Hartley DNA & Genealogy

My Haplogroup is A11134. I share that group with 7 people of Hartley Surname (though one changed his name to Hartley, partly as a result of the testing). An 8th BigY tester in the A11134 group has Nutter heritage. His is the most recent results. Here is where Nutter is under A11134 in the lower right below. This shows he shares A11134 with two other Hartleys

My previous analysis of Nutter’s results and other Hartley results has left me with some questions that I would like to look into further. Previously, I had been working on this list of Variants:

BAMsAway

This is a Chrome Browser extension that looks into positions on the YDNA BigY test that FTDNA may not provide information on. Recently, I was looking at Nutter’s Private Variant with Position number 5672076. It appeared from my download that FTDNA had not tested that location for me. However, using BAMsAway, I see this for that position looking at my results:

This shows that clearly I was negative at this position. While I’m at it, I’ll check all my Variants that I previously thought were not covered by my test:

I’m not so concerned about the last three testers, as I know more about their genealogy back to the 1600’s. However, the first two positions that I checked were clearly negative, so that is a good sign.

6906758

This position is interesting as Nutter showed that this was one of his Private Variants at YFull based on his non-FTDNA testing. I show negative for the Variant:

Here is what Nutter’s results show:

I am not sure why Nutter’s results did not show this as a Private Variant at FTDNA. This may be something to look into further.

BAMsAway ‘No Reads Found’ at 13807922

Here is the first Variant that I looked up with no reads found:

Here is how the Browser displays:

However, the position number does not show. I suppose this would make sense if there were no reads. I showed this result in blue on my spreadsheet:

 

I had previously shown this as not tested and ‘no reads found’ is the same thing. This is the first BAMsAway result that confirms what I thought to be the case previously. Here is what Nutter shows at that position:

Here there were only 2 good reads. Many assume that 10 good reads are needed by FTDNA, so this Position has some logic to not being a Private Variant for Nutter.

My Results Adjusted by BAMsAway

Out of 10 positions I showed Not Tested, 8 of those were tested and found negative. 2 of those positions were actually no reads (or not tested). Those two Positions corresponded with Nutter’s Private Variants at YFull which were not considered Private Variants by FTDNA. When I check Nutter’s Position 19374424, I see that there were no reads at FTDNA:

I am thankful to David Vance at the L513 Facebook Page who steered me to BAMsAway.

Updating My Brother’s Results

My guess is that my brother’s BigY BAMsAway results should be similar to mine. After some copying and pasting into BAMsAway, I get these results for Jim:

For Position #13669903, BAMsAway confirms that Jim only had one read (but that was a negative for the Variant).

Updating Steve’s Results

FTDNA shows that Steve has 5 Private Variants:

The arrow points to the BAMsAway extension for the FTDNA Chromosome Browser. When I choose the extension a popup asks me to add the new SNP name or position:

When I do that, a new position is added to Steve’s list of Private Variants:

I choose the user added position to get this:

This shows that Steve is clearly negative for this Variant. He has no mutation from ‘T’. Here are Steve’s results:

This gives clarity to show that Steve is negative for other A11134 testers’ Private Variants. He gets a No Read for 19374424. This is apparently in a difficult to read portion of the Y Chromosome.

John N’s Results

So far, my chart is shaping up well. John has four Private Variants.

I gave John N a questionable for 13807922 as he had only 4 reads. However, they were all negative. I would say negative. John N also has no reads for 19374424.

Summary of Steve, John N and Nutter

These are the three who tested postive for A11134, but did not form a branch below that level. My major question is why Nutter does not have a Private Variant at 6906758. I will likely write to FTDNA to ask why. I had previously checked Nutter’s results to make sure that he was negative for the 7 SNPs in my Haplogroup. Those are the 7 SNPs at the end of the list above.

Michael, Lawrence and John R

These three BigY testers are in a separate genealogical group that I call the Quaker Line of Hartleys. The ancestor of this group escaped persecution in Lancashire, England and came to Quaker-friendly Pennsylvania around the year 1700. The genealogy of this group can be traced to some time in the 1600’s.

