also around the same time, Rodney upgraded his BigY 500 to a BigY 700. That means that now Rick and Rodney have BigY 700 results and Paul and Jonathan have the older BigY 500 results. Here is the Block Tree pre Frasher/Frazier:

My second cousin once removed Paul is R-Y85652. This is called in general the Archibald Branch. Rodney and Jonathan are in R-Y151390. This is called the James Branch of the Frazer Line. These two lines were previously under R-YP6489. For some reason, another group formed between YP6489 and the two Frazer Branches. This is R-FT421618. As it is usually necessary for a new tester to form a new group, I had assumed that the new Frasher/Frazier test would end up as FT421618.

New Frazier/Frasher Results

Here is the new Block tree from my cousin Paul’s perspective:

The new tester, Richard is listed as R-YP6489 and not FT421618. That means that it is likely that it was Richard that split the YP6489 Block into two. The YP6489 Block must have previously had had six SNPs. Now there are two blocks with three SNPs each.

FT421618 and YP6489

R-FT421618 is the newest SNP and represents the Haplogroup of the Frazers from Roscommon, Ireland. This is the SNP in common with the four BigY Frazers whose roots go back to Archibald Frazer who apparently lived in Roscommon Ireland sometime before 1749. The new Frazier/Frasher tester does not share these SNPs.

Based on the Block tree, it appears that Richard, the newest BigY tester shares three SNPs with the Roscommon, Ireland Frazers. These SNPs are YP6489, YP6490 and YP6493. Collectively, these are called YP6489.

Where and When is YP6489?

When Did YP6489 Form?

This is the big question. We can date FT421618 to about 1690 to when we believe that the first Frazer lived in Roscommon Ireland. That means that the oldest SNP in the Block of YP6489 formed three SNPs before 1690. The question then is, how often does a SNP form? I have seen a number as low as 86 years per SNP as I recall. However, the scale on the left is showing 9 SNPs up to FT421618. If we take that time from very recently then 2020 minus 1690 is 530 years. That means that it looks like a SNP formed about every 59 years.  Let’s use 86 years for the three SNPs in the YP6489 Block. That gives us 258 years before 1690 or 1432 for the formation of the oldest SNP in the YP6489 Block. However, see further down in the Blog as I surmise that there should be more SNPs in this Block which would make YP6489 even older.

When was the Common Ancestor Between Richard and the Roscommon Frazers?

This is a different question. It appears from the Block tree that Richard and the Roscommon Frazers share the top three SNPs in YP6489. That means that the common ancestor would be closer to 1690 than to 1432:

In the image above, “Your branch” is Frasher/Frazier. We know that Richard does not descend from Archibald Frazer probably born in 1690, but he could have descended from Archibald’s father or grandfather. Let’s say that the common ancestor between Richard and the Frazers of Roscommon was 1600. My reasoning is that the most recent common ancestor would have to have a SNP shared by Richard and the other Frazers. That would be the most recent SNP in the group of YP6489. That most recent SNP probably formed about 86 years or so before FT421618.

SNP Tracker

This is a program that gives a rough estimate of dates of and locations of SNPs. Here is what SNP Tracker shows for FT421618:

SNP Tracker has that SNP in Ireland in Medieval times. That is probably based on the 9 SNPs I mentioned above. I think that FT421618 should be 1690. Here is more from SNP Tracker:

Roscommon is in the top three here and the numbers are pretty similar for Armagh, Down and Roscommon. Here is some more information, though I don’t agree with these SNP Tracker results either:

Offshore means continental Europe. That part would be quite certain.

Back Before Frazer with the Stuarts and Grants – YP6488

Whereas YP6489 is the umbrella group for the Frazer/Frasher/Frazier group, YP6488 is the umbrella group for Frazer, Stuart and Grant. The explanation for these relationships is not clear. I can come up with a few guesses:

  • This could represent the period when surnames were adopted. One group adopted Frazer, one Stuart and one Grant.
  • There could have been a Frazer/Stuart marriage and the children of one group could have taken on the Stuart name rather than Frazer for some reason.

Whatever the reason, the YDNA is sorting out the matches between Frazer on the one side and Stuart/Grant on the other.

The Block Tree makes it look like Grant is one SNP away from being a Frazier/Frasher and vica versa. However, that is only because there are not other close matches for Grant and Frazier/Frasher. If there were, that would put their groups further down on the Block tree similar to Frazer and Stuart.

Grant

It is interesting to note that Grant only has three variants bringing him to an equal level with FT421618. I had dated this as 1690. My guess is that Grant had the BigY 500 which did not discover as many SNPs or Variants. If we use the older 144 years per SNP based on the BigY 500 test that would date Grant at 432 years ago or about 1590. This is still early for my proposed 1690 date for FT421618.

Where Was the Common Ancestor for Frazer and Frazier/Frasher – YP6489?

This depends partly on the dating of Richard’s common ancestor with the Roscommon Frazers and partly on genealogy and Frazer history. Perhaps other could speculate better than I. Did the same events that resulted in the Roscommon Frazers moving to Ireland result in Richard’s ancestors move to the New World? Did a common ancestor move to Northern Ireland and then one brother moved to Roscommon and another brother or relative move to Virginia? It is even possible that Richard’s ancestor moved to Roscommon, Ireland and then to America.

Here is a map from Irish Ancestors:

Here is some more information:

Richard’s DNA Testing

FTDNA will do a manual review if a new YDNA branch is formed. Technically, the new branch formed before Richard’s test results were completed. However, this new branch of FT421618 seems to have formed based on Richard’s results.

Richard shows under “Your branch”. What appear to be missing are Richard’s Private Variants.

Richard’s Private Variants

These are the Richard’s SNPs that have no matches at this time called Private Variants. They form Richard’s personal line since the three SNPs in the Block that form YP6489:

This is some of the most important information from the BigY test as these are for the most part new variants that have been discovered in Richard that have never been discovered in anyone else in the World. I haven’t checked Richard’s Private Variants to see if they are all truly Private. However, the number of Private Variants seem to be a reasonable number at six. Above, I gave a possible date of 1600 for a common ancestor between Richard and the Roscommon Frazers. That means that, since 1600, six Variants formed as opposed to the approximately 9 that formed in the Roscommon Frazer Line.

I can look up these positions in YBrowse. 10059190 is too new and does not appear there yet as a Variant:

The same is true for Richard’s next three Private Variants. I found some information on 4056256:

This is a new SNP as of 2021. My guess is that that this “Private Variant” may have come about from Rick or Rodney’s BigY 700 tests.

That leaves one more Private Variant for Richard. Position 5987829 has been named also:

Next, I need to check Rick and Rodney for these two positions. Rick has one of the two:

Rodney has both of these ‘Private Variants’:

Here is my guess of what should happen:

It seems like these two SNPs should go up into the YP6489 Group. Also Rick should lose one of his Private Variants and Rodney and Richard should lose two each. It could be partially due to these discrepancies that FTDNA ordered additional testing for Paul and Jonathan. The other question is, why didn’t Rick show that he had position #4056256? Here are Rick’s results:

It appears that Rick’s BigY 700 testing missed that position number.

For Jonathan and Paul, the results seemed inconclusive for these two positions. Here is what Jonathan’s results looked like for Position #4056256:

Summary and Conclusions

  • Richard’s BigY test represents the first BigY test for a Frazer/Frazier who doesn’t descend from Archibald Frazer of Roscommon Ireland
  • Richard’s BigY test benefits from the prior testing of four Frazers. Without this he would have shown that he is related to two Stuarts and a Grant.
  • Due to the Frazer testing and genealogy, the common ancestor between Frazer and Frazier/Frasher should be about 1600
  • I made some guesses as to where this common ancestor lived, but I don’t know. Finding a Frazer with Scotland-only genealogy who has tested for YDNA would help.
  • I made some guesses as to where Richard’s Private Variants would end up.

