SNP Testing

This section discuses SNP testing.

[I am posting information, which I initially put together for Duncan groups A & F.  The basic of DNA testing, our research objectives and process with them are the same for all groups.

Do not let this information overwhelm you but visit with it for a while.]

I have been trying to find ways to explain our research so everyone can understand what we are doing.  To help everyone get up to speed on our current research I have written some background information (think of it as a refresher) about Y-DNA testing and then details about our current SNP testing.

This information is long so read over it a few times.

added 7/17/2016:
{I have added in the Link section some very good videos on SNP and STR testing given by John Cleary at the 2016 WDYTYR in Birmingham, England intitled: Using SNP Testing & STRs to Enhance your Genetic Genealogy Research Project Part 1-3. These are very good and give a good foundation to our research methods}

Background:

Visualize a family structure.  A family starts in time with two and grows with each generation. As time goes on that family structure grows wider and deeper with more and more generations.

As we research our own family histories we are trying to reconstruct what our ancestry was member-by-member within a generation, and generation-by-generation.  During our research we look for any type of clues that we can find to document and support each person’s placement within our family’s ancestry.

Through all of this general genealogical research we are slowly reconstructing our family’s lineages back in time.

This is exactly what we are doing with the tool of DNA.  We are testing hypothesis about our families and trying to find new clues that may give us new insights and leads/contacts to further our traditional genealogy research.

With Y-DNA testing we are trying to find males that are of the same male lineage as each one of us.  Today we have surnames that have been passed down through the generations.  Surnames have not always been in use as we have them today.  There was no magical date in history when all male lines assumed a given surname.

Before the adoptions of surnames think of males being part of many different genetic pools that as time went on assumed surnames.   Not all men that were from a close genetic pool all took the same surname.  This is part of what we see today with different surnames in our match list especially at the lower marker levels.

Y-DNA testing is a tool to use in conjunction with our traditional genealogical research.  After 15 years of very active testing by the genealogy community we are still pioneers in this discovery process.  Our knowledge and discovery of how genetic information, found in our DNA, is passed down through the generations is still in high gear.

There are two phases to Y-DNA testing and the information each provides gives us insight into our male Y-Chromosome and how we may match to other men who carry a similar Y-DNA signature.  The results of both phases of testing are important to have and apply to our research.  Thus Y-DNA testing is not a single test but an ongoing series of tests each building on one another.

1st phase testing:

The first phase of testing is what we have been doing mostly to date, which is called Short Tandem Repeat (STR) testing.  This testing is focused on a historical/genealogical time frame of about 1000 years.  A time period where there is a chance of records being found to help support and document a DNA connection. From this test we obtained a list of men who match us genetically by the haplotype signature we have at a given STR (12,25,37,67,111) marker level.  A haplotype is the series of numbers we receive as our test results from a STR test.

Think of STR testing as looking from the present towards the past back along ones male lineage.

As you view your match list you see differences among you and your matches.  These differences are called Genetic Distance (GD) and are the random mutations between you and your matches at a given marker.

The closer two male lines are generally the fewer differences in GD they will have. Genetic Distance is an important aspect to know and understand but not the only part in understanding how two men may be related.  When men have tested at 67 or 111 markers a lot of the false positive matches and matches that may be from before surnames will be weeded out.  Thus the resolution for matching and analysis is greatly increased

Some men who are part of a very large genetic grouping of men could still have a few surname matches that could still pre-date the adoption of your specific surname.  We see an example of this happening in Duncan group ‘F’ member’s match lists.

The important thing to remember with the STR test is that the men you match are your closes genetic matches.  These men are the men you need to work with to try and find genealogical records to support what the DNA is saying.  This is collaborative research at its very best. As we all know not every one in Duncan group ‘B’ can find documents to completely tie their lineages together. There are still unknown links within your group.

This brings us to four important things that we have learned from the first phase of Y-DNA testing.

1. STR testing has placed you within a group of your closest genetic matches (out of almost 275 Duncan men tested to date).

2. The need to correspond/collaborate and share information with your matches (that traditional genealogical sharing).

3. That the only way this research moves forward and we gain new information to help us in our genealogical research is to keep doing what you have been doing.  We all must keep DNA testing, and sharing results.

