Looking at Stuart’s Big Y-700

I told Stuart (his last name for privacy) that I would look at his Big Y-700. I hesitate to write this Blog, because I am not an expert on Big Y-700 and describing the differences between Stuart’s Big Y-500 and Big Y-700 is likely to be difficult. Stuart is not part of the Frazer YDNA Project that I am part of, but he is in a line that has had a common ancestor with the Frazer’s before the Frazer were Frazer’s. I am also interested in learning about the Big Y-700 as none of the Frazer testers have tested to that level yet. That makes Stuart a pioneer in this area of YDNA testing.

Stuart at YFull

Stuart has uploaded his Big Y-700 and previous Big Y-500 results to YFull. This is helpful in giving probable dates on when the different family lines had their origin. In the big picture, Stuart is R1a.

I see one difference already due to Stuart’s Big Y-700 test. Here are Stuart’s pre-Big Y-700 results:

Before, the number of years to Stuart’s common ancestors were lower. Stuart’s common ancestor with my Frazer relatives used to be 700 years ago. Now it is 800 years ago. Stuart’s common ancestor with his closest group of R-BY26344 used to be 225 years ago. Now it is 425 years ago. That has implications as there is a Stuart and a Grant in that group. The obvious implication is that the mixup in names could have happened up to 200 years further back in time than previously thought.

Stuart’s Big Y at FTDNA

Here is the same tree shown as a block tree at FTDNA but only up to the YP6479 level:

The thing I don’t like about the FTDNA tree is that it filters out too much. For example, I had my Frazer cousin tested shown as YF09981 at YFull above, but he doesn’t show as a match to Stuart at FTDNA. FTDNA shows a stingy 4 Big Y matches for Stuart

By comparison, YFull does a better job at matching SNPs and gives Stuart 71 matches:

More is better. My 2nd cousin with the Irish Flag shows correctly above, ahead of Hayes who has a common ancestor with Stuart of 1150 years ago.

Stuart’s Private Variants at FTDNA

Stuart shows an average of 13 Private Variants with his match Grant above. I would expect that Stuart would have more private variants than Grant as the Big Y-700 is supposed to pick up more than the old Big Y test.

 

This is the first page of Stuart’s Private Variants. He has 19 altogether. These Private Variants are shown above as position numbers. Once they find a match in another Big Y tester, they will be given a name. In order for Stuart and Grant to have an average of 13 Private Variants, Grant must have 7 Private Variants. As there are two in this YP6488 group, it would be helpful to have a third Big Y tester. This additional tester should refine the results in make a new branch for Stuart or Grant.

Tie-Breaking Candidates

Here is a group from the R1a Project:

The two testers with the green R-YP6488 results above are the ones who took the Big Y tests. The other two testers with the red R-M512 results would be the best bets for an additional Big Y test to match with the existing 26 Private Variants to form a new YDNA Branch on the tree of all mankind. I note that the one with the ancestor of Arthur Grant has genealogy that goes back the furthest. However, this is still within the 425 year timeframe for the common ancestor. In other words, there could have been an adoption or other name-changing event before the time of 1683 which separated Stuart from Grant.

Stuart At YFull

Stuart has two kits at YFull.

Big Y-500

I assume the shorter numbered kit is the Big Y-500. Here are Stuart’s 3 Private Variants:

 

This shows on Stuart’s original Big Y-500 test, he had one best quality Novel SNP and two that were acceptable. This SNP has two different position numbers based on the old system (HG19) and the new system (HG38). Due to newer technology and new SNPs being found, there had to be a new numbering system. It appears that this Private Variant already has the name of Y14660. However, different companies may have different names.

Here are the other two  private SNPs or Novel SNPs as YFull calls them:

 

They are of Acceptable quality. The last Novel SNP has a check by it:

It says that someone did a single test for this and it came up negative. Apparently the person who tested for this was someone other than Stuart.

Big Y-700

I’m curious to see any differences here.

Here are some huge differences. Now Stuart is up to 13 Best quality Novel SNPs. I can see the checked SNP from the previous Big Y-500. This has moved up from Acceptable to Best Quality.

Note that 6 Novel SNPs are marked as Homologous. I’m not sure what this means. I think it means that there is a SNP in a totally different haplogroup that looks the same.

One other difference is that YFull used the VCF analysis for Stuart’s Big Y-500. I checked the Big Y-500 test I had done for my Frazer cousin and the BAM file was used for that. My understanding is that the BAM file should be the one to use if possible.

Note that at FTDNA, Stuart had 19 Private Variants. At YFull, Stuart has 13 Novel SNPs of best quality and three of acceptable quality. This seems to be due to differences in how FTDNA and YFull choose which SNPs they should use.

Here is the side by side comparison between YFull and FTDNA:

For the YFull list, I only used the best quality list. That means that there were 7 Best Quality SNPs that YFull found that weren’t used by FTDNA.

Upon further review, I see that FTDNA has a second page of SNP Variants:

 

Now the comparison is closer. FTDNA has 19 Private Variants and YFull shows 15 Novel SNPs that match FTDNA’s. YFull has 13 SNPs of best quality and 3 SNPs of acceptable quality. These private SNPs are measuring Stuart’s non-matchedness. In other words, these are SNPs that are waiting to be matched, so that Stuart can form a new YDNA branch.

When I look at SNPs under different categories at YFull, it adds one SNP that FTDNA had. This brings up the importance of YFull. It is not necessarily showing that FTDNA is wrong but gives a second independent opinion to the analysis of the results.

YFull STR Matching

Here are the results of Stuart’s STR Matching at YFull:

When I try to choose Stuart’s old Big Y test, I get no results, so these are based on the more recent Big Y-700 test. The results are interesting, though generally not as precise as SNP results. Stuart’s closest match is correctly with Grant with a distance 0.03. After that, there are two Frazer’s, a Hayes and another Frazer. The last Frazer with the Irish Flag is my 2nd cousin once removed. Clearly the Hayes connection is much further back than the Frazer connection:

Extended STR Matching at FTDNA

This is available, but not in one place like YFull has it:

Here are Stuart’s 111 STR matches. If they have taken the Big Y test, then those results will show also. YFull showed 5 extended results. These are all the Frazer results. The rest of the group can be found at Stuart’s 67 STR match page:

For whatever reason, my second cousin once removed seems to have more than the average number of mutations, or that STRs that changed were the faster moving STRs to begin with.

Summary and Conclusions

  • Based on YFull, Stuart had a large increase of Private Variants or SNPs between his Big Y-500 and Big Y-700 test. Based on the Big Y-500, Stuart had 3 Private SNPs. This went up to 16 Private SNPs with the Big Y-700 test.
  • Stuart’s original YFull analysis was based on his VCF file and his Big Y-700 YFull analysis is based on his BAM file. My understanding is that the BAM analysis is more detailed.
  • Stuarts dates for a common ancestor to his Grant match and to his Frazer matches increased. This is apparently due to the increase of Stuart’s newly found Private SNPs. The more unmatched SNPs you have, the further you have to a common ancestor.
  • The new date for the common ancestor of 425 years before present between Stuart and Grant has genealogical implications. That goes back to before the year 1600. That means that the mixup between Grant and Stuart could go back that long, or it could be that these surnames were less set in stone at that time.
  • I don’t know how to look at Stuart’s old Big Y-500 results at FTDNA. It doesn’t seem like the old results are kept separately like YFull does.

 

 

Comparing Grant, Stuart and Frazer by YDNA



In my previous Blog, I looked at Frazer STRs and came up with a STR Tree. It is a bit of a mess, but it tries to show where the STR mutations are:

I like one explanation I read about STRs. STRs are short for Short Tandem Repeats. This excerpt is from an FTDNA article called Understanding YDNA Matches:

Our bodies work as copy machines when it comes to the Y-DNA. You can have a copy machine doing 1,000 copies without a problem, and then, the 1,001 copy may have an “o” that looks more like an “e”. And when we use this copy to make additional ones, all the new ones will now have an “e” instead of an “o”. This is a simple way to explain how mutations occur in our Y-DNA when it’s transferred (copied) from father to son. Mutations don’t happen frequently, on the contrary, very seldom, but they can happen randomly in time, which means that I could be one mutation off of my father. That is why all those matches or close matches on 12 markers will in most of the cases go away when they happen between different surnames, and we increased the numbered of markers that are compared: more mutations showing up, which means way back in time when the common ancestor lived.

Ancestral and Derived – What’s the Big Deal?

STRs are either ancestral or derived. That means that they are older or newer. Older or newer is important if you are trying to figure out timelines. It is also important in creating trees and figuring out who belongs in which branch of the tree.

Grant YDNA

In my previous Blog, I noted that the Frazer marker of DYS710 with a value of 34 was probably ancestral:

Assuming that to be the case, that meant that DYS710 = 33 would define the James Line of the Frazers above.

I wrote to Grant to get the STR values from his Grant BigY test. However, it appears that the Grant STR value for DYS710 is missing along with the STRs from 68-111. I don’t know if this is a mistake by FTDNA or not:

Grant Matches Paul by BigY but Not by STRs

Another surprise is that Grant matches one Frazer by the BigY and not by STR matching. Here is my cousin Paul’s matches by BigY:

Here are Paul’s 67 STR matches:

Here Paul matches a Grant, but not the same one who took the BigY test. Note that the Grant above doesn’t show that he had Big Y tested.