Frazer YDNA Loose Ends and Private Variants

In my previous Blog, I was caught a little off guard as I didn’t know that Rodney had tested for the BigY 700. However, that was good news as now we have a BigY 700 in both the James and Archiald Lines of the Frazer YDNA Tree. One confusing thing about FTDNA is that it is difficult to know when your BigY test has been completed. Here is Rodney’s order history:

This seems to indicate that his BigY was completed on January 14. However there are still more tests ordered by FTDNA. Another way to check is if Rodney’s Private Variants match up with the average Private Variants shown on the Block Tree. [Note: Later in the Blog I show that is not a good way to see if your BigY has completed.]

Here are Rodney’s Private Variants:

Rodney now has 7 Private Variants. These are described by their position numbers to distinguish them from SNP which need to have a match with someone. To get the average number of Private Variants for the James Frazer Line, we need to know the number of Jonathan’s Private Variants:

Jonathan has two. This averages out to 4.5. The Block tree shows an average of 4:

4 is close to 4.5, so I would say that the BigY analysis is complete – except for the Backbone Tests. The number of Average Private Variants went up from 2 to four probably on January 11th when the backbone test was ordered or on on January 14th when FTDNA shows the BigY was completed.

Rick’s Results

Rick shows that his BigY completed in December:

However, Rick has nine Private Variants:

Paul who is on Rick’s Branch has one Private Variant.

That is a total of 10 for Rick and Paul’s Frazer Branch for an average of five Private Variants. The Rick and Paul Branch of the Block Tree shows an average of three Private Variants. That means that FTDNA’s manual review must not be completed yet.

The James Line Private Variants

These should be the variants that have formed since Rodney’s and Jonathan’s common ancestor.

That common ancestor was Thomas Henry Frazer. Thomas Henry Frazer had, for sure, these two SNPs – Y151390 and FT421607:

I say, for sure, but the backbone tests seem to be confirming these. The point is that Rodney and Jonathan’s Private SNPs formed after Thomas Henry Frazer in 1836. By the way, I made a mistake in dating the Block Tree in a previous Blog, so I’l correct that here:

The slightly confusing part is that the 1836 is higher on the tree than the 1804. I think that could change as the average number of Private Variants right now appears to be 5 between Paul and Rick under the R-Y85652 part of the Tree. Say that some of the testers were born around 1950. That would mean that this Tree represents 750 years of Frazer YDNA history.

Jonathan’s Private Variants

Here is Martin’s take on Rick’s initial results. Martin is the FTNDA administor for the portion of the R1a YDNA Tree that our Frazers are on. These have since changed since Rodney’s BigY 700 upgrade came in.

This shows Rick with a BigY-700, but doesn’t show Rodney in that category yet. I mention above, that Rodney has 7 Private Variants. The BigY 700 is more comprehensive and finds more variants. Before Rodney’s BigY 700 results came in, he only had one Private Variant. Jonathan has two Private Variants. They are the last two in the yellow box aove.

Jonathan’s first formerly Private SNP became part of the new James Line Haplogroup:

I don’t see BY84935 on the Block Tree, so if it isn’t there and isn’t on Jonathan’s Private Variant list, where did it go?

Here are Jonathan’t test results:

The mutation should be G to A, but Jonathan shows at least two reads that are G to T.

Let’s see how Rodney tested for this. This is now a named SNP, so no longer a Private Variant for Jonathan. I don’t see Rodney having BY84935:

Based on these two test results, this should still be a Private SNP for Jonathan.

Rick and Paul Have a ? for BY84935

Rick is sometimes positive for this SNP and sometimes not. Also, he seems to have a lot of similar results in this region of the Y Chromosome. Now I see why they took away this Private Variant from Jonathan.

Let’s check out Paul’s results:

Very similar to Rick’s results:

Based on these results, I’m a bit surprised that Jonathan ever had a Private Variant at this position. For Jonathan’s other two Private Variants, I will assume that they are correct. The bottom line is that Jonathan has two Private Variants. These are:

  • 11718822 and
  • 11720223

These had to have formed in Jonathan’s line in either Edward, Walter, or Jonathan:

In a sense, these Private Variants are not important from a genealogical point of view. Jonathan already knew he was a second cousin to Rodney. However, if anyone else ever tests positive for these Variants in the future, it will show that they are from this same Edward Fitzgerald Frazer Line.

Rodney’s Seven Private Variants

There is another use of Private Variants. These can be used to date the common ancestor between two people. A number between 83 and 144 years is generally used. However, that time-frame does not work well in the case of Rodney and Jonathan. Their ancestor is believed to be Thomas Henry Frazer born 1836. Even if we take that date from 2021, that is 185 years ago. That means that, at most, there should have been an average of three private variants between Jonathan and Rodney where there are 4 (and actually 4.5). That means that these Variants were forming about every 40 years or about twice as fast as would be expected, on average.

Here are Jonathan and Rodney’s average of 4 Private Variants:

Rodney’s Private Variant at Position # 11830989

I don’t want to go through each of Rodney’s Private Variants, but I will at least look at one:

I don’t think that FTDNA shows test results in the browser for Private Variants if you are not positive for them. Here is Jonathan’s downloaded results for this position:

It looks like Jonathan’s results were less than conclusive.

Next, I’ll look at Paul’s results:

Paul was not tested at that position.

Let’s see what Rick has. I need to download his ‘csv’ file. I would expect that Rick would have good results as he has tested for the BigY700:

Here is a surprise. This shows that Rick has this Private Variant. That means that it can no longer be Private. That is good because it means that Rodney has one less Private Variant. I don’t know why FTDNA didn’t pick this up:

That means that this should be a new SNP included in the umbrella SNP group of Frazer. At YBrowse Position # 11830989 is FT420438:

The good news is that this will take away one of Rick’s Private Variants as he has too many already.

Rodney’s Private Variant at Position # 5987829

I did a comparison of Rodney’s and Rick’s Private Variants and found one more match:

This brings up another reason that Private Variants are important. If they match with someone else’s Private Variant, they form a new SNP. Usually FTDNA will catch that. In this case, they are still in the middle of some of their reviews and have ordered backbone tests for Rodney and Jonathan. It is possible that FTDNA is not sure where to put these new SNPs. This seems to indicate that they are Frazer SNPs, but perhaps they go back even further?

Here is what YBrowse shows:

These two SNPs are interesting as YBrowse shows that they are from an unknown Haplogroup. That seems to support my theory that FTDNA doesn’t know where these SNPs belong. Here are Rodney’s test results for the position:

Here are Rick’s results:

If Rodney and Rick are positive at this Position, then Paul and Jonathan should also be positive.

Paul’s results above were inconclusive.

How about Jonathan’s?

Jonathan’s test results were also inconclusive.

FT420438 and FT420010 Frazer SNPs?

If it was up to me, I would add these two SNPs to this area:

That means that there would be 8 SNPs in this area instead of the current six. So far, everyone how has tested for these SNPs have been Frazers. However, the six or eight SNPs represent four or five hundred years of history. It would be great to fill in some of the blanks for this time period. It may be that FTDNA hasn’t finished their review or are awaiting the results of the two backbone tests they are doing.

Changes to Frazer Testers’ Private Variants

The other change that should be happening is that Rick and Paul’s Average Private variants under R-Y85652 should be going up. They show 3 currently. Rick has 9 but two of these are shared with Rodney. Rick should have 7 Private Variants and Paul has one Private Variant. That should result in an average of four Private Variants under the Archibald Frazer LIne of R-Y85652.

Rodney currently has 7 Private Variants, but two of those are shared with Rick. That should results in 5 Private Variants for Rodney. Jonathan has two Private Variants. If FTDNA rounds down, that will result in an average of 3 Private Variants for the James Line Branch under R-Y151390.