Because I had added NTs or Not Tested to their list based on their incomplete downloadable files, I would like to correct that information using the BAMsAway extension. That will corrrect my comparison chart of Private Variants.

Lawrence and Position 7153793

One of the first interesting results is for Lawrence in position 7153793:

Lawrence has three positive reads for this position. I could argue that this result should form a new branch of ‘Quaker’ Hartleys. YBrowse has two SNPs for this position, but the first is a G to C mutation where Lawrence has a G to A mutation:

The second SNP is listed twice for some reason, but has the G to A mutation:

My feeling is that Lawrence should be in a new Branch called MF205420. This is also consistant with the genealogy:

John and Lawrence share a branch. However, Michael would have to be negative for this Variant for this to be a true Branch separate from John and Lawrence. Michael had an older test:

His test did not cover that position. That means that it is not clear whether MF205420 would apply to all three testers or just two. So this is a case where there should be an extra SNP, but it is not clear where it belongs.

Here is the end of what I looked up for Lawrence:

I indicated in the notes that Lawrence had 3 positive reads. For 13807922, Lawrence had 2 negative reads which would be expected.

John R’s BAMsAway Results

I have five more NTs to get rid of. There were no surprises with this recent BigY test:

This is what I have so far. It was interesting to look at the results. You don’t know whwat you will find until you look. It would be interesting (but take a little work) to fill in the rest of the blanks.

More on Lawrence

Larwence has 6 Private Variants:

Here I filled in the rest of Lawrence’s blanks including the SNPs from my branch of Hartleys:

 

 

Quaker Line Michael

Michael took the older BigY500 test. I had missed one of his Private Variants last time, so I will add that in:

Michael may find more Private Variants if he updates to BigY700.

Michael had 2 negative reads for one of Lawrence’s Private Variants. He also had no reads for two of my Branch’s newer SNPs which makes sense.

John R’s Results Completes the Quaker Hartley Analysis

• Here we see the difference between Michael’s BigY500 test and Lawrence and John R’s BigY700 test. Michael has many more ‘no reads’.
• Where there is more than one B? in a row, my note at the end is ambiguous
• I probably should have had different colors for the B? designation depending on whether the low read was positive or negative.
• Some results are more important than others. For example, the results within the Hartley Quaker Group is more important than comparing the Hartley Quaker Group with the non-Quaker Group as we know that those two are not closely related by genealogy.

Filling In Nutter

I did see one unexpected result here:

Nutter had 7 positive reads for a Private Variant that John R in the Hartley Quaker Group had. I made the notation withing the cell and added that the mutation was G to A. Here is what John R shows:

That means that it looks like John R’s Private Variant is not really Private. That is why it pays to look at each of these positions.

MF205420

This Position describes MF205420 which I mentioned above. Apparently, this could be another Hartley-wide Variant. Now I want to see the results for the other Hartley BigY testers. Here it looks like I have found a new Hartley SNP:

However, to be sure, I need to go upstream one level to Mawdsley:

He has 9 negative reads for this position. What that means is that John R’s Private Variant of 7153793 should actually be SNP MF205420 in the A11134 Hartley Group:

Here I have pointed to where MF205420 should be added. Here John R had at least 10 reads, so the 10 read rule came into play:

I just need to convince FTDNA to add MF205420 to the Hartley Group. MF is apparently the designation for a Chinese Company. So far, it has paid off to look at all these positions.

Filling in John N’s Blanks

I don’t see any surprises here:

Filling in Steve’s Blanks

No surprises here.

Joel and Jim

Any difference between these two brothers should be from testing coverage.

It doesn’t look like a lot, but it took a while to get all this information. The two recommendations are noted in yellow in the Note Column. The yellow BY is the same as the Y for the last 7 SNPs in the list. The BNR is equivalent to what I thought I was getting in my previous list where I had NT for Not Tested.