How Does Grant Match Jonathan?

Jonathan had fewer STR mutations, so perhaps he matches Grant. Below, we see Jonathan matches many Grants, including the one who took the BigY test:

There is one interesting thing to note here. Look at Jonathan’s match with Stuart who took the big Y. At 67 markers, there is a Genetic Difference (GD) of 3. With Grant the GD is twice as much at 6. However, when the BigY markers are added in, the differences between Jonathan and Stuart are 12 and only 11 with our BigY Grant.

Comparing Grants Extra 435 STRs with Jonathan

Thanks to the Grant family sending me the Grant BigY STRs, I can now compare them. In my previous Blog, I noted these differences between the Frazer Archibald Line and the James Line:

Paul is from the Archibald Line and Jonathan and Rodney are both from the James Line. Grant could be the tie-breaker to tell which values are older for these markers.

FTY299

What do you think? Based on the above, and knowing nothing else, I would say that 12 is ancestral and 13 is derived. That puts FTY299 as a marker for the Archibald Line. I’ll add that to my STR tree after I look at the other two markers.

DYS523 and Good Old FTY269

 

Here we go again. The mutations seem to be skewed more toward the Archibald Line. However, recall that these are mutations that Paul has, so they could have taken place any time between Archibald in 1715 and Paul:

If Rick had taken the BigY test, we could have narrowed that down a bit.

A New BigY 500 STR Tree

With this new information, I can build a New BigY STR Tree:

Here I wrote Paul’s results a little differently as I didn’t have room at the top. The first number is ancestral and should apply to Archibald Frazer born around 1690. The second is Paul’s value. This mutation could have happened between about 1715 and when Paul was born.

Any Other Differences?

It seems that there must be. Jonathan had 5 additional differences in the BigY STRs. However, these may be differences between Grant and Frazer in general.

Here in DYS514, we see a difference between Frazer and Grant. We can’t tell which one is older, because we need a tie-breaker.

Parallel Mutation or Back-Mutation

Let’s consider DYS516. I had said that the value of 18 for STR DYS516 represented the overall Frazer line because it was shared by Paul and Jonathan whose common ancestor was the original known Irish Frazer from about 1690. However, Grant has a value of 17 shared with Rodney. In other cases, we had considered the value to be shared by Grant and Frazer to be the older one. What happened? This is a case of back mutation or parallel mutation. It could be that the old value shared by Grant and Frazer was 17. Then sometime before 1690 it went up to 18 for Frazer. Then Rodney’s branch went back down to 17. That would be a back mutation. For a parallel mutation, the original value that Grant and Frazer shared would have been 18. Then at some time Grant mutated down to 17. In an unrelated (or parallel) way, Rodney’s branch also went down to 17. By getting more information on other people’s BigY results, it might be possible to figure out which happened.

There is a less likely scenario where 17 would be ancestral. That would have to mean that Jonathan and Paul had independent or parallel mutations. As this would have happened over a shorter period of time, it is less likely that this happened.

DYS542

Here is another of Jonathan’s 5 of 435 STR mismatches with Grant:

Note that Grant and Frazer have a difference of two. Again, we don’t know if 12, 13 or 14 was the ancestral value. It could be 13. In that case Frazer would have mutated up and Grant mutated down.

FTY289

This should be the 4th out of 5 differences between Jonathan and Grant.

FTY510

This should be the 5th difference or GD.

Grant Vs Rodney

I would suspect that Grant and Rodney’s results should be similar to Grant and Jonathan’s results.

They are the same except the number of BigY STR results tested are slightly lower.

FTDNA Block Tree Vs YFull’s YTree

Both FTDNA and YFull have SNP trees. Sometime one gets ahead of the other. Here is the FTDNA Block tree from Jonathan’s perspective:

Jonathan matches two Frazers at YP6489. Further out he matchs Grant at YP6488. At at more distant level he matches Hayes at YP6479. That doesn’t mean that Frazer descends from Grant and Stuart who descends from Hayes. It just means that these families descend from a common ancestor.

Another point to note is that the Frazer SNP of R-YP6489 is probably a family SNP. That means that this SNP probably applies to just our Frazer branch. YP3189 is one step below YP6488. That means that it is more recent. YP6488 is older and represents Frazer, Grant and Stuart. Because there is more than one family that shares this SNP, it would not be considered a family or surname SNP.

Here is the YTree version:

R-BY26344 Is for Grant and Stuart

This tree goes back one more level and includes dates. Then there is one important detail I missed previously. It appears that Grant and Stuart have a new SNP called R-BY26344. YFull uses IDs, but it appears that those IDs are for Grant and Stuart. This is the part where YFull’s YTree goes ahead of FTDNA.

My interpretation of the YFull YTree above:

Again, this does not show that Stuart, Grant and Frazer descend from Hayes, but that all four surnames descend from a common ancestor born around 900 AD. This shows that the tested Stuart, Grant and Frazer had a common ancestor from around 1300 AD. I assume at that time, surnames may not have been settled or commonly used in Scotland. According to scottish-at-heart.com:

The use of  ‘fixed’ (or recognized) Scottish surnames appeared occasionally as early as the 10th or 12th centuries, but didn’t begin to be used with any sort of consistency until the 16th century.

Even this, this practice was slow to ‘catch on’, and it took until the late 18th and early 19th century to spread to the Highlands and northern isles.

A New Terminal SNP for Grant and Stuart and a New Mystery

In my previous Blog, I had missed that Grant and Stuart have a new Terminal SNP. They are now BY26344. However, YFull gives a common ancestor for Grant and Stuart at 225 years before present. I roughly called that 1775. The problem is that if Stuart and Grant had a common ancestor in 1775, was it Grant or Stuart? Also, it appears that the Grant and Stuart genealogies don’t match up as to where these families lived at that time.

Grant and Stuart Genealogies

This is an area where I have very little knowledge. I have that the Grant BigY tester’s earliest verifiable ancestor was James GRANT “of Carron”, 1728 – 1790. From a quick Google search, this appears to be Carron:

The Stuart tester has this information:

Charles Stewart/Stuart b. abt 1695 d. 1753 Virginia

This is the problem. If Stuart and Grant had a common ancestor around 1775, then how could Stewart have been in Virginia in the early 1700’s and Grant been in Scotland in the early 1700’s? This suggests that one of the genealogies is wrong or that the common ancestor dating is wrong. The closest reconciliation that I could make up is that Charles Stewart was actually Charles Grant. He had James Grant in Scotland, then came to Virginia and changed his name. I feel uncomfortable making wild guesses for others’ genealogies that I know little about, so I will not go further in this direction.

TMRCA By YFull and FTDNA

What if YFull is wrong with their date of most recent common ancestor? Here is the 6488 Branch:

I don’t totally understand YFull’s dating. However, the reasoning is that the more SNPs in your branch, the older your branch. That makes sense to me. For example, the Frazer R-YP6489 includes 6 other SNPs. The Grant/Stuart branch of R-BY26344 has only two other SNPs. It stands to reason that BY26344 would have a more recent common ancestor than YP6489. The Frazer date checks out well, but three people tested. We think our common ancestor was born in the vicinity of 1690 which is about 329 years ago. YFull gives 375 years as a date. That seems pretty close to me.

A scroll-over of the 375 years before present for the Frazer common ancestor shows this:

This gives a pretty wide margin of error.

For BY26344, there is a larger margin of error:

I assume that the reason is that only two people tested for BY26344.

FTDNA is not as helpful with dates. In addition, FTDNA does not have Stuart and Grant as BY26344. Perhaps if they update their tree, they will and there may be a way to estimate a common ancestor then. However, having said that, the a YDNA project administrator has made this prediction for Grant and Stuart in an email to Stuart:

You had 19 Unnamed variants and now you have 19 – 2 = 17 left over. 

Out of these 17 SNP’s there was 1 SNP which you share with Grant.

So both of you create a new Subclade BY26344 downstream YP6488

(btw. FTDNA has not identified this new subclade yet)

Now my best estimate for your MRCA with Grant is about 1200 AD. 

This is interesting because this is an earlier date than what YFull has. The discrepancy may be due to the fact that Stuart did the Big Y 700 and other testers have only done the Big Y 500. Also, I don’t think that Stuart has uploaded his Big Y 700 results to YFull. It will be interesting to see if that makes a difference with YFull’s common ancestor calculations.

The FTDNA administrator further writes to Stuart:

Up to now you are the only one in subclade YP432 with a BigY-700, thus we will only know where these SNP’s are exactly located when they are willing to upgrade from BigY-500 to BigY-700.

Summary and Conclusions

  • Grant and Stuart are the closest YDNA matches to the Frazer family
  • I used some of the Grant and Stuart STR results to find out which of the STR vaules were older or newer for the two Frazer Lines.
  • Grant and Stuart are in a new Branch of R-BY26344
  • There are discrepancies for the date of the common ancestor between Grant and Stuart. These calculations were done by YFull and an FTDNA administrator. These dates may be fine tuned by Stuart adding his Big Y 700 results to YFull and/or by others in the YP432 Group doing Big Y 700 testing.