Further, I note this under FTDNA:

This says it could be that the two matches I found between Rodney and Rick could be there because they haven’t properly been properly validated yet. Hence the backbone test which is in process.

Summary and Conclusions

  • I started out trying to figure out if Rodney and Rick’s BigY reviews were done or not.
  • I thought that perhaps Rodney’s review was done because the Block tree average number of Private Variants matched with his and Jonathan’s Private Variants.
  • Then, when I started comparing Rodney and Rick’s Private Variants, I saw that they had two in common. That means that if Rodney’s review was over, there was still two SNPs to be assigned to the Frazer Block Tree.
  • I guessed that perhaps FTDNA had trouble placing these new SNPs and that is why they ordered the Backbone tests for Rodney and Jonathan
  • I had thought that if your Private Variants matched with what the average Private Variants were on the Block Tree, then that meant that your BigY manual review was over. But then I found something at FTDNA that said that may not be true.
  • I had thought that the Backbone tests ordered for Rodney and Jonathan were to confirm their new Haplogroup of R-Y151390. Now it appears more likely that the Backbone test is for the two matching Private Variants that Rodney and Rick have with each other.
  • It could be a month or more before the dust settles for Rick’s new BigY 700 test and Rodney’s upgrade from BigY 500 to BigY 700. By then, we will probably have the results from the new Frazier/Frasher BigY 700 test which has been delayed.

Update on Frazer YDNA: Rodney’s Upgrade from BigY 500 to BigY 700

I have been writing quite a bit lately on Frazer YDNA. There are few reasons for this. One is that the information has been changing gradually as the two new Frazer Haplogroups are rolling out. The second is because the discovery of these two new Haplogroups is important. It is important not only for the four testers, but also for all the hundreds of the Frazer “Clan” who descend from Archibald Frazer who lived in Roscommon, Ireland in the early 1700’s. These new YDNA developments are equivalent to a major genealogical find. However, YDNA results are more written in stone than genealogifcal finds. Once you have your YDNA results, it is very clear that if you have these SNPs you are from these Frazer Lines and if you don’t, you are not from thse Lines.

Dating the New Frazer Haplogroups

There are a few ways to date a YDNA tree. I’ll use the dates that we think are right with Frazer genealogy where we know that.

The important dates are for the common ancestors of the four YDNA testers shown at the bottom of the tree above. Those dates are 1690, 1804 and 1836. Here I’ve put the dates on Rick’s Block Tree:

[Edit: The 1792 in the image above should be 1836.]

The tree is reversed from the genealogical tree. Rick is on the right Branch with Paul. From what we can tell, YP6489 was formed about 1200 AD. YP6489 is representative of the three SNPs in the Block. We don’t know which SNP was formed first, but we may assume that these three SNPs formed equally between the time period of 1200 and 1545. Next is the new subgroup of FT421618. This Haplogroup seems to be explained by the Frazier/Frasher test results that we are waiting for. There were quality issues, so his sample is being retested. Perhaps FTDNA had enough information to say he would be FT421618. Again, we don’t know when these three SNPs formed – just that they formed between around 1545 and 1690.

1690 is an important date as that is the date we are using for the birth of our common Roscommon Ireland Frazer ancestor – Archibald Frazer. On the James Frazer Branch, SNPs Y151390 and FT421607 had to form between Archibald Frazer born 1690 and Rodney and Jonathan’s common ancestor. That common ancestor was Thomas Henry Frazer born about 1792. On the Archibald Line, three SNPs in the Haplogroup Y85652 formed between 1690 and 1804. The bottom of the chart brings us down to the birth dates of the three testers. The private variants were formed in the James line between 1792 and the birth dates of the Rodney and Jonathan. The private variants in the Archibald line were formed between 1804 and the birth dates of Paul and Rick.

R-Y85652 – The Archibald Line

Y85652 consists of a group of three SNPs. These were previously Private Variants for Paul. In order for Paul’s three Private Variants to become SNPs, Rick had to test positive for these Private Variants and Rodney and Jonathan had to be negative for these.

Y85652

Here are Rick’s results for Y85652:

The pink column is at the position on the Y Chromosome of 8162400 which is now Y85652. The T in that column shows that Rick had the mutation from A to T.

Paul had similar results:

Every horizontal line is called a read. Paul’s results go off the screen. That means that he had more reads than Rick which just means he had a higher confirmation than Rick of Y85652.

Next, I’ll look at Jonathan’s results. We expect the results to be negative:

Right at the position of 8162400, Jonathan shows no mutations from T to C. That means that he doesn’t have SNP Y85652. To satify curiosity, here are Rodney’s results:

Rodney had fewer reads, but is clearly negative for Y85652 at the position in the middle of the image above under the down arrow. If I went through this exercise for Y102792 and Y112046, I should get the same results.

Y151390 – The James Line

Here are Rodney’s test results:

He is clearly positive. Jonathan has a question mark for this position:

Jonathan didn’t have enough reads at this location. However, for all of his 7 reads, he shos the mutation from C to T at this position.

Paul aslo had a question mark at this position. Here are Paul’s results:

This was a bit of surprise. Let’s look at Rick’s results. He will have to be negative for this position for the James Line to get the Haplogroup of Y151390:

Fortunately, Rick has good results showing that he is negative for Y151390. Because Paul is in a group with Rick, Paul is presumed negative for Y151390 also.

FT421607 on the James Frazer Line

I’m curious about this SNP also. Rodney has good results:

Jonathan has only one read at this position:

But it is positive. That makes it important for Paul and Rodney to be negative for FT421607. Here are Paul’s results:

Paul’s read didn’t make it over to position #7788709.

Rick has much better results:

That means that Paul is again presumed negative based on Rick’s negative results and we end up with the James Line SNP of FT421607. FT421607 is based on only one good positive test and one good negative test. But because the negative test was already in a sold group consisting of Paul and Rick, that meant that Rodney and Jonathan had to be in the other group. The bottom line is that the James Line and Archibald Line Haplogroup results are dependent on each other.

Here is FT421607 which now appears at YBrowse listed as a new 2021 SNP:

This gives the location of FT421607 on the Y Chromosome and what the mutation was (G to T). It also gives the location of the SNP under the Frazer Haplogroup of YP6489 and the James Line Haplogroup of Y151390.

Private Variants

If it weren’t for the Private Variants, I would think that FTDNA’s manual review has been completed. However, the numer of Private Variants of the testers don’t match up with the Private Variants shown on the Block Tree. For example, Rick shows that he has nine Private Variants:

Paul shows one Private Variant:

I’m not sure why Rick has so many Private Variants. It may be because his BigY 700 covered more than the older BigY 500 tests. Their average numer of SNPs should be five. The average number of Private Variants shows three:

Rodney and Jonathan’s Private Variants (James Frazer Line)

The Block Tree above shows that Jonthan and Rodney have an average of 4 Private Variants. Jonathan shows that he has two Private Variants:

Rodney has 7 Private Variants:

This makes me wonder if Rodney actually had the BigY 700. A review of Rodney’s FTNDA history is interesting:

Rodney did have the BigY 700 done. This makes sense. However, it says that his BigY-700 was ordered 8/26/2020 and completed just 1/14/2021. I talked to Rodney’s niece who said that she did order the BigY 700. Mystery solved.