 

Summary and Conclusions

• I had tried to do an analysis of A11134 BigY testers using downloadable files. However, the results were confusing and I found out that these files are not complete.
• I used BAMsAway and found the complete picture
• From my analysis, Nutter needs one more Private Variant than he has.
• Also, the A1134 should have one more SNP in it’s group for a total of three SNPs. The new SNP would be MF205420. That SNP is now a Private SNP that John R has from the Quaker Hartley group. However, 5 other testers who had reads all had positive reads for that SNP (though below what FTDNA usually finds adequate).

 

 

The long awaited Nutter BigY test results came in. As expected by previous testing, he is A1134. The tester’s name is not Nutter but changed along the way at some point. I will call the tester Nutter or Michael for privacy reasons. Here is my list of BigY Matches:

After my brother, the new tester, Michael, is my next match. This may or may not be significant. the listing is based on the number of Non-Matching Variants. I have fewer Non-Matching Variants with Michael (other than with my brother) than with other BigY testers. I will be looking at Variants in greater detail later in this Blog.

I and my brother are fifth and sixth on Michael’s match list. The first 7 testers on the list are Hartleys (other than Michael). After that, there are other surnames. This indicates to me that Michael’s ancestors were likely Hartleys at some point in history. Tester #8 on the list Mawdsley and those after likely have a common ancestor before the time of surnames. Also Mawdsley and others have an earlier Haplogroup than the first 7 testers.

Michael in the Block Tree

One way that FTDNA shows test results is in a Block Tree. Here is the Block Tree from Michael’s viewpoint:

The part that says ‘Your Branch’ actually has three people in it: Nutter plus two of his Hartley matches.

I didn’t show that part of the Block Tree that has Mawdsley. He is further to the right under A11132. This shows that:

• Michael is the only Nutter under A11134
• My branch of FT225247 on the left has 7 variants under A11134
• There are 4 variants under A16717
• Under Michael’s branch there are 3 Private Variants on average
• The people in the bottom block represent now. That means the time back to the A11134 should be about the same for each of the three branches above.

Michael’s Private Variants

Why are these important? These represent Michael’s Line since the common ancestor of the A11134 group that he is in. Above, note that those in Michael’s group have an average of 3 Private Variants. However, right now, Michael’s results show that he has two Private Variants.

These two Private Variants show as numbers which are position numbers on the YDNA. So far, no one in the world has tested positive for these two positions. Once a match is found to one of these two Positions, they will form a new branch of mankind. This would be a branch that is likely in common with the Nutter name.

Position 15646418

This position is already in YBrowse. That is probably from when Michael tested with another company.

That SNP is named Y354187. The Y designation is from YFull.

YFull gave this SNP a name when Michael uploaded his results there last year.

5672076

I suspect the same is true for 5672076. This SNP is called Y354148:

Comparing Michaels Results with Other A11134 Testers

This part may get a bit boring, but it is necessary. There is only one way to match with another tester. However, there are different ways to not match:

• One tests postive and one test negative for a SNP
• One test positive and another’s test does not cover that SNP
• One tests negative and another’s test does not cover that SNP

Then there are incomplete test results which further complicate matter. Usually there need to be about 10 reads to have a good test result. If there are less than 10 reads or some reads are positive and some are negative, you get into a grey area.

Here is what I have so far in comparing Private Variants:

This shows who tested for what:

• Y means positive
• N means negative
• NT means the test did not cover that position
• ? means inconclusive

Above, Joel and Jim are A11134 > FT225247; Steve, John N. and Nutter are A11134 and Michael, Lawrence and John R. are A11134 > A16717. I am not sure what the blanks mean.

Here I’ve added a column for Nutter’s FTDNA results as the previous column was for his other test. I was already tracking SNPs Y354148 and Y354187 which I mentioned above. I would also like to add the SNPs in my branch as there are so many.

Here I have shown that Nutter has none of the 7 SNPs in the branch of Hartleys that my brother and I share. Next I went through the Private Variants of the other BigY Testers and checked to see if Michael tested positive for any of those Private Variants:

This shows that Nutter did not test positive for any of the other testers’ Private Variants. For example here is Nutter’s results for 11071280 which was one of Steve’s Private Variants:

Because Nutter’s Genotype is the same as the Reference, that means that Nutter is ancestral or not positive for that Variant. It is confusing, because these results were found in a download called Derived Variants (which is the opposite of Ancestral Variants).