 

 

Frazer YDNA STRs Compared

Blaine Bettinger recently has started a project comparing STR differences to known relationships. It turns out in our Frazers of Roscommon DNA Project, we have four people who have tested where we know their relationships. Here are those relationships:

Rick has tested 67 STRs and Paul, Rodney and Jonathan have tested for the BigY 500. Here is how the numbers look:

Generally, what we see is that going from top to bottom, the further out the relationship is, the more differences there are in the STRs. The numbers between 0-5 above are the genetic differences. Then as the test gets higher there should be more differences going from left to right as more STRs are being tested.

Paul’s Odd Results

However, Paul’s number goes down when he is compared to Jonathan between the 111 STR test and the BigY 500 test. Why is that? My assumption is that the Big Y test missed one of the STRs tested in the 111 STR test. It should be possible to find this STR looking at the results.

DYS710

Checking Paul’s result, he has a different result from Rodney and Jonathan for marker DYS710. DYS710 is the first marker tested in the 111 STR test. Paul has 34 and Rodney and Jonathan have 33.

Here is Paul’s BigY STR result for DYS710:

Here is Jonathan’s result:

So that is not the answer. I can’t explain how FTDNA came up with a lower genetic distance for the BigY 500 STR results.

A Frazer STR Tree

Over a year ago, I came up with this tree:

This shows the genetic differences. It basically shows that there is a difference of three between the two Frazer lines of Archibald and James. In general, the two lines differ over DYS391 and CDY. At some point between Archibald Frazer of 1720 and James Frazer of 1804, there were two mutations that defined the Archibald Line from the original ancestral Frazer DNA. Then under the James branch of 1804, there are two branches. Rick’s branch is defined by DYS444 and Paul’s branch is defined by DYS576 being 19. However, we don’t know when these mutations occured. For Rick’s branch it could be anyone starting at Richard Patterson Frazer down to Rick. For Paul’s branch it could be anyone between Paul and George Frazer.

An Updated Frazer STR Tree with DYS710

However, the above Frazer STR tree doesn’t explain all the differences. Paul and Rodney have a difference of 5 STRs at 111 markers. I need to add in DYS710. Recall that Paul had a value of 34 for DYS710 and Rodney and Jonatham had 33. But which is ancestral? Or which came first?

The last time I looked for ancestral STRs, I looked at the Frazers more distant relatives: the Grants and Stuarts:

Note that their SNP is R-YP6488. FTDNA now has a block tree:

This block tree was taken from Jonathan’s perspective. However, it shows that R-YP6488 represented by matches with Grant and Stuart is an older SNP. Hayes is from an even older group represented by SNP R-YP6479. I had originally thought that 33 was the older STR for DYS710 but Stuart has a value of 34. Hayes would make a good tie-breaker but he only tested out to 67 STRs.

Checking YFull

Perhaps Hayes has uploaded his results to YFull.

Under Paul’s distant STR matches I see someone who shows as R-YP6479. This is likely Hayes. However, it doesn’t tell me what his value was for DYS710.

Back to the Updated Frazer STR Tree

Assuming that there were no parallel mutations, I’ll try this:

This shows a value of 34 for DYS710 as ancestral. Then on the James line, somewhere between James and Thomas Henry Frazer DYS710 changed from 34 to 33. That means that at least the Thomas Henry Frazer branch is characterized by a value of 33 for for DYS710.

In order to check my tree, I look at Paul and Rodney:

They have a Genetic DIstance (GD) of 5 at 111 STRs. Looking at the tree, we see that the STR differences add up to 5.

  • The Archibald Line has 381 = 11 and CDY = 35-40
  • The George McMaster branch has 576 = 19
  • The James Line has DYS710 = 33
  • The William Frazer branch has 552 = 24

The Mystery of Paul and Jonathan Solved

I posted my question to the Genetic Genealogy – Tips & Techniques Facebook Page. Skip tells me that the 3 of 425 differences are additional differences. That adds up to 7 of 536 STRs. That leads to this observation. Rodney and Jonathan have a GD of 2 of 427. Paul has a GD o f 3 of 425 with Jonathan and 5 of 415 with Rodney. That seems to indicate, if my logic is right, that the extra two mutations are on Rodney’s side.

A BIgY 500 Frazer STR Tree

This leads to another change in the Frazer STR tree. In order to find the GDs between Rodney and Jonathan, I downloaded all the results. These appear to be the two extra differences:

These were on Lines 425 and 475 of my Excel Spreadsheet. This shows that the mutations belong to Rodney. The mismatch column was just to point out any differences between Jonathan’s and Rodney’s STR results.

Here I ran out of room to describe Rodney’s branch at the top of his branch, so the extra descriptors went on the bottom. Keep in mind that STRs can mutate up or down in number. These last two mutations that Rodney had went down in number. In fact, it appears that all the STR mutations on the James Line are going down.

Any Other STR Differences?

Yes. There are a few more differences between the Archibald and James Branches of the Frazers:

Here, Paul represents the Archibald Line and Jonathan and Rodney represent the James Line. Unfortunately, as the newer STR results are not posted on-line, I would not know how to figure out which values are ancestral and which are the newer values.

The Big Picture: SNPs and Haplogroups

The Big Picture is that our Frazers have the haplogroup of R1a:

Most Frazers in general are R1b and not even closely related by DNA. However, before Frazers became Frazers, some of our Scandinavian R1a’s made their way to Scotland and became Frazers when the R1b Frazers were also becoming Frazers.

The R1a Tree

Here is an outdated R1a Tree. It is still nice as it has images on it:

Here is another shot of our Frazer Block Tree:

The trick is connecting the two trees. The Block tree listing at the top mentions R-M198. The “picture’ tree has that at about 6,000 BC, so that is a start.

R-M417 shows as 4800 BC on the picture tree. Next is R-CTS4385:

This shows that before our Frazers were Scots, they were Germanic. Next were the L664 Group:

Our L664 ancestors entered the scene about around 3,000 BC. They still have plenty of time to make it to Scotland. They could have hopped over to England around then, but likely made their way up to Western Scandinavia first.

From there, our ancestors kept branching as families do:

That brings us down to the bottom of the picture chart. S2880. S2880 is right above R-YP432 where the Frazer Block Chart starts:

This shows flags. My interpretation is that during the time of R-YP432 our ancestors were living in Scandinavia. The flag on the right that connects to YP432 is the Swedish flag.

The YFull YTree dates YP432 at 3100 years before present.

Between looking at the Block Tree, the YTree and the R1a Administrator’s Tree, it could be that our ancestors could have made their way to Scotland around the time of Christ. At the time the Frazer Clan was formed, our ancestors were in the area of what is now Inverness, Scotland.

Summary and Conclusions

  • Getting data to a project which compares YDNA STR matches to known relationships gave me a chance to look at our Frazer YDNA STR matches.
  • This lead to a better understanding of what the BigY 500 STR results mean.
  • For the four people who have taken the YDNA test and especially the three Frazers who have taken the Big Y test, I was able to refine the YDNA differences between the different lines and branches.
  • After that I gave a rough overview of how our Frazer ancestors made their way to Scotland from Scandinavia perhaps around the time of Christ.
  • Based on the YTree and other DNA sources, our own Frazer branch of R-YP6489 began around the early 1300’s, but our common ancestor in that branch was from the early 1600’s.

 

 

A Third Frazer Big Y 500: Part 2

Last month, I took a first look at Rodney’s Big Y 500 results. At that time, I was looking for unnamed SNPs that Rodney and Jonathan shared on the James Line. I was unable to find any. It looks like FTDNA and YFull were unable to find any also. When I wrote my first Blog, Rodney’s results were not at YFull yet. YFull is a popular service for interpreting Big Y results. I’ll take a look at Rodney’s YFull Results in this Blog. Before I do that, here is where Rodney fits into the Frazer YDNA testing tree:

Paul, Rodney and Jonathan have taken the Big Y test and Rick has taken the YDNA STR test.

Rodney at YFull

Before Rodney’s results were in, this was the YTree:

Jonathan and Paul were the last two id’s. Here is the present YTree:

YTree Changes

I see two major changes to the YTree. One is that there is a new non-Frazer Branch. The second is that the Frazer branch common ancestor is refined from 475 ybp to 375 ybp. From what we can tell, at the tree above, Archibald was born around 1690. That is roughly 325 years ago. So 375 years ago by YDNA is pretty close. I was expecting a new SNP for the James Line of the Frazers. These SNPs form about every 144 years. Note that at 375 years ago, that should represent 2 or three new SNPs. From my work on the STR side of the YDNA testing, it has seemed like the STR differences have been primarily on the Archibald Branch of the Frazer tree and not on the James side. It seems like this must be true for the SNPs also. This would have to be verified by Big Y testing of someone else in the Archibald Line. The only other possibility is that there is indeed another SNP for the James Line, but the testing results were not clear enough to determine that.

