Friday, 16 December 2016

L2 MHT - Recommendations for further SNP Testing

So far in Lineage II, we have SNP marker data from 10 "Big Y" tests - the tenth one came in last week and is currently being assessed (member G65, 371202, MGG). Together with the STR marker data (i.e. the Y-DNA-37 test most people took when joining the project), this has allowed us to group people into separate branches of the Mutation History Tree for Lineage II (the L2 MHT for short; as discussed in the recent posts).(1) The pioneers of Lineage II who undertook this Big Y testing have paved the way for a more cost-effective, money-saving SNP testing strategy for the rest of the group, so a debt of gratitude is owed to these project members. Thank you, guys! 

As a result, only in rare circumstances will it be necessary for new members to do Big Y testing ... this will only happen if there is a new distant outlier to the rest of the Lineage II group. And this will happen from time to time as more people join our group.

The new SNP Testing Strategy involves collaboration with another DNA testing company - YSEQ. This is a specialist company headed by husband and wife team, Thomas and Astrid Krahn. Both of them used to work at FamilyTreeDNA but left to form their own company to address a gap in the market. Their niche company offers bespoke SNP testing. In discussions with Thomas, we have come up with a highly cost-effective strategy for further SNP testing in Lineage II. This will allow us to achieve our goals and save money at the same time.

The SNP Testing Strategy is in three phases:
  • Phase 1 - the YSEQ Z255 SNP Panel
  • Phase 2 - SNP Block testing
  • Phase 3 - Private SNP testing
All three phases are fluid and a person may jump between Phases 2 and 3 depending on what the results of new testing reveal.


Phase 1 - the YSEQ Z255 SNP Panel
This will be the starting point for most new members, for most people who have only tested to the 37 marker level, and for the 9 members who are currently ungrouped in our L2 MHT.  The YSEQ Z255 SNP Panel includes 6 SNP markers that are immediately relevant to Gleeson Lineage II.

First off, YSEQ is offering us discounted testing with their Z255 SNP Panel. Luckily for us, their Z255 SNP Panel offers more Lineage II-relevant SNP markers than the corresponding Z255 SNP Pack from FTDNA. YSEQ's Panel covers all the six "most downstream" branches identified so far for Lineage II. These branches are represented by the SNPs in the green boxed portion of the diagram below, namely A5631 (aka Y17108), A5628 (aka Y17112), A660, Y16880, A10634 (aka BY5706), & A10640 (aka BY5707). In addition, new branches can be added to this panel over time, so it will adapt as Gleeson Lineage II grows.

YSEQ's Z255 SNP Panel covers all 6 confirmed branches of Lineage II
FTDNA's Z255 SNP Panel (Dec 2016) - only covers 1 of the 6 branches of Lineage II

The usual price of the YSEQ Z255 SNP Panel is $88 (cheaper than FTDNA's panel) but we are getting it for a considerable discount. Not everyone within Lineage II needs to do this as the revised Mutation History Tree predicts which branch many people are likely to fall on. And simply doing a single SNP test with YSEQ (for $17.50 or less) might be all that is needed to confirm the prediction. More money savings! 

So only the following people need do the Z255 Panel (because their placement on the tree is uncertain and needs clarification):
  • the 9 people who are currently ungrouped in the L2 MHT - see footnote (2)
  • Branch E - any one of the 3 members (G91, G75, G84) could do the test - this will tell us whether or not this Branch is more closely related to Branch B or Branch C
  • Branch F - one of G97 or G98 could do the test to confirm or refute their supposed close connection to G65 (371202, MGG)
So at the moment, the recommendation is for 11 people in total to take the YSEQ Z255 SNP Panel. I will be writing to these people individually over the course of the next week in order to organise funding and ordering of the new kits (they will have to swab again as it is a different company).


Phase 2 - SNP Block Testing
For those people whose sub-branch is easily predicted from their STR results, the Z255 SNP Panel is not necessary. Instead they can jump straight to single SNP testing to confirm which of the 6 major branches they belong to. Once this has been confirmed, the next step would be to test for any "phylo-equivalent SNPs" - in other words, SNPs that occur in the same "SNP block" ... and there are 4 of these in Lineage II, highlighted in the diagram below. This stage of the testing is likely to split these 4 blocks into smaller blocks or even single SNPs, and in this way the number of branches associated with Lineage II will increase, possibly to as many as 18 unique "Gleeson" branches.