What this means is that no new branches should be formed based on Private Variants. If my analysis was correct above, it also indicates that none of the other 7 Hartley tests covered the Nutter Private Variants. Nutter should have on average 4 Private Variants, so the two that he has are probably right. That means that the Nutter line had mutations about twice as slowly as the average. On the other hand, my Harltey Branch had 7 mutations during the same time period with mutations about as twice as fast as average.

A11134 Time Tree

Nutter is not yet on the FTDNA Time Tree. That Tree estimates that A11134 formed around the year 1450:

Hartley Branches under that formed at a later date. For example, FTDNA says that A16717 formed around 1650:

This date follows closely the genealogy of this branch:

These are the YDNA testers under A16717.

 

It would stand to reason, that other Hartley Branches formed around the same time as A16717 in the 1600s:

I drew an arrow to FT225127 where my brother and I and two other Hartley Lines are. The Nutter Line will be added in that same area.

Summary and Conclusions

• The new Nutter BigY test shows that he is in the A11134 Branch, a Branch formerly held only by Hartleys
• Nutter has two Private Variants which defines his own private line
• Nutter forms a fifth branch under A11134. However, three of these branches are not named yet and won’t be named until they get matches withing those branches
• My guess is that these branches formed in the 1600’s and represent an explosion of the Hartley surname
• My interpretation is that this Nutter tester had a Hartley ancestor probably in the 1600’s.
• The next step is to see the Nutter BigY results added to the FTDNA Time Tree. I don’t know if those results will make a change to the date of A11134.

 

I was informed recently by a person with Nutter surname heritage that there were some changes at YFull in my area of the YDNA Tree. Here is the current YTree:

YF00890 is Smith. YF106096 is Nutter and the last two ID numbers are my brother and me.  When I press the live button on the tree, I get this:

This is how the YTree looked for A11132 late last year:

This just included Nutter and myself. This must have changed when I added my brother’s kit. Notice that this had a formed date and a TMRCA. Last year’s formed date of 1700 ybp seems way off as that would be roughly the year 300 AD. Here is what FTDNA has:

Changes under A11132

First, I will look at changes under my branch. It makes sense that I would be under a new branch by adding my brother. At FTDNA, that branch is called FT225247. At YFull it is called A11136. What the A11132 tree is telling me that my brother and I share all the SNPs under A11132. They are:

• A11132
• A11134
• A16716
• A11135
• A11137
• A11140

It also tells me that we don’t share:

• A11133
• A11136
• A11129
• A11130

This is consistant with Variants that my brother and I have under FT225247:

 

The difference is that the Mawdsley BigY tester does not have his results posted at YFull. He is the one that split the previous A11132 into A11132 and A11134. As Nutter tested positive for A11134 and A11135, he would be A11134 also.

A11138 to Y82274

Mr. Smith who was in the former A11138 group would be better positioned to do this analysis, but I’ll see what I can see from my viewpoint. Here is the present (non-Live) view of the YTree:

This shows that Mr. Smith with the low ID# shares his group now with two new memebers. One member appears to be from Australia or have ancestors from Australia. The Tree shows that A11138 has three SNPs:

• A11138
• FT22040
• MF205420

This is interesting because A11138 used to be in it’s own group of one.

Here is the new designation under the ‘Live’ Tree:

Now Mr. Smith is under Y82274 (which is under A11138) and the new testers are under Y82274 at Y445810. Mr. Smith’s Y82274 appears to have 19 SNPs, so would be quite old. Y445810 is in a group of 4 SNPs, so would be younger. These new testers must have not tested at FTDNA as they do not show up there. So, as I was writing this Blog, Mr. Smith who was previously A11138, got pulled down to Y82274, then the two new testers were more closely relataed to each other. They left Mr. Smith at Y82274 and moved down to the newer Y445810. The next step is for YFull to come up with TMRCA numbers. Most people greatly appreciate having those dates. This is one case where YFull has more testers directly under this branch of A11138 than FTDNA has, so their estimates should be more acccurate.