3. The need to revisit and re-evaluate your current genealogy.  Step to the sideline and re-evaluate your genealogy again with a fresh and very critical eye, question every component. Ask hard questions about every bit of evidence you read in a book, look for a solid source for every piece of information and not just copying other’s work.

4. The significance of testing as many STR markers as you can afford.  The 67-marker panel should be the new minimum.

2nd phase of testing:

Happening in the background, over the past 20+ years, has been the slow and meticulous process of discovering and vetting newly discovered Single Nucleotide Polymorphisms (SNP).  These SNP discoveries have been slowly reconstructing the male phylogenetic tree.  This is the male tree of all of our lineages from a patriarchal founder.  This is uncovering the ancient migration of our male lines down through time.

Today we have the ability to actively participate in this 2nd phase of Y-DNA testing.

The second phase of Y-DNA testing is now in the main stream as technology has enable us to test most if not nearly all of the testable portions of the Y-Chromosome.  Next Generational Sequencing (NSG) has opened the door of the second phase of Y-DNA testing. We can now participate and help reconstruct branches of the larger male tree by discovering our very own branches and sub-branches down into the genealogical time period.

These are the big SNP discovery tests such as FTDNA’s BigY test and Full Genomes Y-Elite test. They do carry big price tags but will give the most new lineage data.

Think of SNP testing as looking from the very distant past towards the present along ones male lineage.

Every male living today is the leaf on the male tree. All of his very close genetic and genealogical matches must sit right close to him on the tree. Above the leaf is a series of branches leading back to your main branch i.e., “R”, the trunk and down to the root of the male tree.

Now lets go back to that analogy of the family structure I talked about above but let’s this time only considers males.

Pick a point in time say 0 BC/AD where we have a patriarchal male who starts a family and has sons, and those sons have sons and so on.  Over time this male lineage grows in depth (generations) and spreads sideways in numbers.  There could be 75 generations down through 2000 years until our present generation.

What we know about this extended male structure is that every male in this lineage is related on his Y-DNA!

No matter how far they have spread or gotten removed from the place of origin they all descend from the patriarch that started this family. Whatever Y-DNA signature the patriarch had they all carry and are a part of that lineage.

Of course human biology is not static.  Randomly through the past 2000 years some males will have SNP mutations.  A SNP mutation is a change at a single base pair (the four sugar building blocks of DNA) along the Y-Chromosome that changes from an A to (>) T or C to (>) G etc. The current estimates are 135-160 years per SNP mutation. This means that in our example of 75 generations we will have more branching points and subdivision.  A first look at group ‘F’ shows it may be having SNPs at a faster rate than the average.

Now lets say the patriarch had 3 sons and the third son had a random SNP mutation at a point along his Y-Chromosome.  Every male that descends from the 3rd son carries this specific SNP mutation while all the male descendants of the other two sons do not carry that new SNP mutation.

All men that are related at a given SNP point will have all the same upstream SNPs that define their male lineage.  Think of walking down through time, in lock step, sharing a whole string of SNPs until in one generation a male has a random SNP mutation.  From that point forward your male line has branched.

Duncan Group ‘A’ specifically:

So here we are 75 generations later and we have STR tested Duncan men randomly and 24 of them fall into a group we call Duncan group ‘A’.  This is an indication that these 24 men are related on their Y DNA but again no one has a complete genealogy to show that relationship.

In 2013 I participated in a pilot project, with Full Genomes Corp Y-Elite test, to test the full testable portions of my Y-Chromosome.  By previous single SNP testing I had discovered that we were on the U152 sub-branch of the main R branch of the male tree. Over time as a new SNP below U152 was discovered I would test it to see if our male lineage carried it.  If we were derived (positive) for the new SNP then that showed that we had moved below the U152 level.  Alas I remained in a small group of tested males in the world that had none of the new branching SNPs below U152.