The 4 current SNP Blocks of Lineage II

Branch A of the L2 MHT
Currently, there are two people in the project that are at this stage of testing, both of them in Branch A (G54 & G79). These two people are predicted to belong to Branch A (both in the L2 MHT & the SAPP Tree). Both members should test for the single SNP A660 and if positive (95% probability) they should then go on to test for the remaining five SNPs in that particular SNP Block. The chances are that they will be positive for some of them and negative for others. This will "split" the block into two pieces. For example, G54 & G79 may test positive for the first 3 SNPs and negative for the other three. The block will thus be split into 1 section with the first 3 SNPs (with G54 & G79 sitting underneath it) and a second section beneath that with the last 3 SNPs, and the current members (the 3 brothers - G39, G51, G73) sitting underneath that.

In addition, this would identify a new branching point within Branch A, and one (or more) of the defining SNPs could then be added to YSEQ's Z255 SNP Panel. This would benefit future testers.



Phase 3 - Private SNP testing
The third phase is testing of Private / Unique SNPs (i.e. SNPs that are currently unique to one or more specific individuals). These Unique SNPs have been identified via a collaborative effort of many individuals, including Thomas Krahn himself, Alex Williamson, James Kane, the teams at FTDNA and YFULL, various Haologroup Project Administrators, and many others. You can read previous blog posts of how these SNPs were identified below:

The current set of Unique SNPs associated with Lineage II members (3)
(red dots indicate SNPs covered by YSEQ's Z255 SNP Panel)

Currently, there is no one in the project at this phase of testing. But if the Z255 Panel testing of Branch F members confirms a connection between G65 (371202, MGG) and either G97 (524241, PG) or G98 (437908, WG), then G97 & G98 would undertake single SNP testing of the Private / Unique SNPs of G65 (our 10th & most recent Big Y tester). He appears to have 9 Private SNPs (based on preliminary analyses). Testing all 9 SNPs individually would usually cost $351 at FTDNA ($39 per SNP), and $157.50 at YSEQ ($17.50 per SNP = 55% cheaper) but Thomas is offering substantial reductions from the usual YSEQ price if we order in bulk. This SNP Testing Strategy is a lot less expensive than doing the Big Y test at FTDNA (usually $575).

Similarly, if any of the 9 currently-ungrouped individuals (doing the Z255 Panel) test positive for BY5706 as a terminal SNP (and therefore fall into Branch D), they can start single SNP testing of the Private SNPs of members G05 (86192, RLG) & G68 (411177, CG). G68 has 5 Private SNPs and G05 has 1, so it would usually cost $234 at FTDNA, and $105 at YSEQ, but again, Thomas is offering a substantial discount on the usual YSEQ prices if we order in bulk.

Thomas proposes to test for these SNPs sequentially, as this will allow substantial reductions in the cost of doing these tests. And the more people who test, the greater the reductions will be.

Thomas will not test all the SNPs at once. Instead he does sequential testing of single SNPs, usually 1 SNP every 1-2 weeks, and thus the results will trickle in over the course of several weeks or months, and decisions on further testing of the group will be based on the results of the previous test.

In addition, Thomas will add every reasonable new branch to the YSEQ Z255 Panel where new results (e.g. from additional Big Y testing or the above SNP Testing Strategy)  identify at least two people who share the same new branching point (characterised by a new SNP discovery) and are different in at least one other SNP.


Summary
So to recap, the new SNP Testing Strategy involves the following potential steps:
  1. Test with the YSEQ Z255 SNP Panel for those whose predicted placement on the Mutation History Tree for Lineage II needs further clarification
  2. Test for phylo-equivalent SNPs (within the same SNP Block) - this may split the block
  3. Test for Private / Unique SNPs - this may identify new downstream branching points
I will write to all 29 Lineage II project members individually with a bespoke testing plan for each member. I will calculate the price, ask all project members (who are willing to take part) to pay the relevant amount to the General Fund, and then I will pay for the tests via bulk order to get the maximum discount. Thomas will then send new (YSEQ) kits to the relevant people so that they can swab their cheeks and get tested.

In this way, the MHT for Lineage II will continue to grow progressively and will increase in complexity and accuracy. This will allow people to see how closely they are related to everyone else within the group and at what timepoint the common ancestor they share with any of the other members is likely to have been born. This information will facilitate more focussed genealogical research using documentary records. (4)

I will also be writing to individual project members to review the genealogical information they have supplied. Now is a good time for everyone to update that information. At the very least everyone should have supplied their basic MDKA information and their Gleeson pedigree. But to really optimise the chances of breaking through your Brick Wall, you should have the information detailed in my previous post about the MDKA Profile. I will review this information with each project member over the course of the next several weeks.