Y-HAP-Backbone Tests for Rodney and Jonathan

In addition, it looks like two Y-HAP-Backbone tests were ordered and one was completed. The one ordered on 1/11/2021 has not yet completed. Here is Rodney’s Order Status:

Here is Jonathan’s order history:

I’m not sure how to interpret what FTDNA is saying. It appears that more tests were ordered for Rodney than for Jonathan. Here is some information from FTDNA. I don’t know if itis up to date:

I checked Paul and Rick’s order history and no backbone SNP Tests were ordered there. That is interesting because it tells me a few things:

  • FTDNA is sure of Paul and Rick’s new Haplogroup of Y85652
  • FTDNA came up with Rodney and Jonathan’s Haplogroup based on one positive test from the James Line and one negative test from the Archibald Line
  • FTDNA would like more positive testing for Rodney and Jonathan to confirm their Haplogroup of Y151390, so they ordered Y-HAP-Backbone tests.

This should mean that we will have a pretty good Haplogroup for Rodney and Jonathan, that will be proven once the backbone tests have been completed.

This shows Jonathan’s pending results:

Here are Rodney’s pending results:

This seems to indicate that Rodney’s BigY700 is not yet complete. However, these are Rodney’s matches:

This seems to indicate that as Rodney matches Rick (who has taken the BigY 700) in the 800,000 level (under Shared Variants above) and Jonathan (who has taken the BigY 500) at the 600,000 level that perhaps Rodney’s BigY 700 is completed except for the Backbone test.

Another Thought on the Backbone Test and the Frazier/Frasher Results

It is possible that the need for these backbone tests came about due to the pending results of the Frazier/Frasher BigY 700 tests. At least, the tests were ordered around the time that a new Haplogroup appeared on the Frazer Tree:

This new Haplogroup which seems to be a result of the pending
Frazier/Frasher BigY results. This new Haplogroup appeared around the time of the backbone tests were ordered for Rodney and Jonathan. So these backbone tests may have been ordered to back up the new Frazier/Frasher results, to verify the James Line Haplogroup of Y151390, or both.

Summary and Conclusions

  • While looking at Rick’s new test results and the resulting new Haplogroups for the James and Archibald Frazer Lines, I was surprised to see that backbone tests had been ordered for Jonathan and Rodney from the James Line
  • Also I was surprised that Rodney had a BigY test that was only recently completed (or is being completed).
  • Now that I can see the SNP test results and the SNP results at YBrowse, it makes it easier to see how FTDNA has made/is making their decisions.
  • I can probably see the results of the testing because Rodney’s BigY 700 seems to be completed. That testing in conjunction with Rick’s recent BigY 700 testing is likely the reason why there is a new James Frazer Line Haplogroup.
  • It appears that the results of Jonathan’s and Rodney’s backbone tests should come out around the time that the Frasher/Frazier BigY 700 test results are due.
  • The result of all this testing is that we will have a really good Frazer YDNA Tree solidly documented by BigY testing.

 

 

 

 

 

 

A New Proposed James Frazer Line YDNA Haplogroup

In my previous Blog, I mentioned how Rick’s new BigY 700 test results created a sort of tipping point. His test in conjunction with the previous three BigY tests resulted in three changes in the Frazer YDNA Tree. One of those changes was the likely creation of a new James Line YDNA Haplogroup of R-Y151390. I say likely, because FTDNA’s manual review has not yet been completed.

However, when I look at the Frazer Block Tree today, I see that there is already another change from yesterday:

For some reason, FTDNA has split the old Frazer umbrella group of R-YP6489 into two. YP6489 is now the older group with a younger group of R-FT421618 under it. This is very unusual, because without an additional tester, there should be no way to know that FT421618 is younger than Y6489.

Some Speculation on R-FT421618

This is another mystery, as I don’t know how FTDNA could know that there were two groups unless someone else has tested. The only thing I can think of is that they may have access to other information such as the initial Frazier/Frasher BigY results that we have been waiting for. This test had quality issues and the results are now due around the end of February.

Let’s assume that FTDNA is looking at initial Frasher/Frazier results. Previous dating by the FTDNA YDNA administrator for our Frazer group had set YP6489 at around 1200 AD. The two Frazer Lines (Archibald and James) had to have started around 1720. This is about the date we are guessing Archibald and James were born, though we believe that Archibald was older. From looking at the two groups of Y6489 and FT421618, they both have three SNPs in each. That means that FT421618 could have formed about halfway between between Y6489 and the James Frazer and Archibald Frazer Haplogroups. 1200 to 1720 is 520 years. That means hat we should be able to date FT421618 at the halfway point between 1200 and 1720 or at 1460.

R-Y151390: The New James Frazer Line YDNA Haplogroup

This is what I set out to look at but got side-tracked. In my previous Blog, I was struggling to see how FTDNA had arrived at the conclusion that this would be the new Haplogroup for the James Frazer Line based on my inability to find test results for certain SNPs or Private Variants. I brought my questions to the FTDNA – BigY Facebook Group and got some great results. This was the bottom line answer after much discussion from David Vance who is very accomplished and respected in the field of YDNA:

ok so YFull thinks Paul is positive for Y151390; FTDNA thinks not. That’s something you’d probably have to delve into the BAM file to figure out, but the only difference would be that Y151390 might belong above as an equivalent in the R-YP6489 block rather than only above Rodney and Jonathan. Based on their negative results for the R-Y85652 block and equivalents, the basic branching structure either way is still as shown on the Block Tree.

Here is some more background. Here is Jonathan’s results show in the non-block tree diagram:

FT421618, which I discussed above, is in yellow because Jonathan was Presumed Positive for this SNP. That means that his test results were not as thorough as needed for Jonathan to be positive for this SNP. However, based on others being positive for this SNP, he had to be positive for it also. Although I can’t find Jonathan’s detailed test results for Y151390 (the new James Frazer Line Haplogroup), the green dot means that Jonathan tested positive for this SNP. FT421607 is much more confusing as the grey dot means Presumed Negative. If Jonathan is showing as having this SNP, why wouldn’t he be Presumed Positive for it? Furthermore Jonathan is showing Presumed Negative for Y85652, Y102972 and Y112046. I know that is not the case, as I have looked at his results for these three SNPs and he shows as Tested Negative. Here is Jonathan’s results for Y85652:

I had to shrink my screen to show all of Jonathan’s reads that show he tested negative for Y85652. If he had tested positive, there would be a letter T in the column under the tiny arrow above. That tells me that, despite what the grey dots say, that Jonathan tested negative for this SNP and the other two under Y85652. This negative testing by Jonathan and Rodney made it very clear that Paul and Rick were in Y85652 and that they were not.

Is Paul Presumed Negative for Y151390?

That appears to be the case, but I showed above that these dots are not always right:

Here Paul shows as Presumed Negative for Y151390 and FT421607. I looked up FTDNA’s definition of Presumed Negative:

Presumed Negative – You are presumed negative for the primary SNP or variant. A person is presumed negative for sibling branches of SNPs for which you have tested positive.

It seems like the definition could have been stated more clearly. David Vance wrote to me:

so presumed negative, but not confirmed negative.
Are Rodney and Jonathan confirmed negative for R-Y5652 and the other two equivalent SNPs in that block? I’m starting to think those are the driving force for this split, and Paul and Rick are presumed negative for Y151390 because they’re positive for those three SNPs and Rodney and Jonathan are negative so that drives the branching decision rather than Y151390.
It seems that what FTDNA is saying is that Rick and Paul are clearly in Y85682 and that Rodney and Jonathan are clearly out of that group. That means that if Jonathan and Rodney are in FT151390, then Paul and Rodney have to be out of that group even though Paul had some indications on his test that he might be positive for FT151390. At least I think that is what happened.
Let’s see what Rick shows for his newer BigY 700:
The results are similar to Paul’s except that Rich test positive for the new Frazer SNP FT421618.

Another help at Facebook was that someone found Y151690 at YBrowse when I could not. I was doing the search wrong. Here it is:

This seemed like an older SNP based on the Y prefix and it is dated at 2018. The Y prefix on the SNP means YFull.