A New Parallel SNP Line to the Frazers

Here is the new line of R-BY26344:

While I’m thinking of it, there is another interesting point. The YTree shows that YP6488 was formed 1100 years ago. [The date that the SNP was formed is earlier than the common ancestor dates listed above. For the formed dates, see the YTree above.] The two branches below YP6488 were formed 700 years ago. However, the Frazer branch of YP6489 consists of six total SNPs listed here:

From 1100 to 700 years ago is 400 years. SNPs are formed on average every 144 years but in 400 years somehow the Frazer seemed to get 6 SNPs. On the other hand, BY26344 has is only represented by two SNPs over 400 years. That could mean that the Frazer line had all it’s SNP mutations between 1100 and 700 years ago, so now they are just coasting, so to speak.

Who Does BY26344 Represent?

YFull uses ID’s, so it can be difficult to tell who these people are. In the past, I have been tracking the Grants as their YDNA STRs have had similarities to the Frazers. That appears to be the case. However, there is also a Stuart as well as a grant in the YP6488 Group.

Here Grant and Stuart are still listed as YP6488, so that means that FTDNA may be a bit behind YFull for Grant and Stuart.

This is interesting as it shows us that Grant and Frazer had a common ancestor about 1300 A.D. To me, this would be before the time that surnames were in common use. However, by 225-375 years ago, surnames should have been in common use. This should mean that the two SNPs at the bottom of the tree should represent Grant and Frazer respectively. This also has interesting parallels to my wife’s line. A surname that was related to hers was also found to be a common ancestor about 700 years ago.

As a reminder, here is a map showing how close the Frasers and Grants lived in 1587:

My assumption is that this is where the common ancestors of the Grants, Stuarts and Frazers lived around the year 1300. This is to the Southwest and West of Inverness. The Frazers had the Grants surrounded. Also the Grants and Frazers surrounded Loch Ness.

I also note that one of the YDNA Grants testers mentions Carron. If I have the right Carron, it is to the Northeast of Glasgow. The Frazers were believed to be from the area of Ayr. I have also added dates to the various areas that the Grants and Frazers may have lived these areas.

Note where I have Grant above, I should have also included Stuart.

Further Questions on the Grant/Stuart Line

Assuming that the two IDs at YFull on the YTree are indeed Stuart and Grant, that poses additional questions for those two lines:

  • A common ancestor of 225 years ago is within the surname era. That means that there was some mixing of the two surnames due to adoption or other event.
  • Stuart appears to have been in Virginia before 225 years ago and Grant in Carron before that time. If this is correct, then the 225 years for a common ancestors may not be right.

I point this out partly, because it shows some common issues that could arise in a surname project. Fortunately, the testing of the Frazers so far has not resutled in similar issues.

Big Y 500 STRs

YFull looks at STRs deduced from the Big Y test. Here is how Rodney matches Jonathan and Paul:

This shows that, by STRs, Rodney is much more closely related to Jonathan than Paul. I think that there is a way to convert the distance to years, but I can’t find it right now. However, it appears to show that Rodney is more than twice as closely related to Jonathan as Paul is. This makes sense based on the genealogical tree at the top of the Blog.

Rodney is Running Out of SNPs

Here are Rodney’s novel SNPs at YFull:

Note that Rodney has no best or acceptable quality Novel SNPs. Novel SNPs are the ones that don’t match others. That means that all of Rodney’s good SNPs are already matched up with Paul and Jonathan as they should be. This makes sense as the time between the birth of Rodney, Jonathan and their common ancestor of Thomas Henry Frazer is likely less than 144 years.

For comparison, here are Paul’s Novel SNPs:

Paul has 10 Best or Acceptable Quality novel or private SNPs. It is likely that one or more of these SNPs could become an Archibald Line SNP if another Archibald Line Frazer descendant tests for the Big Y.

Perhaps a better comparison would be with Jonathan’s novel SNPs:

Jonathan is really out of Novel SNPs. He has no novel SNPs of any kind of quality.

Summary and Conclusions

 

  • Rodney’s Big Y 500 test has refined the YTree and dates of common ancestors
  • Many new SNPs prior to about the year 1300 may account for no identified SNPs after that date for the James Line
  • Another Big Y tester on the Archibald Line may create a new SNP for that branch
  • Assuming that the new Branch of BY26344 was for Stuart and Grant, that raises questions about the origin of those lines and about the date of the common ancestor for those two surnames.
  • The common ancestors for the Frazer distant relatives of Stuart and Grant has been moved up from 800 years ago to 700 years ago.
  • The common ancestor for the three Frazer testers has also been moved up 100 years: from 475 to 375 years ago.
  • The STR testing confirms the relative DNA closeness of Rodney and Jonathan who are in the James Line. This is also confirmed by autosomal DNA test results.

A First Look at Rodney’s BigY500 Results – a Third Frazer BigY

I had some good news recently. Rodney’s BigY500 results were in ahead of schedule.

Rodney’s Genealogy

Here is Rodney with other Frazer that have had YDNA testing. Paul, Rodney and Jonathan have taken the BigY test and Rick has taken the STR test.

Frazer SNPs

Currently, the SNP that defines this whole Frazer line is R-YP6489. This is part of the R1a group. With the addition of Rodney to BigY testing, we should be able to get a new SNP that defines the James Line Branch and more specifically, the Thomas Henry Frazer Branch. This testing is bringing us into relatively modern times.

Paul Compared to Rodney and Jonathan

When I compare my cousin Paul to Rodney and Jonathan I see this:

Paul has these Non-Matching Variants compared to Rodney and Jonathan:

  • 7947875
  • 8162400
  • 16784516
  • 20957961
  • 21457649

These are likely Variants on Paul’s side (the Archibald Line) which are not on the James Line side of the Frazer tree. The problem with these Variants is that they will not be named as SNPs unless someone else tests positive for them. There are two ways that this could happen. One would be that Rick (from the Archibald Line) takes a BigY test. Or, tests could be requested for each of the variants above and Rick (or another Archibald direct line male descendant) could test for the individual SNPs once there is a test protocol.

Looking for the James Line Variant

Where is the Variant or Variants that will define the James Line? Here is what Rodney’s niece Kim sent me. This is how Rodney compares to Jonathan and Paul. The comparison is by non-matching variants which is a bit confusing. The non-match could be on Rodney’s side, Joanathan’s or Paul’s sides:

 

What I am looking for is where Rodney does not match Paul. I want these to not include the Variants that I have listed above representing the Archibald Line. That leaves:

  • ZS3186
  • 20102008

These would be potential candidates for the James Line

Here are Jonathan’s matches:

These appear to be unique to Jonathan:

  • BY26998
  • BY28746
  • BY28749
  • BY28761
  • F4038
  • ZS3186
  • 11718822
  • 11720223

I was hoping that these lists would match up better. Rodney’s results have been uploaded to YFull for analysis, but the analysis is not yet done. It could be that there is an issue on how these variants were reported. The only Variant in common is ZS3186. However, this is a named variant which would probably not be used for a new branch.

Further, Jonathan has this list of Unnamed Variants:

Here it seems we are dealing with a lot of double negatives. Jonathan’s results report Variant 11103209. As this is not on Jonathan’s list of Non-matching Variants, should I assume that Jonathan has this variant in common with Rodney and Paul? I’m confused.

Here is Paul’s list of unnamed variants:

This matches pretty well with my original list for Paul, but it does not include 20957961.

ZS3186

ZS3186 was shared by Rodney and Jonathan but not Paul. However, this is already named. The YBrowse website has this information:

This was found in 2014 but never added to a YTree. It is in the J1 Haplogroup. For this reason, this SNP may be not considered good. Or, it may be determined that the original sample was in error(?) Again, we need some help from FTDNA or YFull in figuring this one out.

Variant 20102008

I had listed this Variant above. Is this the defining James Line Variant? This is not on Paul’s list of unnamed variants. This is good as Paul is from the Archibald LIne. 20102008 is shown as a non-matching variant between Paul and Rodney, so that leads me to believe that Rodney has this variant. However, 20102008 is not a non-matching variant between Paul and Jonathan. This would lead me to believe that Jonathan does not have this variant.

Frazer Variant Summary

This left me a bit confused, so I found out Rodney’s Unnamed Variants. Here is a summary of the three tested Frazers:

Hopefully, I can explain the inconsistencies in blue. The first row is YP6489. All the Frazers have this SNP and it currently defines the project.

Variant 1103209

The second row shows that Jonathan has Variant 11103209. This is actually a double discrepancy. Rodney and Paul do not show this Variant listed on their results but neither do they show this as an non-matching variant with Jonathan. Here is what I believe happened. The results for Rodney and Paul were inconclusive. As a result, the first go at looking at this variant was not enough to list this variant for Rodney and Paul. However, due to the uncertainty, it could not be clearly said that this was a non-matching variant between Jonathan and Rodney and Jonathan and Paul. By looking at the raw test data, it may be better to come up with a better analysis. Right now, this does not look like a defining Variant for the James line if there is some question as to whether Paul has this Variant.

Variants 11718822 and 11720223

These Variants appear to be Jonathan’s private SNPs. Jonathan is positive for them, but Paul and Rodney are not. That means that these likely formed in Jonathan, his father or grandfather after the time of Rodney and Jonathan’s common ancestor Thomas Henry Frazer born 1836. Once YFull has done their analysis, they will give an estimated date of SNP formation and an estimated date of common ancestor. The SNP formation is always the older date. In this case, we know the date of the common ancestor: 1836.