Maurice Gleeson
Dec 2016


Footnotes:
(1) the current pdf version of the L2 MHT is available in three parts:

(2) Here are the 9 currently-ungrouped members who should test with the YSEQ Z255 SNP Panel (listed by G-number, kit number, and initials for ease of reference):
  • G99 ... 437986 ... MIG
  • G81 ... 458407 ... BEG
  • G89 ... 498597 ... OMG
  • G77 ... B78262 ... SG
  • G70 ... 371145 ... DG
  • G78 ... 446153 ... AG
  • G92 ... 438324 ... TOG
  • G95 ... 437988 ... TEG
  • G94 ... 437987 ... GMG

(3) These are based on Alex Williamson's analysis from the Big Tree 

(4) Incidentally, Judy has rearranged the order of project members displayed on the DNA Results page of our WFN website to match the current new groupings in the L2 MHT. See below ... 


The DNA Results table for Lineage II on our WorldFamilie.Net website
(click to enlarge)








Wednesday, 14 December 2016

L2 MHT - "difficult to place" people

When we put together the revised Mutation History Tree for Lineage II (L2 MHT), there were 9 people who could not be confidently allocated to sub-branches of the tree. We are going to use two techniques to attempt to place them on the MHT and the first of these is Dave Vance's SAPP programme. We will explore Robert Casey's methodology in a subsequent post.

The SAPP programme is like a turbo-charged version of Fluxus especially designed for genetic genealogists. Fluxus is the software programme I used to help generate the first version of the MHT last year. It is a programme that uses STR data to generate a phylogenetic tree (a.k.a. cladogram or phylogram or Mutation History Tree). The SAPP programme also generates a phylogenetic tree based on STR data, but it has some additional features that make it way superior and far more elegant and user-friendly: 
  • the output is more like a family tree, and less like assembly instructions for Swedish furniture (it's an oldie but a goodie)
  • unlike Fluxus, it incorporates SNP data so that the upper branches of the tree can be anchored effectively 
  • it recognises similar STR signatures and takes these into account when grouping people 
  • it recognises people with known genealogical relationships and groups them together
These features make the SAPP programme a great time-saver and an excellent way of double-checking your work if you have created your MHT manually, as I have. It takes a lot of trial and error (40 minutes in my case) to get the data input "just right" but once you have done it correctly, the output is impressive.

Below is the SAPP Tree output from the SAPP programme for L2 (with some of my own graphic additions) and below it (for comparison) the output from my manually created L2 MHT. You can download higher quality pdf versions of these files from Dropbox by clicking on the captions below each individual graph. And that's the first point - the detail in the images is not easy to see. There is a lot of information concentrated in a small space and that makes reading it very challenging. We have the same problem when trying to navigate through our family tree - it will never all fit on the same page. Best to click on the Dropbox link (the caption below each graph) so you can view it in a separate bowser window, or download the file and open it in a separate programme on your computer.

This SAPP Tree includes all 29 members of Lineage II. The 9 previously ungrouped individuals are indicated by a dashed red border around the relevant boxes. Most of them are sitting away from the SNP-confirmed branches of the tree - the exceptions are G77 under Branch A and G99 & G81 under Branch D.

What you can just about make out without enlarging the image is the colour-coded branches in each version of the tree. There is good concordance between the two trees with regards to Branch A & Branch B (both SNP-confirmed branches) - both have the same membership, the same (or complementary) STR mutations listed, and similar placement on the larger tree in relation to each other.

However, although Branch C (also SNP-confirmed) & Branch E have the same membership in both trees, & the same (or comparable) STR mutations listed, their placement in the SAPP Tree is different - SAPP says Branch E could be genetically closer to Branch C than Branch B. Further SNP testing will be needed to determine this.

Branch F is split in two in the SAPP Tree, with members G97 & G98 sitting quite distantly away from G65. Determining which tree has the correct placement will only be decided by additional SNP testing. The split in Branch F  has also caused a split in Branch D - this is not too surprising as the two members on this branch (G05 & G68) are very distantly related and I am sure this particular branch will split into several smaller branches in due course as more SNP testing is undertaken. In addition, Branch E has also split Branch D and has been placed very differently compared to the other tree.