Summary and Conclusions

  • By reaching out to the BigY community on Facebook, I was able to find more resources to answer my Frazer YDNA questions.
  • At the very least, I am documenting the changes as they are happening with the Frazer YDNA tree
  • I tried to explain how the James Frazer Line was formed. However, without seeing the testing data for some of the SNPs, it is difficult to accurately describe the process
  • There was an unusual split in the umbrella Frazer Haplogroup of Y6489. This seems to be only explained by FTDNA using the partial results of the Frazier/Frasher results for which we are waiting.

 

Two New Frazer YDNA Haplogroups: R-Y151390 and R-Y85652

Family Tree DNA has issued the Frazer family two new Haplogroups as seen in Rick’s block tree below:

R-Y151390 and R-Y85652

I was only expecting one new Haplogroup for the Archibald Frazer Branch (shown as “Your branch” above. Previously, I was disapointed that Rodney’s previous test did not form a new branch for the James Frazer Line. Apparently Rick’s BigY test also gave FTDNA the confidence to create a James Frazer Branch shown in the bottom left portion of the Block Tree above.

The James Line and the Archibald Lines were previoiusly under R-YP6489 which is now an umbrella group over the two new Frazer subgroups.

R-Y85652

This Archibald Frazer Branch came out as predicted by the R1a – L664 FTDNA Project Administrator Martin. The Archibald Frazer Branch is the one below near the date 1804:

I added the dates in black above from my previous Blog. Apparently the manual review has not completed (or started?) yet. My understanding is that there is a mechanical/automated review first before the manual review. Note that the Private Variants do not line up. Martin has Rick with 10 Private SNPs. The Block tree shows an average number of three private variants between Paul and Rick. Rick’s Private Variant List at FTDNA has gone down to nine pressently:

It’s a puzzle trying to find the difference between Martin’s list and FTDNA’s. Martin has the additional Private Variant numer of 11683336. If Rick had 13 private variants and three went to the new Archibald Frazer Line, then he should have 10 left.

11683336

Here is 11683336 at YBrowse:

This must be a new Private Variant as it has no name yeat at YBrowse. This Private Variant may have gone up to the umbrella group of YP6489. Here is Rick’s previous Block Tree:

The old YP6489 had five SNPs. The new group has six:

FT421618 is the new SNP in that group. That means that Rick’s BigY results ended up changing the umbrella Frazer group of YP6489 as well as creating two new groups (for Archibald and James Frazer) under that group.

More on FT421618

The FT series is FTDNA’s newer SNPs. As seen by the fact that YBrowse is not yet aware of this SNP, this must be a brand new SNP. In order for this position to be a true Private Variant for Rick, it has to show as negative in Rodney, Jonathan and Paul. FTDNA probably looked at their results and saw that Rodney, Jonathan  and Paul tested for this posisiton and it wasn’t clear that they didn’t test positive for this position.

Here is Rick’s results:

What this shows is that Rick is very positive for this SNP. 10 good reads is usually OK. He has many more than 10 good reads.

Here are Paul’s results:

There is a little arrow where the results should be, but there is nothing there. That is probably what is called a no-call.

Here are Jonathan’s results:

Jonathan has four good reads. Remember that for Rick to have this position as a Private Variant, the others have to be negative for this position. Jonathan didn’t have enough reads to give him this SNP on his own, but because Rick tested really well for it, then Rick and Jonathan must both have this SNP. That is how it got added to the Frazer Umbrella Haplogroup.

Finally, we look at Rodney:

Rodney has only one good read for this SNP, so Rick confirms this single read.

Where Does R-Y151390 Come From?

This is the new James Frazer Line Haplogroup that FTDNA is showing on their Block Tree, I am having trouble finding this SNP perhaps because it has not been on a tree before. When I search on YBrowse:

When I search for Y151390 at FTDN, BY151390 shows up which is a different SNP. Without knowing what position Y151390 is, I cannot do further analysis on it. I have one more place to look. Here is Jonathan’s non-Block Tree at FTDNA:

When I hover over the SNPs under R-Y151390:

The first is Positive and the second is presumed negative. However, I still don’t know what position that Y151390 is at. That means that I can’t figure out how FTDNA arrived at their decision.

A Google search for this SNP revealed that I had mentioned Y151390 in at least one of my old Blogs:

The answer appears to be at YFull. After clicking around a while at YFull, this appears to be the position of Y151390:

For some reason, this named SNP was perhaps never uploaded to YBrowse:

So it appears that FTDNA got the name of its SNP for the James Frazer Branch from YFull. I believe that the Y prefix is from YFull. Further it is unclear how my cousin Paul was listed under Y151390 at YFull and is now not in that group at FTDNA.

FT421607

This is the other SNP in the new YDNA Tree for the James Frazer Line. I can’t find it right now listed as being tested for either Jonathan or Rick. That means that it must be still listed under the position number. As I don’t know what the position number was, I can’t find the test results for the position. An FT prefix refers to a new SNP by FTDNA. Here are the search results for Jonathan:

 

Summary and Conclusions

  • Recently FTDNA came out with three important developments for our Frazer group. One was expected and two were not.
  • What was expected was that there would be a new Haplogroup for the Archibald Frazer Line based on three different SNPs
  • The first unexpected thing was that there would be a new SNP added to the now umbrella of R-YP6489. This group is now over the two Frazer Lines of Archibald and James. This new SNP could theoretically make the age of YP6489 older by about 100 years.
  • The second unexpected thing was that a new Haplogroup formed for the James Line. I had expected this to happen when Rodney did a BigY test but it didn’t happen. This new Haplogroup is R-Y151390. I was unable to see how FTDNA arrived at this conclusion. I think that it will be clear as the manual review progresses.
  • Hopefully, subsequent review will confirm this new James Line Haplogroup
  • Rick’s new test results in conjunction with the previous three Frazer BigY tests has resulted in a quantum leap in the Frazer YDNA Tree. These results are helpful in a quite recent timeframe. They cover the time from ancient history up to the 1800’s when the genealogical records became more reliable.

 

My Look at an R1a Administor’s Review on Frazer BigY Results

Sorry for the awkward title on the Blog. Things are moving quite quickly after a 4 month wait for Frazer BigY results. I wrote my first review the day the initial results came out on December 29th. Martin’s initial review came out on January 2, 2021. Happy New Year.R1

Martin’s New S2880 Tree

Martin, who live in the Netherlands, is the L664 Project Administrator for FTDNA’s R1a YDNA Project. Here is L664 on the left of the image below:

 

This is from a 2015 R1a Tree.  At that time, L664 was dated around 3,000 BC.  L664 is in blue on the bottom left of the image above. Martin has updated what he calls Section 2b or S2880 as of January 2, 2021. Here is where that is on the bottom left side of the 2015 tree:

 

Here is where S2880 is on Martin’s new tree:

The date for S2880 is about 1800 BC:

Here are the four Frazer BigY testers on the tree:

Here is a more close-up version:

Above YP6489 is the date 1200 AD. Below that box is 1600 AD. That is an important jump as it brings us into more of a genealogical time-frame. It is also important to understand the what these two dates mean. It says that the SNP YP6489 (which is actually a group of SNPs) formed about 1200 AD. The shared group of Frazers go back to 1600 AD (by DNA). This is probably 1690 or so by our genealogy, so a pretty good agreement. However, others outside our group who descend from our 1690 Roscommon Frazer and who share YP6489 could have have an earlier shared date. We are currently awaiting BigY results for a Frazier/Frasher who may fit into this category. His results should show where he fits in.

The last four vertical lines are the Frazers in our group. They are Rodney and Jonathan in the James Frazer Branch. The last two are Paul and Rick in the Archibald Frazer Line. They are the two with all the projected private SNPs.