More on Dating

While I’m on the subject of dating. Here is the present Frazer tree going back over 3,000 years:

Jonathan and Paul are at the bottom of this YFull YTree. Based on their BigY testing alone, it was estimated that the SNP YP6489 was formed 800 years ago and that Paul and Jonathan had a common ancestor 475 years ago. This is to illustrate that the SNP formation is before the common ancestor. Going up one step is YP6488. This was formed 1050 years ago. There was a common ancestor there 800 years ago. I assume that this date fits into the formation date of YP6489 800 years ago.

Paul’s Private Variants – The Archibald Line

Paul has four private variants. These formed in the Archibald line between the time of Archibald Frazer born around 1690. The Archibald Line needs another person to test to have some of these Variants named as defining SNPs for the Archibald Line.

Rodney’s Variants

Rodney’s first Variant 2012008 has a question mark under Jonathan. That means that there is some question on Jonathan’s read. However, the fact that Paul was negative for this Variant makes it looks like this could be the new defining Variant that gets named as the SNP for the James Line. Rodney’s second Variant is common to only him at this time. Like Jonathan, this variant formed in either Rodney, his father or grandfather.

This appears to be Rodney’s only Private Variant:

What’s Next?

Kim has uploaded Rodney’s BigY500 to YFull for further analysis. YFull will get this information onto their tree. They will give age estimations and produce 500 STRs from the results. FTDNA will also be doing further analysis on the results. In addition, the R1a administrators will take a look at the results. However, they will like be interested in seeing what FTDNA and YFull have to say.

Summary and Conclusions

  • Rodney’s results show that there are some clear SNPs that could be added to define the Archibald Line. However, as Paul is the only Archibald LIne BigY500 tested person right now, these SNPs will not be named.
  • The James Line results are not as clear. Interpretaion of the results are needed. It is likely that Variant 2012008 will be a new defining SNP for the James Line for the Frazer DNA Project. It appears that this SNP occured between James Frazer born about 1720 and Thomas Henry Frazer born 1836.
  • We need to wait and see if FTDNA and YFull come up with further analysis.

Another Frazer Joins YDNA Testing

Joanna, who has had her brother tested for the BigY. informed me of a new YDNA match for the Frazer family. This is big news when a new Frazer match appears. The new match is Richard.

Some of Richard’s YDNA Matches

Here Richard shows up as the fifth match to my cousin Paul:

The new tester, Richard, has tested for 37 STRs. The first three on the list are known to be related to each other by genealogy. Those three and Paul all have ancestors from Northern County Roscommon by the early 1700’s.  Here is how they are related as best we can figure:

How Richard Shows Up on Jonathan’s List

Richard shows up as a Genetic Distance (GD) of 2 on Jonathan’s list. On Paul’s list, Richard has a GD of 4.

More YDNA Comparisons – YDNA TIP Report

On Jonathan’s match list, I ran the ‘TIP’ report. This is an estimation of how far away Richard and Jonathan’s common ancestor is:

This report makes it look like Jonathan and Richard are related in the not too distant past. The likelihood that Jonathan and Richard have a common ancestor in the last 5 generations is close to 90%. A 67 STR test would give better results as it is possible that Jonathan and Richard have more STR differences in the second tier of STRs. If these results are born out, there would be a good chance that Richard’s ancestors were from North County Roscommon Ireland.

TIP Report for Richard and Paul

If Richard is from the James Line of the Frazer Tree, then I would expect that Paul would be 6 generations to the common ancestor of James.

Looking at Richard’s STRs

One thing that jumped out at me was STR 447:

Those in green have a Frazer or Frasher ancestor. They also have a 447 STR of 24. All those above are Grant, Chisum, Hayes or Whittaker and have a STR value of 25 or higher. That could mean that among families that are closely related to the Frazers, the Frazers alone have a STR of 24 at this location. This gives me some confidence that Richard is related to our line of Frazers. The question then becomes whether his ancestors were in North County Roscommon or whether our common ancestor goes further back to Scotland.

STR 391

Another interesting STR is 391. Rick and Paul are both on the Archibald Line and have a STR value of 11:

Jonathan and Rodney are known to be on the James Line and have a STR value of 10.

This shows that the first Frazer known to be in North County Roscommon had a STR value of 10 at location 391. Somewhere on the Archibald Line on the left between the first Archibald and James born around 1804, the value of that STR changed from 10 to 11. This doesn’t prove that Richard is from the James Line as Grants, Chisum, Whittaker and Hayes also have a 391 value of 10,

Frasher and Frizelle

Jonathan also matches a Frizelle at 37 STRs at a GD of 1. Putting Jonathan and Frizelle into the TIP report also shows a probable close relationship. The Frizelle that Jonathan matches by YDNA has an ancestor of William Frizelle. I wonder if there is a connection between this William Frizelle and Richard’s William Frasher.

Further Options for Richard

Richard may want to upgrade to the 67 STR test. An autosomal DNA test would also be interesting to see if he matches anyone in the Frazer DNA Project. The autosomal test would be the less expensive option. If Richard is from the James Line, it is likely that the autosomal test would reveal that. If no matches with the Frazer DNA Project show up in the autosomal DNA test, then further YDNA testing may be of further use.

Summary and Conclusions

  • Richard’s recent YDNA test appears to show a pretty close relationship to Frazers from North Roscommon County, Ireland
  • Autosomal DNA testing, if taken, could reveal more matches to those already in the Frazer DNA Project for descendants of those Frazers from North Roscommon
  • Richard shares a STR that has been found to be unique to the Frazers up to this point
  • There is also a Frizelle who has found to be fairly closely related by YDNA to the North Roscommon Frazers, however his results have not been posted to my knowledge
  • It will be interesting to see what additional genealogy or DNA testing will reveal

A New Frazer Tested for YDNA

People say that YDNA is complicated. It is not too complicated. YDNA gets passed on from father to son unchanged. Except it does change on average about once every 144 years or so. That reminds me of how to have a good lawn. Plant grass seed. Wait 100 years and you will have a good lawn.

Rodney Added to the Frazer YDNA Tree

 

There is some confusion on the Archibald line (left side)  as to whether there should be two Archibalds or one under the top Archibald. Some researchers added one to make the dates look better, but I am thinking of taking one back out. For example, an alternate tree has one Archibald but has Philip born 1758 instead of 1776.

Here is the alternate tree:

 

If nothing else, the symmetry is better on this one.

Rodney’s STRs

Rodney tested for 111 STRs. That is a good amount. Jonathan also tested for 111 STRs. Rick and Paul tested 67. STRs are Short Random Repeats. These are repeats of certain markers on the YDNA. They may increase or decrease every so many 100’s or 1,000’s of years. Some markers change faster than others. Over a large amount of time these markers could go up or down and we wouldn’t know it as we weren’t around 1,000 years ago to test them. However, this tree only goes back to about 1690 or so, so we shouldn’t have to worry about that.

Rodney’s Vs Jonathan on the Thomas Henry Line

Jonathan’s sister asked me about Rodney and Jonathan’s STR comparisons. Rodney and Jonathan had a perfect match at 67 STRs but a one difference at 111 STRs. That was because their only difference was between STR 68 and 111. The actual marker for this difference is at DYS552. Rodney has a value of 24 and Jonathan has a value of 25. That means that Jonathan has one more Short Random Repeat compared to Rodney. Out of all the STRs, that is the one that distinguishes Rodney’s Line from Jonathan’s line.

Which Line Changed: William or Edward Fitzgerald?

And does it matter? It would be nice to know who changed, because that would mean either 24 or 25 would be ancestral, meaning that Thomas Henry either had 24 or 25 for that marker and one of the lines changed. I did not have the 111 STR test done for my cousin Paul, but he has taken the BigY. When he had that test done, I uploaded his results to YFull and they extracted some of the STRs from the BigY test. Unfortunately, the extraction from the BigY test does not get good reads for all the STRs. Fortunately, Paul did get a result for DYS552. He had a result of 25.

That means that 25 is likely the ancestral value. 25 would also likely be the value for Archibald Frazer born around 1690.

This is the way I’ve heard STRs explained. Pretend at every conception along the male line through the ages, the YDNA is going through a copying machine. All the different STRs are being copied. Every three generations or so, one of the 111 STRs has a copying error and one more copy or one less copy is made. In Rodney’s case, one less copy must have been made of DYS552 in either Rodney, Rodney’s dad or his grandfather, William Frazer.

There is one implication concerning the mutation in Rodney’s line. When Paul is compared to Rodney and Jonathan, it looks like he is more distantly related to Rodney than Jonathan. These differences are called GDs or Genetic Distances. However, based on the tree, Paul is related no more closely or further away from either Rodney or Jonathan.

It’s Simple

That is why I said at the top that YDNA is easy. Rodney and Jonathan have a common ancestor of Thomas Henry Frazer born 1836. Jonathan and Rodney have a GD of 1. That means that change happened after Thomas Henry Frazer as he had only one value for each of his 111 STRs. Because we know Paul’s result for DYS552, we know Thomas Henry Frazer’s value at location DYS552. There is only one catch. It is possible for STRs to go up and down. What if DYS552 changed more than once since 1690? This would be highly unlikely. If DYS552 was a fast-moving STR or if there were several thousands of years to the common ancestor, this would be more likely, but that is not the case here.