The SAPP Tree for Gleeson L2
(click image to enlarge, click caption to download pdf)
My L2 MHT for Gleeson Lineage II
(click image to enlarge, click caption to download pdf)

The SAPP Tree raises some important considerations for the Gleeson L2 MHT:
  • It revealed a few data omissions on my part (so it was a good way of verifying my data)
  • It generated Genetic Distance tables which I found very useful (see below). The maximum Genetic Distance (GD) between any two members in L2 was 12/37, 12/67, and 18/111 … and Adjusted GDs (taking into account Back & Parallel Mutations) were a staggering 30/37, 29/67, & 29/111
  • In Branch A, the SAPP programme identified a "more parsimonious" configuration of the branch, as a result of which I have slightly modified my version of Branch A (in other words, it identified a better configuration that made better sense of the data - see diagram below). The revised L2 MHT is available from Dropbox here.

The Old & New Versions of Branch A
  • In addition, all 9 people who could not be placed on the tree previously have now been allocated (provisionally) to specific sub-branches. This allows us to see to whom they are (potentially) most closely related. However, the confidence with which these 9 members have been placed on the SAPP Tree is relatively low (compared to the other members, who have either been SNP-tested or have relatively unique Y-STR Signatures and/or supportive Genetic Distance data). Thus their positions on the SAPP Tree have to be taken with a grain of salt. To confirm whether or not these 9 members have been accurately placed on the tree will require additional SNP testing. 

I have been in discussions with Thomas Krahn from YSEQ and have negotiated a specially-priced SNP Testing Strategy for the Gleeson's of Lineage II. And that will be outlined in detail in the next post.

Maurice Gleeson
Dec 2016


Outputs of the SAPP Programme for Gleeson Lineage II





Wednesday, 7 December 2016

Building the Mutation History Tree - Placement

In the previous post we looked at how we can group people together within Lineage II to form sub-branches. Once we have our sub-branches, the next step is to place each of them on the larger Tree of Mankind.

The starting point is the Modal Haplotype (MH) of the Z255 subclade. I obtained this from two sources - the R-L21 Haplogroup Project and Nigel McCarthy's Group E. Both are in complete agreement apart from marker CDYb which has a value of 39 in Nigel's version and a value of 40 in the Z255 Project's version. I arbitrarily chose the value of 40 for my version of the tree.

The Z255 Modal Haplotype (red text) & Branch Modal Haplotype (mutations in green highlight)

I then defined the modal haplotype for each individual branch (which I called the Branch Modal Haplotype or BMH in the Results Spreadsheet) and highlighted the differences between it and the Z255 MH (in green highlight). This identified those mutations which were common to all or some of the sub-branches, and which therefore potentially occurred quite early on (i.e. relatively far upstream) on the Tree, after the Z255 mutation/marker. These included the following:

  • a value of 19 on marker 20 (dys448) for all sub-branches
  • a value of 13 on marker 9 (dys439) for all sub-branches except Branch D
  • a value of 16 & 8 on markers 13 & 14 (dys458 & dys459a) for all sub-branches except Branch F
  • and so on ...

I then visually inspected each sub-branch in turn, marker by marker, and identified which marker values differed from the Z255 MH and if these marker values were unique to that branch. Thus marker 4 (dys391) has a unique value of 10 in Branch F, a value that is unique to this group and therefore helps define this branch. Similarly, marker 2 (dys390) has a value of 23 for each member of Branch F and thus is also potentially branch-defining (it is also present in Branch A and thus could potentially occur further up the tree as a common mutation to both).

Branch-defining mutations on Branch F (bold outline)

I also identified mutations that were specific to individuals and were therefore not branch-defining. Examples include ...

  • the marker value of 14 for marker 1 (dys393) in the results of member G-68 (row 28)
  • a value of 15 for marker 3 (dys19) in member G-79 (row 15)
  • a value of 14 for marker 9 (dys439) in member G-79 (row 15)
  • and so on ... 


The end result is a draft "tree" for each sub-branch. This exercise is best done with a paper and pen initially because there will be a lot of crossing out and moving markers around. You can see in the diagram below that the marker values that are shared by all members of Branch F are written in the upper part of the tree, and the values that are unique to specific individuals result in a branching pattern in the lower part of the tree. Marker values that also occur in other branches and might therefore be better placed further up the tree are indicated with arrows pointing upwards.

Identifying Branch-specific & Individual mutations for Branch F

Once the mutations for each sub-branch had been defined, the next step was to try to hook the various sub-branches together. This was a game of chicken and egg, trying to figure out if some mutations could have occurred earlier in the tree than others. If placing them earlier in the tree resulted in a simpler version of the tree, then the particular mutation was moved up accordingly (this is analogous to the "maximum parsimony" approach used in the Fluxus software programme). Doing so often required additional upstream branches to be created in order to "fit them in".