Martin’s Review

Rick and Paul’s Shared Private SNPs

This is the most important part, because these shared private SNPs willl become a new Frazer YDNA branch. Martin writes:

You have 13 private SNP’s and I found that you share 3 of your private SNP’s with the private SNP’s of Frazer #[number deleted for privacy]. This means you both create a new subclade downstream Subclade YP6489, which I have called Y85652.  

In my first review, I only found two private SNPs that Paul and Rick shared. Martin was able to find three:

These three are shown in the block where the bolded Y85652 is. Here were the two variants that I found:

Positions 8162400 and 21457649

These were the two that I found. Martin has these as SNPs Y85652 and Y112046. In my previous Blog, I had identified that Rick and Paul had matching SNPs Y85652 and Y112046. So that looks like we agree.

Position 16784516 aka Y102972

This is the posiition that Martin found and that I didn’t see in my initial review. Here is my spreadsheet:

I Show that Rick and Rodney have position 16784516 as a non-matching variant but that Rick and Jonathan do not. I may have deleted this entry by mistake. Actually I see this variant above on Jonathan’s list, so I just did not match these correctly:

You have to think backwards with these lists. So if Rick has non-matching variants with both Rodney and Jonathan who are in the James Line. That means that he must have matching variants at those locations with Paul in the Archibald Frazer Line.

Here is Richard Frazer born 1830:

Here is George Frazer born about 1838:

Assuming that this is right (and it appears to be) that means that there was on average one SNP mutation every generation for Archibald Frazer born 1720, Philip Frazer born 1758 and James Frazer born 1804. Also this assumes that we have the genealogy right. We don’t know which ancestor had which mutation. However, it would be possible to find that out if we had descendants from each of these lines test. That is also assuming that there is an unbroken male descendant in each of these lines.

Here is one of Martin’s comments:

Normally we find in the BigY-700 on average a number of 100 years per SNP (or one SNP mutation in every 4-5 generations). So when we assume the Frazer family splits around 1600 AD in 4 branches, then you expect on average for each about 4 private SNP’s. You and #444958 have now about 12-13 SNP’s downstream subclade YP6489 and the other two Frazer’s only 1-3 SNP’s. But sometimes we see large differences in the SNP mutation rate in individual cases.

My opinion is that a male generation was longer between 31 and 38 years so on average 34.5 years. Of course this varies at different times and in different places. Still, with my version, there would be a new SNP every three generations as opposed to the one generation we are seeing here.

The bottom line is that I see my mistake and Martin and I are in agreement on the number of matching private variants that Rick and Paul have in the Archibald Frazer Line.

A Side Thought on Male Frazers

A little ways above, I mentioned the need for an unbroken male line for Frazer YDNA testing. Here is the line of Archibald Frazer born about 1778 and Ann Stinson. This Archibald was the son of Archibald born about 1720 and Mary Lilley:

Out of about 27 or so who tested for autosomal DNA under the Archibald Line born about 1720, I see only about two who would be eligible for YDNA testing. If these two tested, it would confirm this line by YDNA. Their common ancestor would be Archibald born about 1778.

On the James Frazer Line the first two circled on the bottom have taken the BigY test.

There are two others on the left hand side who haven’t taken the YDNA test.

Rick and Paul and Private Variants

To me the private variants are not as important as the shared SNPs. These are variants that should describe a line after the shared ancestor of the two testers.

So Rick’s Private Variants would describe his line starting with Richard Patterson Frazer. Paul’s private variants describe his lineage starting with George Frazer born about 1838. George is my second great-grandfather.

Here is what Martin has to say about Rick’s Private Variants:

You and #444958 have now about 12-13 SNP’s downstream subclade YP6489 and the other two Frazer’s only 1-3 SNP’s. But sometimes we see large differences in the SNP mutation rate in individual cases. I have also checked your 10 private SNP’s in the Yfull results of #444958, but for these 10 private SNP’s of yours, 8 gave a negative result and 2 gave a “no-call” because these two were not tested in his BigY-500 test.  

I am a bit confused by Martin’s use of what he calls downstream SNPs or private SNPs.

These are the numbers in the last yellow boxes for Rodney, Jonathan, Paul and Rick. Paul currently has 4 private SNPs. Because of his three matches with Rick, that will go down to one. However, Martin adds in private eight private SNPs identified by YFull.

Here are some of Paul’s ‘Novel’ Variants at YFull:

I highlighted the first Private SNP that Martin has identified on Paul’s yellow box above. Paul has two more Novel SNPs under his Best quality tab. I see that some on the YFull list say private and some say up to R-YP6489. According to YFull:

The words up to [name of subclade]  after a Novel SNP means that the eventual location of the SNP may be as far in the past as the named subclade or closer to the present than the current Terminal Hg.

That means that they aren’t sure if those SNPs belong in with YP6489 or after it. Just another way to slice and dice things. For the SNPs that say ‘private’, they must be after YP6489 for sure.

Rick then shows 10 private variants. These also don’t make sense in a way. If these are valid, then these would all be in five generations of his Richard Patterson Frazer line. That would mean that there were two mutations per generation. I’ll just depend on Martin’s analysis for now and wait to see if FTDNA’s manual review reduces these SNPs at all.

Dating the YDNA Tree

We can use what we know about Frazer genealogy to get better dates on this tree. The date of ca 1600 is probably a bit early. We think that the father (probably Archibald) of the Archibald and James Lines was born around 1690. Our best bet at dating is from the Elphin Census:

For sake of argument, we’ll say that Archibald Sr was born in 1690 and died at age 50 or so around 1740.  Perhaps Mary was younger and born in 1695. Let’s say she had Archibald in 1718 and James in 1720. We’ll say they both married at age 25. We know that James married in 1745. He had two children by 1749. We’ll say they were only age 1 and 3 at the time. Archibald could have married in 1743 and had children aged 1 3 and 5 in 1749. Just a guess.

All this to say that Archibald Frazer Senior could not have been born 1600. I would stick to 1690 and put that date in where the 1600 is. Then we know that the common ancestor for Rick and Paul is James Frazer who was born about 1804:

Summary and Conclusions

  • I appreciate Martin’s quick and thorough review of Rick’s test results and his incorporation of those results into Setion 2b of his L664 Tree
  • The new name Frazer Branch in the Archibald Frazer line will include three SNPs
  • I was able to identify four people who would qualify for YDNA testing from my charts of Frazers who have already taken autosomal tests. These people are rare because they have to have unbroken male line Frazer ancestry
  • I looked at Rick and Paul’s private variants briefly and will wait for the FTDNA manual review on these.
  • I looked at fine-tuning the dating of the Frazer YDNA BigY Tree based on what we know about our Frazer genealogy.
  • Next on the horizon is the Frazier/Frasher test we are waiting for and Rick’s FTDNA manual review.

Addendum on 16784516 and New Information from David Vance

This is the extra SNP that I missed. Here it is at YBrowse:

This would have been discovered at the time of my cousin Paul’s initial BigY test. David Vance recently posted a chart with the regions of the Y Chromosome:

DaveidVance has this as a good region even though it shows in a darker region on the YBrowse browser.

So SNP Y102972 is a SNP that Rick and Paul share. We’ll have to wait and see which SNP FTDNA calls this portion of the Archibald Frazer Branch.

8162400

David Vance lists this in not the best region:

Here is more from David:

21457649

David doesn’t list this as the greatest either. Based on David’s chart Y102972 would be the best SNP name for this section of the Archibald Frazer Line. Whatever the name, I think that it is interesting that the BigY test has defined a specific area of the Archibald Frazer Branch of the Frazers from Roscommon, Ireland.

 

A New BigY Test for the Archibald Frazer Line

Back in August of 2020 a BigY test was ordered for Rick. I was just notified that his results have started to come in. Rick’s STR results came in last August and I wrote about them here. However, now we have the more important SNP results. SNPs are the part of a man’s YDNA that mutate in a way that give a precise indication of his line back to the earliest men on the planet.