When my NGS results were posted I learned that I had indeed moved down two branch points with the SNPs PF6658 and Z193.  My other U152 men moved another step down to SNP Z192 a SNP that I did not have.  This is where our small group of U152 males separated with our male lineage continuing with only SNP Z193 and not branching with the Z192 SNP see (Figure A).

In my test data I had 24 singleton (private) SNPs that no other male to date had.  This takes our male lineage down we think into the historical time period.  After my Y-Elite test I then tested Donald Duncan #11804 with FTDNA’s version of a NGS test their BigY test. When Donald’s results came back he matched, as he should on 8 of my 24 singleton SNPs.  The reason that we have a difference is based on the coverage difference between the two NGS tests.

To view the current U152 Tree visit this link; http://www.r1b.org/docs/Full_Y-Chromosome_U152_Samples.xlsx

Figure A: U152 Tree with the Duncan cluster shown.  This is where we currently sit and all of Duncan group A men will be.  We need more NGS testing of men in group A to find the additional sub-branches that could gives us our most recent genetic families.  This view is small but visit the above link for a full excel view.

Donald and I are a 110/111 marker match on our STR tests.  We are emphatically closely related but we still have not identified our common ancestor.

I now want to test more men in Group A with these NGS tests to gain more clarity about our male line sub-branching.

What is interesting about my particular male ancestry is that I document back to my 2nd great grandfather, Brantly Duncan, born about 1820 in the Saluda area of South Carolina.  Beyond 1820 there is an unproven three additional generations that I have been DNA testing and have shown a genetic connection between us.  The oldest generation of these unproven ancestors is a Samuel Duncan, listed as from Dundee, Scotland born about 1722.  Of course I cannot find records of this Samuel in Scotland.

Then about three years ago Duncan group A had new Duncan matches from two distant cousins.  Gordon and Joe Dunkin were Y-DNA tested to see if they matched as their geologies show them to be cousins.  In looking at their genealogies they list a possible descent from a circa, later 1600, Duncan of Anne Arundel County, Maryland.

Now this is very interesting. If these genealogies are proved then there may be a case for at least two progenitors for our specific Duncan group A lines into Colonial America which emigrated at different times.  If we are able to SNP test Gordon and Joe’s line we may get some SNP differences that could show some family branching.

I would like to have a Y-Elite test done on Gordon Duncan and at least one or two more BigY tests done on other Duncan men from group A.  If we can get a good sampling of NGS tests for Duncan group ‘A’ then we should be able to see some family branching that is specific to our lineages.

Below is information about similar research with NGS testing taking place in Duncan group F.  They have been SNP testing with FTDNA’s BigY test.  Follow the discussion below to get more information about what I would like group A to be working toward.

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Example with Duncan Group ‘F’:

Our next research step was to start using NGS technology and SNP test three men from group ‘F’ to see if we can uncover some structure within their lineages.  Last December group ‘F’ stepped forward and pooled financial resources and we tested Dean #36576, Jason #28358, and Wayne #307780 with FTDNA’s BigY test. The BigY test is Family Tree DNA’s version of a NGS test.  The BigY is optimized to test about 60% of the testable portions of the Y-Chromosome at a lower price point.

Remember that NGS SNP testing is a discovery type of test that is looking to find new SNPs down into the historical/genealogical time period.

When the SNP results came in we found that two men Jason and Wayne had some SNP differences.  When Dean’s results were posted we also found he had a few differences from Wayne and Jason.  The meaning of these SNP difference is that we have found branching points within Duncan group ‘F’.

Now we have sub-divided group ‘F’ into three new subunits.  Remember all men in-group ‘F’ are genetically related on their Y-DNA but now we have found some lineage sub-division.  This is just like in a typical family structure where after multiple generations we have first, second, and fifth cousins etc., but they all can be traced back to a common male ancestor.

We now feel that we have discovered some SNPs and sub-branching in Duncan group F that is down into the historical/genealogical time period.  This is what we want to find so we can align men into their most recent family units.  If we are able to date one of these new SNPs into the 1700’s then we know that all the men who have that particular SNP are part of a male line since the 1700’s

We then will have given ourselves a better view of the sub-groups in Duncan group F and can redirect our genealogy research into the new and more recent family units.  We can test how well our genealogies hold up and if we have been incorrectly trying to tie the wrong Duncan lines together since a 1700 time period.