And lastly, once the tree had been accurately defined on paper, it could be easily transferred into a digital format using Excel to draw the tree.

Simples!
Maurice Gleeson
Dec 2016



The Mutation History Tree for Lineage II (L2 MHT)
(click to enlarge)

A more detailed account of the Grouping & Placement process can be found in this YouTube video.







Building the Mutation History Tree - Grouping

The process of generating the Mutation History Tree for Lineage II (L2 MHT) is not an easy one. It involves many steps and hours of work. I have made a video of the actual process to give you an idea of what is involved and to help other Project Administrators who might be interested in undertaking the same exercise. You can watch it via the embedded video at the end of this post, or directly on YouTube.

The Results Spreadsheet
The basis of the work is an Excel spreadsheet generated from the DNA Results page on the FTDNA or WFN (WorldFamilies.net) webpages. Luckily for us we use both webpages in the Gleason/Gleeson DNA Project - each have their pros and cons. The Results Spreadsheet generated from these results pages is below (for the first 37 markers only. The spreadsheet for the full 111 marker dataset can be downloaded from Dropbox here).

Lineage II DNA Results in the Results Spreadsheet

So what's the difference between this and the results as seen on FTDNA or WFN?

Well, FTDNA & WFN appear to group the Y-DNA results by ascending marker value, column by column. So for example, on the FTDNA results page, the 2nd column is arranged by marker value in ascending order - the 23's first, the 24's after. The ascending order is again seen in the third column - 14's first, 15's after. This biases the listing of members in favour of the values of the markers that occur at the start of the row. In other words, the order of values in any given column is dependant on the order of values in the preceding column. This does not give the best representation of who is most closely related to whom.

Lineage II DNA Results on the FTDNA website
Lineage II DNA Results on the WFN website

The Grouping Process
In my Results Spreadsheet, the project members are organised into specific sub-branches, with a number of ungrouped members at the end of the spreadsheet. The 6 distinct branches (A to F) identified thus far are relatively clearly defined. The grouping process relies on several distinct pieces of information, namely ...
1) Known Relationship
2) Downstream SNP markers
3) Genetic Distance (GD) & GD Demarcation
4) Y-STR Signatures (relatively unique marker values)

1. Known Relationship
Several members are known to be related (highlighted in yellow) and can therefore be grouped together. For example, members G-75 (371160, MG) and G-91 (438302, DG) are known to be second cousins.

Known Relationships (yellow highlight) & Downstream SNPs (red & orange highlight)

2. Downstream SNP markers
The first four branches include members who have tested positive for specific SNP markers (namely A660Y16880BY5706, & BY5707). These SNP markers help place these specific members on specific branches. They also help anchor the upper reaches (the earlier, more distant parts) of the tree. Of note, on Alex Williamson's Big Tree, he places Branch D members G-05 (86192, RLG) & G-68 (411177, CG) on the same branch and so I have done the same in the Results Spreadsheet.

Gleeson Lineage II on Alex Williamson's Big Tree

3. Genetic Distance & GD Demarcation
Some of the members who have not tested for downstream SNPs can still be confidently grouped together. For example, in Branch E, member G-84 (412320, THG) is a Genetic Distance of 1/37 from G-75 & G-91 (known second cousins), but in addition, there is a clear demarcation in the Genetic Distance these three people have to each other and to the rest of the group. In the last line in the text box in the diagram below, you can see that the Genetic Distance jumps from a value of 0 or 1 for all three of them to a value of 3 or 4, demarcating them from the rest of the members in the DNA Project. This information, in combination with relatively unique marker values that they all share, supports their being grouped together.

GD & GD Demarcation

4. Y-STR Signature (relatively unique marker values)
If you look carefully at the spreadsheet, you can see certain patterns associated with specific subgroups. Thus, for example, Branch B is the only sub-branch that has a value of 15 for marker 30 (aka DYS 456). And Branch E has distinctive values of 17, 14 & 17 for markers 23, 31 & 32 (aka DYS 464b, 607, & 576). A similar distinctive pattern of marker values appears in Group F with values of 10, 17, 9, 9, & 17 for markers 4, 13, 14, 15, & 32. These distinctive Y-STR Signatures (together with Genetic Distance data) help to group these people together into their relevant sub-branches. This process is explained in some detail in the video below.