Frazer YDNA

This is the YDNA tree for the Frazers who were from Roscommon, Ireland. They have lived there since the early 1700’s. It is believed that there were two brothers at that time: Archibald and James:

The older brother was Archibald. I am not a Frazer by YDNA as my grandmother was a Frazer, but I had my second cousin once removed Paul take a test. Paul, Rick and I and many others are on the Archibald Line. Rodney and Jonathan and many others are on the James Line. Paul, Rodney and Jonathan already have BigY tests, but they are the older BigY 500 tests. Rick has the newer more accurate and thorough BigY 700 test. Rick was needed to better define the Archibald Line specifically.

Rick’s New Results

Family Tree DNA (FTDNA) will likely perform a manual analysis of Rick’s results which will result in a further wait, but I’ll look at what the results show so far. Based on the tree above, Rick and Paul’s matching SNPs should show what SNPs their common ancestor James Frazer (born about 1804) had.

Rick’s Block Tree

Here is Rick’s Block Tree:

 

Right now, Rick is shown with Frazers from the Archibald Line and James Line. They share the SNP name of R-YP6849. I am hoping that, after FTDNA’s manual review, that Paul and Rick will form a new YDNA line with a new SNP name.

Rick’s BigY Matches

The next step is to look at Rick’s matches. He shows matches to Rodney, Jonathan, Paul and the Grant above. These results can be misleading due to the criteria that FTDNA uses for matching. For example, the Frazers, Stuarts, and Grant testers all share the common SNP of R-YP6488. Rick also matches Hayes with whom he shares the even older SNP of R-YP6480. However, Rick shows as a match to Grant and Hayes, but not to the two Stuart testers. This may be because the Stuarts also took the more expansive BigY 700 and thus have more Variants that don’t match.

Here are some more BigY match details:

 

FTDNA lists non-matching variants between Rick, Rodney and Jonathan. That may seem confusing but it is easier than listing the 600,000 plus matching Variants that go back to genetic Adam. A non-matching variant may be several things which is also confusing. It may be a variant that Rodney has and Rick doesn’t have. It may be a variant that Rick has and Rodney doesn’t have. It may be a variant that Rick’s newer test covered and Rodney’s didn’t. Then there are test results which may be inconclusive that complicate things.

What I should be looking for is a SNP (or Variant) that Rick and Paul share and that Rodney and Jonathan don’t have. That would create the new Archibald Frazer Line that I am looking for. The goal is to get the newest or most recent SNP possible for the Frazer family.

Variant by Variant Analysis

Here are Rick’s non-matches to Rodney, Jonathan and Paul by Variant in a spreadsheet:

This shows why Paul shows as a match that is further away to Rick than he really is. Paul and Rick have the most non-matching Variants. Another point to the exercise, is that Rick will have have Variants that he validly does not share with Rodney, Jonathan and Paul. Those will be the Variants that Rick has that define his own line since James Frazer born about 1804.

Next, I separate out the Variants and compare them.

 

Candidates for a New Archibald Frazer Line

I would like to look at the two variants I have highlighted below:

It stands to reason that for a new branch to formm Rick should have non-matching variants with Rodney and Jonathan but not with Paul. The two highlighted Variants could meet that criteria. In order for these two or one of the two to meet that criteria, Rick and Paul would both have to have tested positive for these Variants and Rodney and Jonathan would have had to be tested negative for thes Variants.

Variants 8162400 and 21457649

Rick currently has 13 Private Variants. I think that these should change after FTDNA’s manual review. I’ll show what they look like now:

On Rick’s second page I see 8162400, so that is a start. 21457649 is on Rick’s first page of Private Variants.

Next, I have to log into Paul’s results:

Paul has 8162400 and 21457649 which mean that they are not really Private Variants after all. Or, they will no longer be Private Variants now that Rick’s results are in. That is because we are looking at preliminary results that will change.

To be really sure, I need to show that Rodney and Jonathan both tested for these two variants and the results showed that they did not have them. However, that is a little difficult. It involves looking at all their results. I know I have access to Jonathan’s results, so I’ll give that a shot. I think that I need to download Jonathan’s results as a csv file. That is a very large file.

Here is 8162400. The reference and Genotype are the same, so I think that means that Jonathan is not positive for mutated DNA at that position. Or in FTDNA terminology it is not derived. I assume that the fact that this Novel Variant is on Jonathan’s list means he was tested for this Variant. That means that 8162400 should form a new branch for the Archibald Frazers.

The same is true for 21457649 on Jonathan’s test list:

This makes sense because if Paul had these two Variants on his Private Variant list, it likely meant that Jonathan and Rodney did not test positive for derived Variants at these two positions. I included a known SNP above in Jonathan’s list to show that FTDNA only shows the derived information for those known SNPs. Both of these Variants show beyond line 600,000 on the spreadsheet for Jonathan’s BigY results.

Here is what my cousin Paul’s results look like for the same Novel Variant:

The reference T has changed to C. That is what should define the new Archibald Frazer Branch.

What Will Be the Name of the New Archibald Frazer Line?

Assuming my analysis is right, we can go to YBrowse to find the names for these two positions that Paul and Rick share. YBrowse is a YDNA Chromosome Browser.

This shows the Y Chromosome with over 50 million positions. The lighter regions are the ones best used for genetic genealogy. I put in the Variant that Rick and Paul share that is around 8,000,000 – where the red vertical line is on the depiction of the Y Chromosome. It turns out that 8162400 has two names:

I”m guessing that this name came out when I first did the BigY 500 for Paul in 2017. Note the derived is from T to C. That is what Paul had at this position:

This is also within the R1a Haplogroup which is where the Frazers are.

Here is the other SNP:

This is BY155971. Here the reference T has changed to G. Aslo the haplogroup is unknown. I would rule out this Haplogroup for the Archibald Frazer Line.

I’ll try the other position:

This only has one SNP associated with it but it is in a dark region. I thought that was not as reliable.

That means that the new branch for the Archibald Frazers (or even more specifically the James Frazer Line of 1804) will be Y85652 and Y112046. One of the two will have to be chosen to be representative of the line.

Anything Else?

Rick also has a bunch of Variants that don’t match with Rodney, Jonathan or Paul:

My guess is that these Variants are mostly due to Rick taking the BigY 700 test and testing regions that were not tested. These Variants may come into play when the results of the other Frazier test come in. Those results should be due any day now.

Rick Solves a Problem

The problem is with the existing R-YP6489. Here is what SNP Tracker shows:

This has R-YP6489 forming in the Middle Ages. That is because there are other SNPs within the group of R-YP6489:

Each one of the SNPs takes time to form. Up to 144 years based on the older BigY 500. Somewhat less with the newer BigY 700. Say it took about 100 years for each SNP in the top block to form. That would be 500 years. Then that is to the common ancestor who may have been born around 1690. That seems to compare well with what the SNP Tracker has:

That brings us to about the year 1200. According to thefraser.com:

The earliest Fraser found on record was Gilbert de Fraser, who, in 1109, witnessed a charter to the monastery at Coldstream, along the southern border. In 1160, Sir Simon Fraser, who possessed half of the territory of Keith in East Lothian, made a gift of the church to the monks of Kelso Abbey. Through marriage the Frasers acquired Castle Oliver on the Tweed and became the Sheriffs of Peebles.

That means that there were Frasers around before the year 1200. The question is, were they our Frasers and were our ancestors Frasers at that time? Some of the early Southern Frasers were interesting as I had thought that the earliest Frasers were from around Inverness. At any rate, the point is that even though our Frazer testers’ common ancestor was from around 1690, the origin of R-YP6489 is around the year 1200. If Rick creates a new Archibald Frazer branch, that should bring the Frazer YDNA ahead about 600 years to 1800.