The Bigger Picture

Using the same principles, I should be able to get some ancestral values for our common ancestor, Archibald Frazer. However, let’s start with a smaller part of the Archibald tree, like we did on the James Line.

Here is Rick and Paul on the Archibald Line of the Frazer YDNA tree. Where Rodney and Jonathan had 3 generations to have YDNA changes from their common ancestor, Paul has 4 generations and Rick has 5 generations from their common ancestor of James Frazer born about 1804.

Rick has taken the 67 STR test but not the BigY test. Paul has taken the 67 STR test and the BigY test. As a result, he has some results from the 111 STR test, but is missing many of the STR markers between 68 and 111. Here are the differences between Paul and Rick:

Getting the Ancestral STR Values

Now I want to know what values James had for his STRs for 444 and 576. These are the values that Rodney and Jonathan have going up to the orignal Frazer ancestor born around 1690.

That means that Rick’s STR of 444 went down one repeat from 14 to 13 and Paul’s  STR of 576 went up from 18 to 19.

Putting it Together

Now we know that Archibald , born about 1690 had 444 = 14, 576 = 18 (oops, typo above) and 552 = 25. However, there are two other differences from the Archibald Line and the James Line.  It will be easier to show this on a tree:

Now there is a tie, so how do we tell which values are ancestral? (That should be CDY above.) In order to figure out the ancestral values, we have to go outside the Frazer project and bring in some more distant relatives: Grant, Hayes, and Stewart. Fortunately, I have already done this in a previous Frazer YDNA Blog:

This shows the ancestral value to be 391 = 10 and CDY = 35-38. Now we have our five ancestral values for Archibald.

Here is the final Frazer STR Tree:

 

Observations:

  • If I drew this right, Jonathan has no mutations going back to Archibald, born about 1690.
  • Paul and Rick both have three mutations going back from the same Archibald.
  • There are more mutations on the Archibald Line than the James Line, but they average out.
  • Paul and Rick have a GD of 2. That represents differences in marker 444 and 576.
  • Paul has a GD of three compared to Rodney and Jonathan. This is based on markers 391, CDY and 444. 552 was not counted as Paul did not test at FTDNA for 552.
  • This tree contains some 67 STR results and some 111 STR resuilts.
  • Other direct male Frazer descendants that have YDNA STR tests should be able to tell what branch of the Frazer tree they are in based on this tree.
  • This gives an idea of how the mutations occur. There were two mutations that happened rather quickly between about 1690 and 1804 on the Archibald Line. So that was one every 57 years.  Rodney had one mutation. I’m not sure when he was born, but let’s say one mutation in 260 years. Let’s say Paul and Rick had a mutation about once per 87 years. An average between Paul or Rick and Rodney would be about one mutation in 173 years. This is comparing a bit of apples and oranges as some tested at 67 STRs and some tested at 111. I don’t know how to average Jonathan in as he has no known mutations.

 

Dating Using the McDonald TMRCA Calculator

Rodney and Jonathan

That should say generations at the bottom. Jonathan and Rodney have a common ancestor at three generations.  This calculator’s first choice for a GD of one at 111 markers is 2 generations away. Three generations would be the third choice.

Paul and Rick

This graph tops out at 5 generations. Paul and Rick are 4.5 generations away from a common ancestor, so that is close enough.

Paul Compared to Rodney (and Jonathan)

Paul and Rodney are 7 generations to a common ancestor. At least they are on the tree without the extra Archibald. This shows 8 as the first choice, but almost the same chance as being 7 generations away. Rick and Rodney should be at the same genetic distance (GD) and they show as 7.5 generations away from a common ancestor. These would also apply to the matches between Rick, Paul and Jonathan.

Summary and Conclusions

  • Rodney’s YDNA test has added some symmetry to the Frazer YDNA Tree
  • The YDNA test does not appear to be precise enough to tell us if the Archibald tree is correct or not. Either configuration would be reasonable based on the YDNA.
  • The Frazer STR tree sets down some results that places the four tested Frazer descendants in their different branches.
  • A Frazer that is unsure of his branch would be able to test his STRs and find out which branch he is in.

 

 

Frazer YDNA Update and Some Early Frazer Research

A few things have been going on the Frazer DNA and genealogy front:

  • Results are still coming in from our Frazer-related Stewart/Stuart BigY test results
  • A new YFull Tree has come out
  • A Frazer researcher has shared some of his information with us on Frasers in Scotland

Stewart/Stuart Big Y Results

In my last Blog on the subject I gave more information, so this is just an update. Once our Stewart tester got his Big Y results, there was still more analysis by the R1a YDNA project administrator, Martin. I was interested to hear what Martin has to say as these administrators are talented and take their volunteer position seriously. I found this part of Martin’s analysis interesting:

Around 1000 AD this subclade YP6488 splits in 3 family lines Grant, Stuart and Frazer. The date 1000 AD is not very certain because we see a wide variation in the number of private SNP’s in these family lines. Normally we calculate with 130 years per SNP (or one SNP mutation in 4-5 generations), but this average figure is only valid for a large number of samples. The total average number of SNP’s downstream M417 is on average about 50 for Subclade R1a-L664. However Grant and you have only resp 42 and 45 (see red number at bottom of chart) and the Frazer’s have more or less the average number of 50 (excluding the extra SNP’s found in the Yfull analysis). So the best guess for the MRCA of the Grant/Stuart/Frazer families is for me still 1000 AD, but with a large margin.

Here is the new R-YP5515 portion of the tree with Stuart added:

I erased the FTDNA kit numbers for privacy. I hadn’t realized that the red numbers were important at the bottom of the tree. Now I realize that they are, so I have included them. [See the explanation above in italics.] The addition of Stuart to the group has the effect of changing the separation date of the Frazers, Grant and Stuart to the year 1,000 A.D. Before Stuart, it showed Frazer and Grant separating at the year 900 A.D. Not a big difference, but it does show the effect of the Stuart test on  Grant and Frazer.

I was also in touch with Martin and he was seemed excited about a new member to the group:

Today we have new member, which I think is interesting for the members of subclade YP5515>YP6479  It is #______ from Sweden and he has the typical STR haplotype for this subclade. Up to now all members of YP5515 had their roots in Scotland/Ireland, but we expect YP5515 came originally from Scandinavia. This new member could be a proof that YP5515 came from Scandinavia if he is willing to do a BigY test.

So we will have to wait to see how this plays out. It appears that if this person were to do the BigY test, this could give us a more exact time of when our ancestors came from Scandinavia to Scotland. Speaking of this, I thought about Martin’s comments to our Stuart tester and came up with this drawing:

I used a little bit of guessing. It seemed like the best route from Sweden to Scotland would be by water. Perhaps our ancestors made some stops in current Norway before settling in the Inverness area. Their route from Inverness to the shore SE of Glasgow is based on some Frazer traditions. I noted that it is a pretty straight shot from there to County Roscommon where they certainly were according to the 1749 Census. They could have traveled by boat again, but there have been Scots known to be in Ulster also.

A New YFull YTree v 5.06

YFull analyzes Big Y results. For those that use their service, they come up with a tree and other analyses. Here is the current version of YFull’s YTree:

Compared to the last YTree, this has added YP6488 and YP6489. The Stuart tester is not yet included in this analysis. So his analysis should come out as YP6488. Note that YFull has a TMRCA of 800 years before present for YP6488 or roughly 1200 A.D. This is an important date as it is where there is a split between the Grant, Stuart and Frazer families. I feel that Martin’s tree may be more accurate. On his tree, the analogous date appears to be 1,000 A.D. That seems to get into those red numbers that I mentioned above. Perhaps YTree saw the fewer SNPs for Grant and Stuart and figured that represented a more recent date. Martin, being a real person, was able to take ambiguities into account and give a more plausible date.

Early Frazer Research

I am grateful to Alan for bringing together and to light research on Frasers in Scotland that might link to our Frazers in County Roscommon, Ireland. Alan’s research appears to indicate the following:

  • James Fraser of Knock married Mary Ramsay in 1628.
  • That James was the son of John Fraser of Knock
  • Mary Ramsay was the daughter of “Mr Andrew Ramsay one the ministers of Edinburgh
  • James was associated with “…Montrose during the sojourn of the royal forces in the west of Scotland. The laird of Knock [James] denied having had any concern in the protection…”
  • “James Fraser of Knock
    March 13, 1649: Presbytery of Irvine: it was reported on this day to the Presbytery that “upon the day of tendering the Covenant, the laird of Knock, because it was told him that he wald not admitted to the Covenant, absented himself from the kirk in the afternoon”. For “his scandalouslie absenting himself fra the kirk the day of swearing the covenant”, the Session of Largs were ordered not only to proceed in the process against the laird, but that this latter offence should be taken into the process. Paterson states ‘that in 1650 the process was still continued against him, though meantime he had fled to Ireland to escape the persecution to which he and others were subjected’.
    [Paterson, James: History of the County of Ayr, Vol. II, p. 309]”
  • Apparently this same James shows up in 1673 in Aberdeenshire as a “minister of word of God at the Church of Ellen

Knock is part of Largs Parish:

Here is a modern view of the updated Knock Castle:

Alan informs us that the modern day spelling of Ellen is Ellon:

This looks like it would be an interesting place to visit.