As another example we have also been SNP testing in the very large Duncan Group ‘B’ group.  This Duncan group is also of a colonial time period most likely as is group F.  We have found an Isle of Bute, Scotland Duncan that matches group B and has become their genetic anchor back to Scotland.  In our SNP discovery testing we have found a SNP (A1147), which only the Americans in-group B have, and not the Duncans in Scotland.  We currently see this as a SNP that most likely happened in a Duncan male on this side of the pond.  If we are able to confirm this then we will have an American genetic family that we can base our genealogies around.  If we find a Duncan in-group B that does not have the SNP A1147 but has a genealogy based in America then we will know that their Duncan progenitor came to America, from Scotland, after the colonial progenitor of the main group for Duncan’s in-group B.

What’s Next?

I would like to test at least two more Duncan group F men with NGS testing to try and determine if there is some more sub-branching. Ideally we would like to NGS almost all the men in-group F but the cost would be very high.  Pooling your financial resources into a few NGS tests, followed up with additional SNP pack testing, is an effective way to gain SNP information.

I definitely want to test David Duncan #N53481 who was born in Dundee, Scotland as he currently is group F’s Scottish anchor.  I expect there will be more subdivision between David and the rest of group F as his male line stayed in Scotland.  The rest of group F’s men are mostly from the American Colonial time period so we have enough time for several SNPs to develop.

What is interesting about one of David’s STR markers is that he carries the same DYS 390 = 25 value as does Dean Duncan.  Dean’s has documented his male lineage in America into the 1770’s but most of the men in-group F have the DYS 390 = 26 value.

I also would like to test a descendent of Seamore Duncan or a few of the men with more GD for the group’s average of marker values.

After we get the NGS testing done our next step will be to have YSEQ develop a SNP Pack for Duncan Group F.  This SNP Pack will be composed of those private SNPs that the NGS testing has given us for our SNP test subjects.

Then we will test all the other non-NGS tested men in-group F with this new SNP Pack with a much lower price point.  Out of this we will be able to align some men under Dean, Wayne, Jason, and David’s group.  Our hope is that we will have these male groups broken out so we can better align our genealogies to them.

The main points to remember are:

  1. Each SNP you see in your test represents a branching point somewhere along your male lineage.
  2. All men below any given SNP will carry that new SNP
  3. If you do not carry a SNP that someone else carries then your male lines have branched (separated) from one another i.e., think related but as cousins.
  4. Each of you shares 1000’s of SNPs, which means that you are part of the very same male lineage. Not until more resent times have your male lines separated which is marked by a SNP mutations.  You are emphatically close cousins!
  5. Now we want to choose some of these new private SNPs that each of you have and test the other men in-group ‘F’ with them.  We then should see some men falling into Jason group, some in Dean’s group and some into Wayne’s group.
  6. We can now pick up our genealogies and look at them anew.  We have removed some ambiguity and placed each of us into a much closer sub-group of Duncan group ‘F’.
  7. That DNA testing is a process and we must gain information from both STR and SNP testing.

I would like to see all the men in Duncan Group F also join the Z253 project when they do any SNP testing.  The administrators in this Haplogroup Project are the subject matter experts on your SNPs below Z253. I learn from them.

Once any NGS testing is done we like to have some third party analysis done on your NGS raw data BAM file.  Along with the Admins of the Z253 project we like to have you share you raw data with The Big Tree (see below).  We also have ordered analysis done by Full Genome on the FTDNA BigY raw data BAM files.  The more eyes we can have looking at the raw data files the more we stand to glean for your test.

Any pooled funds for a BigY test within group F can be donated to the Donnachaidh General Fund (located on your myGroups page).  This is how we have been doing the test upgrades and orders.  Once funds are raised I then can order the test and apply the donations to that test.

I have attached several documents to help show what our current understanding of the SNPs discovered to date show us.

One is an excel file, from the administrators of the Z253 project which group F is under. I have personalized, this chart for group F showing Duncan group F’s decent down through time.  Follow the red line down through the different major SNP branching points down into more recent times with Jason, Wayne, and Dean’s current SNP results.  Dates are broad estimates.