As there are four SNPs in Y445810, that could indicate that SNP is from around the 1600’s. However, it may be earlier if the two new testers have private variants. My guess is that there will be little difference between the date of A11138 and Y82274. YFull previously had A11138 around the 350AD and FTDNA has it at around the year 500AD.

Why So Many SNPs for Y82274?

Or, the question could be, why does Smith have so many SNPs now? My guess is that is because he took the older BigY500 test. This test covered less of the Y Chromosome compared to the newer testing. When the new testers tested, it was clear that they shared many of their SNPs with Smith. Under the older testing at FTDNA, Smith had 11 Private Variants since A11138:

Now, he is showing 20 SNPs at YFull:

In addition, Mr Smith likely has Private Variants in parallel with the 4 extra variants that the new testers have. That means that as a result of the new testing, Mr. Smith’s Variants have about doubled.

Summary and Conclusions

• R-A11138 is under a state of flux due to two new testers
• A11138 used to be held by Mr. Smith. He is now at one level down at Y82274.
• The two new testers are one level below Y82274 at SNP Y445810.
• YFull has not come out with new date estimates for A11138, Y82274 and Y445810. This will be important as the new testers are not at FTDNA.
• My brother and I are now shown as A11138. However, FTDNA has many more teseters in this area. That means that their tree and dating should be much more accurate than what YFull has.

 

 

I wasn’t sure what to call this Blog. I have been following the YDNA test results of a Nutter descendant with interest. His YDNA results have been showing a connection to my general branch of the Hartley Family. The results of other Hartleys who have taken the BigY test show like this:

All those so far under R-A11134 are Hartleys. One tester who is A11132 is a Mawdsley. The connection between Mawdsley and Hartley could be right around the time that surnames were coming into use.

Nutter’s 111 STR results

While we are awaiting Nutter’s BigY results, I will look at his 111 STR results. STR results are much more difficult to interpret compared to the BigY SNP results. That is because STRs can mutate backwards or forwards. In other words, the mutations can increase or decrease.

Here are the STR results of those Hartleys in my general line who have taken the test and have joined the Hartley YDNA Project at FTDNA:

My brother and I are in the last group. The group above us are Hartleys with a Quaker ancestor who left England to move to Pennsylvania in colonial days. The top person is Mawdsley who is closely associated with the Hartleys at R-A11132. The rest are Hartleys in the R-A11134 category. The first two in the A11134 group have only tested to 12 STRs which is not very helpful. Note that many of the genealogies get stuck in the 1700’s. It is very difficult to do the genealogy in England at that point due to the number of Hartleys in the Colne, Lacnashire area. This is where many of the Hartleys came from.

I have an arrow in the column where the new Nutter results are. The person above Nutter tested to 111 STRs. The person on the list below Nutter tested to 37 STRs. Nutter and the Hartley below him have a match on this STR:

They both have a value of 20 for DYS458. Of the 12 Hartleys who have tested to this level, only these two have a value of 20 for the STR named DYS458.

Here is a comparison between Nutter and the Hartley tester listed above him:

At STR DYS710, both these two have a value of 36. This may be more difficult to interpret as two of the Quaker Hartleys and the more distantly related Mawdsley tester have this value.

Building a STR Tree

These trees are difficult to build and interpret, but I will give it a shot. These trees are easier to build when the BigY SNP results are in, because those results are so much easier to interpret. Previously I have considered two models to intepret the STR results. Here is the first:

This tree only has six people in it, so I think that some are missing. I count 9 Hartleys who at the FTDNA Hartley YDNA Project who have tested to 111 STRs. I see also that other changes will be needed as I don’t see DYS710 listed in the tree. Also I don’t see DYS458 listed.

Here was my second model:

It looks like a major overhaul of this tree is needed. It looks like I only did the tree for those who took the BigY test.

111 STR YDNA Hartley Tree Overhaul

This appears to be the raw data involved:

I had trouble matching the STR names to the columns. Previously, I had used a program called SAPP to try to analyze these STRs. I’ll try that again. I downloaded the information for all testers in my Hartley group except for the two that tested for only 12 markers. This goes into a text file where the first line is /STRDATA.