Having said that, SNP Tracker has a new feature for the ‘British Isle’:

This seems to contradict the previous SNP Tracker Map. However, the legend at the top says ‘SNP Formation Eroas for Descendants of YP6489’. So this SNP Tracker feature has a bit of prediction to it. I can’t say I get how this works but it is interesting.

The problem that Rick solves is that his test should form a Haplogroup for the Frazers that is undoubtably Frazer and even specific to the Archibald Branch and James Frazer Line of 1804.

Paul’s Private Variants

Right now Paul has 4 private variants which is a lot considering the time between his birth and 1690 is about 260 years. It would have been more likely that two SNPs would have formed in that time.

Here are Paul’s current Private SNPs:

As mentioned above, Paul’s private Variants should go down to two. That means that in 140 years, Paul’s line had two SNPs which seems a little more reasonable. On the other hand, the James Frazer Line seems to have had fewer SNPs or Variants, so perhaps it all averages out.

Summary and Conclusions

  • Currently the YDNA defining SNP for Roscommon Ireland Frazers is R-YP6489. This haplogroup is assumed to be unique for these Frazers but that is not known for sure due to the age of its formation.
  • Now that Rick has tested, it appears that there will be two new defining SNPs for the Archibald Frazer line and even more specifically the James Frazer Line of 1804. This gives a concrete date that will define these two SNPs.
  • I think that the FTDNA manual review will confirm my findings.
  • The next BigY 700 test for Frazier that is coming in should further define early Frazer genealogy and history.

 

 

 

 

 

 

 

Another Frazer DNA Match at 23andMe

I get emails from 23andMe on a regular basis telling me I have new DNA matches.

I don’t usually recognize who they are. This time I saw a closer than usual match with a name I recognize: Frazer.

My other new matches were predicted 4th cousins and shared less DNA. 23andMe’s Relatives in Common helped me figure out who he is:

Stan is related to Katherine and Brenda. In fact, Brenda is Stan’s sister. I wrote about Brenda here. Here is where Stan fits in:

All these people have had their DNA tested. I am at the bottom left as I descend from the eldest son and Stan is on the right as he descends from the youngest son of George Frazer. According to this chart, I am a 2nd cousin once removed to Stan. Stan is Paul’s first cousin.

Here is a photo of the five brothers:

Hubert is back right. I have more and better photos of Hubert, but I have not scanned them.

Stan’s DNA

I see that I now need Stan’s permission to see his DNA results. Here is how I match Stan’s sister Brenda on Chromosome 6 and 7:

I share three segments with Stan, so my DNA match with Stan could represent Frazer DNA that I have not yet identified. The other yellow matches are other matches with people who descend from George Frazer and Margaret McMaster.

Stan’s YDNA

23andMe gives a haplogroup for Stan’s YDNA. YDNA is interesting as it is only from the male line – in this case Frazer.

My R-L21 Haplogroup represents my Hartley lineage. Stan is R-L664 which represents Frazer YDNA. We know a lot about Frazer YDNA. There have been three Frazer BigY DNA tests done which describe Frazer YDNA in great detail. Every hundred years or so, there is a mutation in the YDNA which is passed down from father to son. Based on these changes, we can create a YDNA tree.

L664 is actually a Germanic Haplogroup going back to about 3,000 BC. That means that before our family was from Scotland, it was from Germany:

However, much has happened in the last 5,000 years. Here are some of the SNPs that have formed in the past 5,000 years:

Here are Paul’s matches:

Paul and his two Frazer YDNA matches are all R-YP6489. We awaiting two BigY tests to refine this tree. One test is from a Frazer with known ancestry. He is more closely related to Paul than to Rodney and Jonathan. The other tester is a Frazier. We don’t know how he is connected, but the connection probably goes back to Scotland before our Frazers moved to Ireland.

Here is the SNP Tracker map:

Here are some more details since L664:

Summary and Conclusions

  • It is somewhat rare to find a 2nd cousin once removed show up as a DNA match
  • Stan’s YDNA type fits in perfectly with other Frazers who were from Ireland
  • If Stan shares his autosomal DNA results, I will be able to tell how we match. This matching DNA is the same DNA that we inherited from Stan’s great grandparents and my 2nd great grandparents George Frazer and Margaret McMster.

 

 

 

 

 

A New Frazer STR Tree with Associated Families

First, I don’t like to make STR trees. They take a while to build and then when the SNP results come out, I can be proven wrong with my previous STR trees. Nonetheless, I’ll forge ahead based on the new 111 STR results from a Frazier relative.

First, Who Are the Associated Families

My understanding is that our Frazer ancestors came to Scotland at some time around the time of Christ. They probably formed a small group of people around the Inverness area. At the time when people were taking on surnames, they probably took on the surnames of the people who were surrounding them at the time. This would likely account for the names of Riley, Hayes, Stuart, Grant and Frazer/Frazier below. There were likely other names adopted. The name of Chisolm comes to mind and perhaps other names that haven’t had YDNA tests.

Building a STR Tree

First I extracted STR results from Frazers and other more distantly related families:

These are 25 STR results for Riley, Hayes, Stuart, Grant and Frazer/Frazier. From this, it appears clearly that a DYS447 of 24 defines Frazer/Frazier and a DYS447 of 25 defines the families above. It appears that the value of 25 is older as there are more of that number and it is applied to three different families.

Without getting into the details, here is a simple tree:

The important thing here is that our most recent Frazier tester falls solidly in with our North Roscommon Frazers.

Further, there is a clear break between Riley and Hayes/Stuart/Grant:

This is just with 25 STR testing.

Frazer and Related Families at 37 STRs

Here is the testing up to 37 STRs:

I took out the markers that were all the same. There was a further distinction I didn’t note above in the first 25 markers that identifies the Archibald line of the North Roscommon Frazers. That is a DYS391 of 11. This is where I was before Richard’s 111 STR results came in. It looked like he was fairly closely related to the Roscommon Ireland Frazers. At the 37 STR level, one of the Stuarts drops out as he only tested to 25 STRs.

111 STRs

At this level, some more families drop out:

There is still one Riley and one Stuart left. In the last column, there was a 16, 17 and 15 for results. In that case, I assumed that the 16 was the ancestral value and that Riley mutated up and Stuart mutated down. I made a similar assumption in the column that had 12, 13 and 14.

It is in the lighter blue 38-111 STRs that Richard shows some of his differences from the North Roscommon Frazers in DYS710, 717 and 712. These are the three markers that appear to put Richard further back as a match with our Roscommon Frazers before they were in Roscommon. Again, the SNP results should give a better idea if this is indeed the case.

This is my best guess for a STR tree:

The big question is whether Richard is under Archibald Frazer or further back as I have it in the above diagram. The main reason for putting Richard’s common ancestor with Archibald Frazer descendants back before the Irish Frazers is that Jonathan’s matches with other known Irish Frazer descendants appears to be closer than with Richard. Here are Jonathan’s STR matches:

Jonathan matches known North Roscommon Frazer descendants at a GD between 1 and 4. He matches Richard at a GD of 7 which is about the same level at which he matches two Stuart descendants.

Summary and Conclusions

  • I built a Frazer STR tree which tries to take into account other related families of Riley, Hayes, Grant and Stuart.
  • Frazier seems solidly in the Frazer camp based on one of the STR markers
  • However, based on genetic distance, it seems like Richard should have a common ancestor with the North Roscommon Frazers at some point before they moved to Ireland.
  • These findings seem consistent with what I looked at in my previoius Blog on Richard’s 111 STR results
  • My guess is that Richard’s BigY SNP results will confirm what appears to be happening with his less reliable STR results