You will see (Figure 1) that there are two surnames, Powell and Brignall/Bridgnell, that track with the Duncans.  Mr. Bridgnell is one of those odd surname matches that a lot of you have in your Y-DNA match list.  Powell does not show up, as a match as his GD is outside of the matching criteria because the time of your common ancestor is must older.  This represents a genetic pool, which I mention before, from which your males ultimately descended.  This is from the time period well before our current surnames evolved. You will then see Powell branch off and the Duncans and Brignall/Bridgnell lineages continue for a period of time.

Figure 1: Z253 Tree: Snippet of Duncan, Powell, & Brignall/Bridgnell lineages. See attached excel file for full view.

Then Brignall/Bridgnell branches off and our current three group F BigY men continue together, see (Figure 2).

At some point in the more recent past you see that Dean, Wayne, and Jason’s lines each branch from one another.  This is a real time example of how a family sub-divides and creates cousins.  We have not been able to see this detail of family structure within our current genealogies.

Figure 2: Sub-grouping of Duncan’s in-group ‘F’ via BigY SNP test. See attached excel file for full view.  The SNPs listed in blue (and bottom three orange) are those found only in each Duncan male tested.  Some of these could be within the historical/genealogical time frame.

As we get more NGS testing done on group F and then get the other men tested to these private Duncan SNPs then we will be able to place men into their respective sub-families that I talk about.

The second chart see (Figure 3) is from The Big Tree maintained by Alex Williamson.  This tree shows the evolving SNP tree with branching below the important P312 SNP.  This tree is growing daily but you can find Wayne, Jason and Dean listed along with Powell and Brignall/Bridgnell.  The website for the big tree is www.ytree.net. Stroll down to find Z253 and then open that page and then go over a few to find our Duncans and see the SNP branching. You can also use your browser search/find function.

Figure 3 – The Big Tree: Snippet of the Z253 part of tree specific to Duncan Group ‘F’ and their Powell & Brignall/Bridgnell genetic matches. See the full placement of SNPs under Z253 on The Big Tree website www.ytree.net

We are not at the end of the journey yet but we are now getting closer.  For with every NGS test taken we stand to have the arrangement shuffled some but the SNPs that have been identified for you…. you will always have.

The 2015 FTDNA holiday sale has the BigY test marker down to $525.  There are some $25, $75, & $100 coupons, floating around, which can also be used to reduce the price even more (this is what we did last year). See your mystery rewards button on your myFTDNA page for your current weekly coupon.  These coupons are changed every Monday during the holiday sale.  If you have a $75 or $100 coupon for a BigY test you can share it if you do not plan on ordering a BigY test.  Post the coupon code to the Duncan-group-f gogglegroups.com forum and me so it can possibly be used.

The Full Genomes Corp NGS test is their Y-Elite 2 full Y-Chromosome test. This test covers 98-99% of the testable portion of the Y-Chromosome.  It would be ideal to have at least one-man in-group F with this test.  This test cost more than the BigY test.  The Y-Elite 2 test is currently reduced to $675 with a $100 off coupon.  Full Genomes is a different company than FTDNA so you will need to submit a new DNA sample (they use a saliva sample).

We do not want to donate through the Donnachaidh General Fund for any Full Genomes Y-Elite tests.  The current project’s general fund is only for FTDNA’s list of products and not their competitors.  All donated funds in the project general fund based with FTDNA are held by FTDNA until dispersed.  Projects administrators do not handle any of the donated funds.  We only apply their use towards payment for selected FTDNA’s products.

We will need to find a way to collect these Y-Elite donations and keep them separate.  One possible way, if there is interest, is through a Donnachaidh Project General Fund set up with PayPal.  Thus administrators would not be holding these funds but we could apply them towards any DNA test.

As normal when a donation is made please give instructions in the note field about the intended use.  Let me know if there is more interest in pooling funds during these price reductions.

Also, as a reminder, the current balance showing the receipts and disbursements of the Donnachaidh General Fund can be seen on the project website.

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