Here is what pops out:

The program comes up with four main branches. Here is some further identification:

It seems like the results are generally accurate. Nutter is near the middle of the chart. He is with the other Hartley I mentioned earlier with a DYS458 value of 20 (red arrow). My brother and I are on the bottom row. I would say that the depiction is generally correct. Between Nutter and his closest match on the tree, the Time to Most Recent Common Ancestor is 1750. Here is what FTDNA shows for the GD of 2 between Nutter and his closest Hartley 37-tested STR match:

The third line indicates a GD of 2. FTDNA estimates a aTMRCA of 1650 for that GD. However, whether this is more or less accurate than the SAPP tool, I don’t know.

For the Quaker Hartley group, the TMRCA is 1550 according to SAPP. The known common ancestor is from 1666. However, it is within the SAPP Tree range of 1350-1700. There are more than the usual mutations for this line which make the TMRCA seem older.

The TMCRA for this group of Hartleys is shown by SAPP to be 1550. This does not seem unreasonable to me. I did not include the Mawdsley STRs in this analysis as he is from an earlier SNP group of A11132.

One other point is that there are other adjustments that can be made on the SAPP Tree. One would be to add SNP values where known. Another interesting feature is the thickness of the lines on the tree are meant to indicate confidence of relationship. For example, the thickest line is between me and my brother. The program does not know that we are brothers, but it does know that we both tested to 111 STRs and have a close match.

SAPP Tree with SNP Data

For the kits, I have added this insformation:

This reflects the BigY testing. Here is how the SAPP interprets my input:

Here is the tree that it produces:

Notice that many of the lines are now in darker blue showing more certainty. One somewhat surprising result is that it projects that two of the Hartley kits are outside of A11134. Those are the two yellow kits on the second row above. I had assumed that all Hartleys that were in this group were A11134. Based on SAPP these two kits may not be A11134.

Here is some further output from SAPP:

I watched a video explaining the program. The red numbers in the second chart show the adjusted genetic distance due to parallel STR mutations. So for example, it shows me at kit 275990 as being a GD of 12 from Quaker descendant 617805 instead of the GD of 9 that FTDNA shows. That is because the Quaker descendant had some of the same mutations that I had but they happened in a parallel manner on different branches.

Once Nutter’s BigY results are in, the SAPP Tree could change also as we will have more SNP information. The only further modification would be to add Mawdsley to the tree.

SAPP Tree with A11132 Mawdsley Added

• Now the Quaker Hartleys are on the bottom left. Oddly, the tree now shows the correct sub-branching for the three Quaker Hartley descendants.
• Now there are four Hartley testers showing outside the A11134 realm on the third row from the top. These four are in groups of two each.
• I did not add any genealogical information for the chart. I could have added some for the Quaker Branch, but the program sorted that out before I did that.
• This seems to be as good as I can get the SAPP Tree with the information that I now have.

Actually, I do have a refinement I could make to the chart as the Nutter descendant is A11134. This is from previous testing at another company. Here is the results:

This pulls Nutter with the ‘B’ kit back into the A11134 realm (both circled). This should be now the best SAPP Tree I can come up with given the information I have.

Nutter Genealogy

I have covered Nutter Genealogy in past Blogs. It appears from the STRs, that Nutter’s closest STR match has Hartley genealogy:

The SAPP tree predicts a common ancestor around the year 1750 which is interesting. That means that either the Nutter genealogy or the SAPP Tree prediction for a TMRCA could be wrong. The Hartley tester who has James Hartley as his ancestor has not posted a further Hartley Ancestry Tree at FTDNA.

Summary and Conclusions

• The Nutter 111 STR results add important information to a part of the YDNA tree of mankind
• If correct, the STR results link Nutter with a kit who traces his genealogy back to James hartley born 1788.
• Running the SAPP Tree with different inputs gave interesting results. One result was that it showed a possibility that not all tested Hartleys are neccesarily A11134 as I had previously supposed.
• I await Mr. Nutter’s further BigY testing results