Unique marker values (outlined in bold) define a unique Y-STR Signature for Branch F


Ungrouped people
There are a number of people who have not been confidently allocated to sub-branches as yet. Most of these have only tested out to 37 markers. For these people, using Fluxus software (which I used to generate the first version of the Mutation History Tree) or Dave Vance's SAPP programme or Robert Casey's methodology can help give some indication of where they might sit, and we will look at that in a subsequent post. But ultimately, additional SNP marker testing will provide definitive answers for these particular individuals. And because we already have a lot of information from the people who have previously undertaken the Big Y test, a cost-efficient SNP-testing strategy can be devised for the rest of the group and future members.

Placement
Once the members have been grouped into sub-branches, the next step is to see how these various sub-branches are placed on the larger Tree of Mankind. More on that in the next post.


Maurice Gleeson
Dec 2016



The Mutation History Tree for Lineage II (L2 MHT)
(click to enlarge)










Friday, 2 December 2016

L2 MHT - The Updated "Family Tree" of Lineage II (Dec 2016)

There are currently 31 members in the North Tipperary Gleeson group (Lineage II), 8 new members since August this year and several more on the way. All of them contribute data from at least 37 STR markers to the project. Over the last few months, several people have upgraded their results from 37 STR markers to either 67 or 111 markers.

In addition, we have SNP marker data from 9 Big Y tests, with the results of 1 more test expected shortly (end Jan 2017). This SNP data has identified 4 distinct branches of the North Tipperary Gleeson "Clan" so far, and supplementary analysis of STR data has identified an additional 2 probable branches. This brings the total to 6 distinct branches within the North Tipperary group.

With all this new data, the "Family Tree" for Lineage II can be updated. This tree is also known as a Mutation History Tree (MHT) - in essence it is a Descendancy Tree that combines data on SNP markers and STR markers with traditional genealogical information such as place of birth of MDKAs (Most Distant Known Ancestors) and family nicknames.

A list of all the members of Lineage II is included in a table at the end of this post and includes their "G number", their kit number, and their MDKA (Most Distant Known Ancestor). Find your G number from the table and then see where you sit on the tree.

Below is the updated version of the previous MHT for Lineage II - the North Tipperary Gleeson's. It is in two parts - the first part is the actual tree itself, the second part is the known genealogies associated with each branch. The best way to see the detail of the tree is to click on each image to enlarge it or, better still, download high resolution pdf versions of each part from Dropbox on the links below and refer to it as you read what follows:
The Mutation History Tree for Lineage II (L2 MHT)
(click to enlarge)

The Pedigrees of the North Tipp Gleeson's
(click to enlarge)

So what are we looking at?
The tree starts 4300 years ago, at a branching point in the Tree of Mankind characterised by the SNP marker Z255. The particular individual who carried this mutation became the Great Grand-Daddy of the Gleeson's ... and their various genetic neighbours (including the Treacy's & Miller's, and more recently the McCarthy's, Carroll's, and McMahon's - for further information, refer to Nigel McCarthy's Group E tree here). Further DNA mutations occurred among the descendants of the Z255 individual before one branch became a gaggle of Gleeson's. Where on the tree this actually happened is still not immediately clear, but apparently some time after the BY2852 group of mutations (crudely estimated to have occurred about 200-400 AD) and probably at or after the A5627 group of mutations (crudely, 490 AD), and probably at or before the A5628 mutation (crudely, 1125 AD).

The tree is based on a combination of SNP marker data (in bold brown text) and STR marker data (in black text). How the tree was generated is the subject of a YouTube video here. Back Mutations are highlighted in yellow, and Parallel Mutations are highlighted in green - more about them in a separate blog post. A crude timeline based on SNP data is on the left of the diagram (blue numbers), and the timings for more recent branching points are calculated from STR data - these appear as red numbers below each branching point (or node) and are expressed in terms of the estimated number of generations back to the common ancestor at that particular branching point. These latter estimates use the values closest to the midpoint (50%) estimate from the TiP Reports for the various project members. To convert these to years, I generally assume 30 years per generation and I also assume that the average year of birth of each person tested is about 1950. Thus 5 generations back would be approximately 1800; 11 generations back would be roughly 1600; 14 generations, about 1500; and 22 generations back, about 1300. A key point to remember about all these time estimates is how crude they are - they only give very approximate timepoints, with a very large range around each one.