  • There is mention of an Archibald and William Frazer in reference 11 compiled by Alan. This appears to be in a document signing over the property at Knock. However, the relationship of Archibald and William to James and his younger brother Alexander are not apparent.

So where does this leave us? Alan’s research adds some clarity to the traditions of the Frasers of Knock circulated among some of the Frazer descendants. It shows that there was a controversial figure named James Fraser of Knock who held the Knock Castle and property. He got into some trouble with the authorities in the area of Largs, fled to Ireland for a while and showed up in Aberdeenshire as a minister where he apparently died.

My assumption is that the Frazers that moved to County Roscommon were familiar with James of Knock and probably were living in the same area before moving to Ireland. What is not sure is whether our Irish Frazers were closely related, distantly related or unrelated to James Frazer of Knock. Joanna of our study group has mentioned that there are Frasers and Frazers still around in the area of Largs. It would interesting to find out if there is any DNA connection between these Fraser/Frazers and our Frazers.

Any comments are welcome in case I have misinterpreted Alan’s research.

Stuart Added to the YDNA Group of Frazer, Grant, Hayes and Patton

I just found out about some exciting news. A Stuart that likely originates from the same area in Scotland as the Frazers has gotten his BigY results back. This is one of the best tests for YDNA. It places people in YDNA trees and shows how families originated. I’d like to look at those results to see where this Stuart fits in with Frazers and other related families.

BigY and YDNA Basics

The important thing to remember about YDNA is that it is very simple. You are only dealing with one Chromosome versus the 22 autosomal chromosomes. Then you are only dealing with one line of ancestors. That is your father’s, his father’s father’s and so on. The Big Y tests SNPs. SNPs are mutations that happen every four or so generations on average. The Big Y tests these SNP and how they have changed since our original ancestor – called genetic Adam. When you get your Big Y results you get a lot of SNP names. These are the SNP differences between you and Adam:

You will have the first SNP that differentiated you from “Adam” up to the one that got you into the R group. Our group of Frazer, Hayes, Grant, Patton and Stuart are in a still very general group called R1a. The understanding is that this group traveled a bit to the North of the R1b group. The thought is that our R1a group made their way up through the current country of Germany to Scandinavia. From there they made their way somehow to Scotland.

snps and variants

These SNPs carry down to what is called a terminal SNP. This is the last or most recent SNP that is named and is usually shared with another person. After that, the SNPs are not generally named and called Variants. These are the newest of all. Once others test and these Variants can be placed in a tree, they will extend the branches of the tree further into the present and will also be named.

what is confusing about YDNA?

STRs are a little more confusing, but I won’t be looking at them here. They can be confusing because the values for these can go up or down. SNPs however happen once and then they are set in stone. One of the major confusing things about SNPs are their names. The SNP names are based on the lab or group that discovered the SNP. That means that there is no logical progression in the name that shows the change from an older SNP to a newer SNP.

Here is an example from the R1a Project spreadsheet:

This shows two Frazers and an unnamed tester. The turquoise heading shows the progression of the SNP names. They start at M417 and end at R-YP6489. The unnamed person did not have his SNPs tested, so he has a conservative red designation for his SNP based on the values of his STRs which appear to the right. He is probably actually R-YP6489 based on his STRs, but he hasn’t taken the test, so he has a SNP value that is likely thousands of years older than R-YP6489. I’ll try to address a few more items of confusion as they come up. However, in general they have to do with the naming of SNPs.

So far:

  • YDNA SNPs are simple. According to YFull, there is a new high quality family SNP in your line every 144.41 years. They change about every four generations just on the direct male line. In my 2nd cousin once removed Paul’s case, four generations takes him back to his 2nd great grandfather. Between Paul b. 1944 and his great grandfather James Frazer b. about 1804 there are 140 years. Between those 5 people there is likely a new SNP. Or maybe none or two. But most likely one.
  • Based on these changes back to Genetic Adam we can make a YDNA tree.
  • The SNP names are complicated and don’t represent the progression of the SNP changes in the YDNA Tree.

Three Different YDNA Trees

There are three different YDNA trees for our R1a Group all trying to show the same thing. They are:

  • FTDNA Haplotree
  • FTDNA administrator Tree
  • YFull YTree
ftdna haplotree

FTDNA is the Big Y testing company. They have a tree that shows the end result of the Big Y testing. They call their tree the Haplotree. Here is the current tree for my Frazer cousin that I had tested:

There are several levels above this, but this is the current bottom of the tree. It ends in R-YP6489. This is consistent with the FTDNA R1a Project Spreadsheet above. A lot has been happening since I wrote my last Blog on the subject just two months ago. At that time our Frazer terminal SNP on this tree was YP432. Now we are four levels below that.

ftdna administrator R1a tree

This is a good tree, but it is private, so it is not published anywhere. I had referred to it in previous Blogs by taking out some of the ID’s. The other issue is that I got to see it when our Frazer Big Y test results came in, but I haven’t gotten any updates. Here is what I had before. It looks like FTDNA has since caught up with the FTDNA R1a Administrator tree:

One good thing that the Administrator does is put dates on the SNPs. So for example the date of our common Frazer ancestor is 1600. That is very close to the actual date of 1690 which is when we believe the common ancestor to have been born. Another good check is to see if the date between different surnames is before the advent of surnames. Notice that the year 900 A.D. splits off Grant (and now Stuart) from Frazer. I recently heard that the advent of surnames was around 1,000 A.D. and they came into use for several hundred years after that depending on the region and other factors. Another point is that, if the 1600 A.D. date is correct for this SNP, it would ensure that this is indeed a Frazer Family SNP. Any male Frazer that want to prove his Frazer lineage, would just have to test for this SNP. This SNP should separate the Frazers from non-Frazers – or at least our brand of Frazers.

From a recent Stuart email, I gather that his new result is R-YP6488 which is what Grant is also. That would place Stuart next to the Grant in the middle line above. Time to pull out the Clan map of the Inverness and South. This shows Fraser (Frazer), Grant, and Stewart (Stuart). For me, the geography pulls together what the DNA is showing us. That is, that at least this group of Frazer/Grant/Stewart had a common ancestor probably before the beginning of taking on of surnames in this area South of Inverness.

According to the R1a Administrator: “It looks like between 1400 BC and 400 BC some (or maybe only one) YP432 people migrated from Scandinavia to Scotland.” I am guessing they hung out there for 1,000 years or so. In 900 A.D., one of those former Scandinavians had children. Their descendants stuck around in the Inverness area for several hundred years. When people were taking on clan names, they took on the names of Fraser, Stewart or Grant probably based on where they were living at the time. We have another Chisolm/Chisum who has tested STRs but not the Big Y. He appears to fit into this pattern also.

Yfull Ytree

I wrote my last two Blogs on Frazer YDNA in mid July and the new YFull YTree v5.05 is dated 30 July 2017. It is big news when this tree comes out. Here is the latest version.

On YTree’s web site, they say they try to come out with a new YTree every month, but it seems more like two months before they come out with a new one. So it is now that YTree is lagging behind FTDNA. The Frazers are shown as being at R-YP6479. That is correct, but outdated. They actually are YP6479>YP6488>YP6489. When the new YTree comes out, this should be corrected. Note that next to YP6479, it says, +12 SNPs. When you hover over this box, the additional 12 named SNPs appear. They include the SNPs YP6488 and YP6489 which now form branches. By seeing these new SNPs, it is like we are going back 1200 years or so and seeing these new branches and families form.

What people wait for is the YTree’s dates. YFull has YP5515 as formed 3200 years ago and the TMRCA which is time to the most recent common ancestor as 2200 years ago. It will be especially interesting to see what YFull comes up with for dates on YP6489. At this time, YP6489 seems to be a Frazer family-only SNP as no other families have laid claim to it.

One of the down sides of YFull is that they don’t have all the testers. They only have people in the tree that have signed up for their service. Another issue is that YFull uses ID’s only, so in order to find out who the ID’s belong to you need to message the ID contact. In the tree above, my Frazer cousin is the ID without the ‘new’ designation after it. However, they do have advantages over FTDNA which make them a worthwhile option to use in Big Y analysis.

FTDNA SNP Matching and the Mystery SNP L1012

FTDNA’s Big Y SNP matching is one of those things that doesn’t work well. As I mentioned, my cousin Paul and (by inference) I share our terminal YP6489 with one other Frazer tester. However, when I choose to look for SNP matches at zero difference, it appears to give me 35 entries. Our new tester Stuart is not included in those 35. It appears that the SNPs have not been updated for this search. I think that FTDNA tried to correct this by putting in a subclade search option at the top of the SNP matching area:

 

This feature usually works. However, the R-Y2894 SNP seems out of place as it is several layers above R-YP5515. Here is the result when I choose R-YP6488:

The right people come up (Grant and Stuart), but it shows that there is not a match on L1012. When I look Up L1012, it appears to be an early “Adamic” SNP:

I suppose that there a few kinks in the FTDNA system, unless I am missing something.