The main feature of this updated tree is that there are 6 distinct branches (or sub-branches) of the North Tipp Gleeson "Clan". Let's take a look at each branch in turn:

  • Branch A is characterised by a block of 6 SNP markers, starting with the A660 marker. The project members in this group include 3 brothers (G39, G51, G73) whose ancestors emigrated to Ontario, and 2 other members whose ancestors emigrated to the Antipodes (New Zealand & Australia). The common ancestor for these individuals is about 9 generations ago (in crude terms) and so is beyond the reach of paper records.
  • Branch B is characterised by the SNP Y16880 and is shared by 4 people (two of them uncle-nephew). Two families are relatively closely related (with a common ancestor about 5 generations ago or roughly 1800) but both are more distantly related to the third family (the common ancestor being 8 to 11 generations back, i.e. born about 1600-1700).
  • Branch E members have not been SNP-tested yet but are grouped together on the basis of a relatively unique STR marker pattern (signature). Two of them (G91 & G75) are second cousins and are related to the third member about 5 generations back. The two cousins have Gleeson ancestry going back to the townland of Curraghaneddy in the early 1800s. This may be the ancestral homeland for the other member of this sub-branch.
  • Branch C consists of 3 people, two of them related within about 4 generation and the third about 6 generations back. Interestingly, the townland of Garryard occurs as a common location for the respective MDKAs of the first two people (G71 & G22).
  • Branch D is a bit unusual. The two members are very distantly related (about 14 generations back) and each has many mutations not shared by the other. These are likely to be quite ancient branches of the Gleeson "Clan" and I suspect that over time (as more people undertake SNP testing), both of these branches will be subdivided into further sub-branches.
  • Branch F is also a very ancient branch, going back anywhere from 14 to 22 generations ago (crudely, 1300-1500). However, 3 people sit on this particular branch, and two of them (G97 & G98) are related about 5 generations back (about 1800). Our illustrious Chairman (Michael G) sits on this branch and his Big Y results (expected end Jan) will throw further light on the origins of this particular branch.

You can read more about how the tree was put together on the following two blog posts which deal with Grouping of members and Placement of the resultant groups on the tree respectively.

Altogether, the new tree incorporates 20 of the 31 members of Lineage II. What of the remaining 11 members? Well, two of them are Treacy's and belong on the A557 branch (in the top right of the tree). The nine remaining members could not be accurately placed on the tree due to the absence of SNP data and/or distinguishing STR data - we'll take a look at these in a separate post. These members will need to undergo further SNP testing to see where exactly they fit on the tree. But because we already have a lot of SNP data (thanks to the 10 project members who have already undertaken Big Y testing) we will be able to pursue a cost-efficient SNP testing strategy for the remaining members of the project. And that will also be the subject of a subsequent post.

The 31 members of Lineage II
(with "G number", kit number, MDKA, & terminal SNP)
Maurice Gleeson
Dec 2016






Tuesday, 22 November 2016

New DNA Results from the Clan Gathering

Back in August this year we had a very successful Gleeson Clan Gathering in and around Nenagh, Co. Tipperary, the heartland of Gleeson territory. You can view the various presentations of our Lecture Programme on the dedicated YouTube Channel here.

A gaggle of Gleeson's

Altogether, 35 people had their DNA tested at the Gathering and the last of the results are now in. Twenty seven people did the Family Finder test (autosomal DNA) and eleven did the Y-DNA test, nine of them Gleeson men. In addition, since the Gathering, three additional Gleason/Gleeson males have joined the project, bringing the total to twelve who have recently joined the Gleason/Gleeson ranks. 

Of these 12 men, one is a member of Lineage I (the English Gleason's), 8 belong to Lineage II (the North Tipperary Gleeson's) and 3 of them are currently ungrouped. Thus the vast majority of those who tested in Nenagh recently are all related to each other along their direct male line. Somewhere back in the dim and distant past they all share a common Gleeson patriarch in Tipperary.

These new results have expanded the numbers in Lineage II and currently we have 31 members in this group and in the next blog I will give an update on the current status of Lineage II together with an updated version of its Mutation History Tree (this is in essence a Descendancy Chart for the people in this group).

We also have Big Y data from 9 people within the Lineage II group and we will shortly be receiving the results of a tenth person (our Gathering Chairman, Michael G Gleeson). Thanks to the generosity of the people who have tested, the rest of the group has benefitted. The Big Y data has helped define the branching structure within the group and will help segregate all current and future group members into different subgroups or sub-branches within the overall Lineage II group. 

Based on the Big Y results so far, I have been making enquiries with YSEQ (another DNA testing company) about the feasibility of future cost-effective SNP testing for the group and the CEO Thomas Krahn has proposed a very streamlined approach. This will ultimately save a lot of money for group members and will help further define the finer branching structure within the group. In the next post, I will make specific recommendations for further testing for individual group members.