Implications of R-YP6489

YP6489 is a fairly recent SNP. So far, this SNP has been dated at about the year 1600 by the R1a Administrator. This SNP came about because of tandem Big Y Frazer tests. As a result, we were able to get a SNP that represents the Frazer family. This SNP can be used to verify that a Frazer male is part of our Irish Frazers. There is another possible use of this SNP. Say that a Frazer with no known Irish history were to test positive for this SNP. That would forge a link between Ireland and the part of Scotland that the Frazers moved from. There may be no further paper records to be found that would link the Frazers to Scotland. There were no immigration requirements for moving from Scotland to Ireland. Many of the vital records have been lost or destroyed. However, the DNA could be the “record” that would link our Frazers to other Frazers that never moved to Ireland.

The YP6488 SNP does not show a single family origin for Grant and Stuart. YP6488 is also shared by our two Frazer testers. The Grant and Stuart families likely have a SNP at the level of YP6489 that represents each of their families. To get to this level would require an addition Grant or Stuart Big Y test. However, if another Stuart or Grant were to test positive for YP6488 by just doing a single SNP test, they would have proof that they are looking in the right area.

Summary and Conclusions

  • Our new Stuart tester is a welcome and enthusiastic addition to our part of the YDNA tree.
  • The Stuarts, Grants, Frazers and others have shared early ancestry. This has now been determined by YDNA testing
  • The area that the Stuart, Grant and Frazer families originated from was likely just South of Inverness
  • Single testing of YP6489 should indicate Frazer ancestry.
  • Single testing of YP6488 should indicate at least Grant, Frazer or Stuart.
  • The next step is to wait for updated YDNA trees from YFull and the R1a Administrator.

A New Frazer Tests for YDNA

It is big news when a Frazer tests for YDNA. YDNA is what is passed down from father to son only. So it is the perfect test for a family surname study like we have for Frazer of Roscommon, Ireland. The other reason that it is big news is that there are not that many male Frazers around to do the testing. We previously had 2 tested for YDNA. Now with Rick’s new test, we have three.

Frazer YDNA and Genealogy

I (and others) have pieced together a Frazer genealogy. It is not perfect, perhaps. That is why DNA testing is needed to affirm the work that has been done. Autosomal DNA is good, but the effectiveness tapers off as we go back more generations. Also autosomal DNA is not specific to a surname, so it could apply to any of hundreds of ancestors the further we go back in time. YDNA on the the other hand, is specific to one male line – in this case Frazer. There are two types of YDNA. One is STRs which Rick tested for. These are good, but there are some problems in interpreting them as I will explain later in the Blog. SNPs are the most exact YDNA test. The other two Frazers, Paul and Jonathan have tested for SNPs through the BigY Test.

Rick descends from George Frazer from Martinsburg, NY. George Frazer moved his family to Canada and left many descendants. I have more on that family here. [Edit: Rick’s cousin Pat replies, “It was Richard Patterson Frazer that brought his family to Canada from Martinsburg.   George was born there but came to Canada with his family as a child.”] Many years ago, I convinced Bill, one of those descendants,  that he and I were related based on genealogy. Even though I wasn’t 100% sure myself, I argued my point with Bill and he finally agreed that we were related. Later, I convinced Bill to take an autosomal DNA test which did show that he was related to my family and many other Roscommon, Ireland Frazer Families. Since then, others have tested and confirmed the relationships. Now we have Rick who has tested his YDNA proving a more certain link on the male Frazer line. So this has been a several year journey starting with traditional genealogy, followed up with autosomal DNA and YDNA testing. Here is the tree of the three male Frazers who have tested for YDNA:

This genealogy is the best that we could do with what we have. There are some uncertainties about it. We have other’s research with names but no references. We have the Elphin Census of 1747 and this includes a widow Mary Frazer. She is presumed to be the widow of Archibald Frazer born around 1690. There are two other Frazers in that Census who represent the Archibald and James Lines. Further, I have supposed that James Frazer b. about 1804 is my ancestor. However, this requires the marriage of two first cousins. This was not that unusual apparently back in the day. Those belonging to the Church of Ireland wanted to marry other Church or Ireland people. In fact, there were laws in place requiring that. However, those from the Church of Ireland were in the minority.

According to the chart above:

  • All the testers have the top Archibald as a common ancestor. Rick and Paul also have James Frazer b. about 1804 as their common ancestor.
  • Rick is 9 generations from Archibald b. about 1690. Paul is 8 generations away and Jonathan is 7 generations away from the first Archibald.
  • Paul and Rick are third cousins once removed
  • Jonathan is a 6th cousin once removed from Paul and 6th cousin twice removed from Rick.
  • Assuming that Rick, Paul and Jonathan were born around 1950, there would be about 260 years from the first Archibald to our three YDNA testers.

Rick’s New YDNA STR Results

Based on the above tree, we would expect that Rick would be more closely related to Paul than Jonathan. That is the case. Ricks closest match is to Paul with a Genetic Difference (GD) of 2. His GD to Jonathan is 3. The GD is the difference in STR mutations between two people. Here are all of Rick’s matches by STRs. He has more matches than Paul or Jonathan:

Here is how Rick’s STR matches compare with Paul’s and Jonathan’s. The numbers are GDs. So a larger GD is a more distant YDNA match. A blank means more than 7:

  • I put the matches together that matched all three Frazers.
  • The light blue highlighted names have taken the BigY Test
  • The SNP Tree below based on BigY SNPs shows that Grant is a closer match to Frazer than Hayes. This seems clear from the STR matches above also
  • The chart points out all the Grant matches. Half of the 10 Frazer STR matches are with Grants.
  • Rick is the only Frazer matching Hayes. This backs up the SNP tree below.

These are the same names that I have been tracking by SNPs. So that is good that the SNPs and the STRs agree with each other. Here is the new SNP tree that was developed by the R1a L664 Administrator Martin:

  • Patton is the most distantly related to Frazer and doesn’t show on any Frazer’s STR match list.
  • Grant shows as the closest match, then Hayes.
  • Chisum doesn’t show on the SNP map as Chisum has not taken the BigY Test.
  • Stuart doesn’t show yet, but he is in the the process of taking the BigY Test, so he will eventually show on the SNP Tree.
  • If Rick had taken the BigY test, he would have formed a branch under the Archibald line on the lower right of the tree. Rick and Paul would likely share some of the SNPs now shown as private SNPs for Paul and both Paul and Rick would then have their own new private SNPs.
  • Rick must share all the SNPs in the yellow box above the ca 1600 A.D date. These are the five brand new SNPs YP6489 through YP6493 that are right now Frazer only SNPs.

A Simple New Frazer STR Tree

A STR Tree for the Frazer should follow the genealogical tree and the SNP tree. Here are the STRs and where Jonathan, Paul and Rick differ:

Normally, the mode would be taken as the oldest STR. However, in the case of DYS391 I believe that based on comparison with other STR tests for Grant, Chisum, Whittaker and Stewart, that the 10 value of DYS391 is the older value. Likewise for CDY which changes more quickly than other STRs, I took 35-38 to be the older value. Prior to Rick’s results, I had this tree for Jonathan and Paul:

In this simple tree, Paul had all the STR changes since the 1690 Frazer ancestor and Jonathan had none. However, there is some guesswork in drawing this out. One rule is to make the chart as simple as possible, which is what I did. This means having the least amount of changes. It is sometimes called the rule of parsimony. Ambiguities in STRs is why some people prefer the SNP trees as there is little or no ambiguity in SNPs. Now note the above chart. Paul and Rick share 391 = 11 and CDYa = 35-40. Here is the new Frazer STR Tree with Rick included:

This shows:

  • Paul has his own STR mutation of 576 = 19 which happened sometime after 1804.
  • Likewise, Rick has his own STR mutation of 444 = 13 which defines Rick’s relatively recent branch.
  • The GD of 2 noted above between Paul and Rick are for markers 576 and 444.
  • The GD of 3 between Paul and Jonathan are for markers 576, 391 and CDYa.
  • The GD of 3 between Rick and Jonathan are for markers 444, 391 and CDYa.
  • The STR tree gets more difficult to draw further back from the present time. This is because more variables come into play such as parallel mutations and back mutations.
  • It would be possible to draw a STR Tree for the Grant, Hayes, Stewart, Chisum, Whittaker Tree, but I will leave that for another time.

Summary

  • The Big Y test for Paul and Jonathan have defined shared SNPs for the Frazer line and Private SNPs for the Archibald and James Lines
  • Ricks STR test has defined shared STRs for the line of James Frazer who was born about 1804. Any future testers from this line should be able to confirm descent from this line by testing for 391 = 11 which is a slower moving STR. CDYa would be a less reliable STR as it is a STR which changes much more often than most.
  • STR mutations that are unique to Rick and Paul cannot be dated precisely as they could have happened anytime after James Frazer of 1804 was born until Rick and Paul were born. That would be roughly between 1830 and 1950.
  • At the 67 STR testing level, on average, one STR change takes place about every 140 years. Jonathan shows no STR changes the way the chart was drawn. This would be less than average for him. Paul and Jonathan should have had 2 changes each, but each had 3 changes. This means they got the extra two STR changes that Jonathan should have had since 1690. It all averages out.
  • All this DNA testing makes me feel more close to my Canadian Frazer cousins.