I'll also be writing a separate blog post about the autosomal DNA results (the Family Finder test). It turns out that many of the people who tested at the Gathering are related to each other! They are turning up in each others matches ... and I hear that people are having a lot of fun trying to figure out how they are related.

For now, all new members are encouraged to read these three essential Blog Pages and in particular, supply their Most Distant Known Ancestor (MDKA) information and Gleeson pedigree (you can simply email me with the information at mauricegleeson@doctors.org.uk) ... 

Maurice Gleeson
Nov 2016





Sunday, 13 November 2016

The Chairman joins Lineage II

There's been a recent development with Lineage II. A very distant relative has just joined the group.

Michael G. Gleeson
Chairman of the Clan Gathering
Michael Gleeson (MGG-1202), Chairman of the recent Gleeson Clan Gathering, has been sitting in the Ungrouped section since he joined the project some 6 months ago. On his Y-DNA-37 test, his Genetic Distance to members of Lineage II was 8/37 or greater, suggesting no close relationship.

However, on reviewing Michael's results, it became apparent that the terminal SNP markers of his closest matches were usually below Z255, the upstream SNP marker shared by everyone in Lineage II. This got me thinking ... could Michael possibly be a distant match to everyone else in Lineage II?

We set out to explore if this hypothesis could be correct.

First off we tested him for the single SNP marker Z255, just to confirm that he was indeed positive for this upstream SNP. And he was. 

Then we did the Z255 SNP Pack which contains 108 SNP markers below Z255 (i.e. further downstream on the Human Evolutionary Tree, the Tree of Mankind). And (surprise, surprise) he tested positive for the downstream SNP markers Z16437 and BY2852. This is illustrated by the green text in the diagram below (green text means he tested positive for these particular SNP markers, red means he tested negative, muddy yellow means he is "presumed positive" for those SNPs, and blue are downstream SNPs that he has not as yet been tested for).

Michael's current position on the Tree of Mankind
(he's making good progress)

The SNP marker BY2852 (red arrow below) is also shared by all the Gleeson's in Lineage II, but not exclusively so. There are two Carroll's who share this SNP marker. So theoretically, whilst it looks most likely that Michael does indeed belong in Gleeson Lineage II, there is an outside chance that he could be a Gleeson by name and a Carroll by DNA. For example, some time back in the 1500's, a Carroll baby might have been adopted by a Gleeson neighbour. The baby was Carroll by DNA but became Gleeson by name. And so too all his descendants ... Carroll by DNA, Gleeson by name. 

However, this seems unlikely because Michael is more genetically distant from the Carroll's (minimum GD = 11/37; calculated from the Z255 Project Results Page) than he is from other Gleeson's in Lineage II (min GD = 8/37). And in addition, an alternative explanation could be that the two Carroll's are Carroll by name but Gleeson by DNA. It is difficult to know which came first - the Carroll chicken or the Gleeson egg.

The Gleeson portion of the Tree of Mankind
(from http://ytree.net/DisplayTree.php?blockID=16)

Furthermore, shortly after Michael's results came in, a new member joined the project (PG-4241), and this member was a close match to Michael (Genetic Distance of 4/37). They appeared in each other's matches list. And shortly after that, another close-ish match (5/37) joined the group (WG-7908; someone who tested at the Clan Gathering in August). So it looks like the three of them have formed their own particular sub-branch of the Gleeson Family Tree, with a common ancestor born sometime around 1600-1700 or so.

Confirmation that they belong in Lineage II could be achieved by further testing with the Big Y test. This would identify which further downstream SNP markers they test positive for. And it would also help give us an estimate for when this particular sub-branch broke away from the rest of Lineage II (it may have been shortly before 1600).

In any case ... welcome to Lineage II, Mr. Chairman.
Maurice Gleeson
Nov 2016

Update (19th Nov 2016)
I am very happy to announce that Michael has just ordered the Big Y test in the FTDNA Christmas Sale. The price is reduced to $525 from $575 but we used an additional $100 off coupon to get it for $425 - the cheapest it has ever been.

The results should be back some time after Christmas and I suspect they will create a whole new branch on the Tree of Mankind above. And if we are very lucky, they may even split up the SNP Block at the A5629 level (which currently consists of 4 SNPs). The results will also help us get more accurate date estimates for the various branching points in this portion of the Tree. And they will also help in putting together the SNP Panel for Gleeson Lineage II which will make it easier and cheaper for project members to do downstream SNP-testing. I am currently putting this panel together with Thomas Krahn from YSEQ.