Uploading your new Big Y-700 results

The Big Y test changed to a completely new technology earlier this year. It now covers 50% more of the Y chromosome than previously. And so it is anticipated that the new test will discover additional SNP markers that the old technology did not detect. Furthermore, the new SNPs should be able to more accurately date the various branching points on the Tree of Mankind.

It also gives us approximately 700 STR markers whereas the previous test only gave approximately 500 STRs. As a result, the old test is called the Big Y-500 and the new one is called the Big Y-700. Going forward, all new Big Y orders will use this new technology.

For those who did the old test, it is possible to upgrade from the Big Y-500 to the Big Y-700. There are several people within the project who have done this upgrade. But for everyone who does the new test, or upgrades from the old version to the new version, it is essential that you upload a copy of your results to the Big Tree so that we can get some essential additional analyses. You will find instructions for doing so on the Big Tree website here and on the Y-DNA Data Warehouse website here but I include a briefer summary below.


What do you get from your Results?

Your results should be analysed within a week or two and you can check them by navigating to your particular portion of the Big Tree. For members of Ryan Group 2 (for example), your Terminal SNP is M756 and you will find this branch on the Big Tree here (see screenshot below). The diagram nicely illustrates your placement on the Tree of Mankind and the surnames of the people sitting on neighbouring branches to your own. This information can be very useful for determining the geographic origins of your particular direct male line and for determining if your name is associated with an Ancient Irish Clan.

Project Administrators can use programmes like the SAPP tool to generate Mutation History Trees and determine the likely branching structure of your particular "genetic family" from the time of surname origins up to the present day. This process can also help identify which Ryan's are more closely related to you and which are more distantly related. It is also possible to date the branching points within the Mutation History Tree using SNP data as well as STR data. This process is likely to become more accurate with the advent of the new Big Y-700 data and the identification of new SNPs. It is anticipated that the new data will reduce the number of "years per SNP" from about 130 to about 80 years per SNP. You can read more about this here.

You can also click on your surname above your kit number for an analysis of your Unique / Private SNPs. These may prove useful in the future for defining new downstream branches in the Mutation History Tree and for dating new branching points. But this very much depends on new people joining the project and undertaking Big Y-700 testing (so that we can compare apples with apples). And as this is a new test, it is likely that we will have to wait some time before we begin to see real benefits from it.

Creating a Link to your Big Y results

In order to create a downloadable link to your Big Y results, first log in to your FTDNA account and go to your Big Y Results page ...



Then click on the blue Download Raw Data button ...

Then you need to create a link to two separate files - your VCF file and your BAM file. The VCF file is used for placing you on The Big Tree. The BAM file is used for high-end technical analysis by the folks at the Y-DNA Data Warehouse. You can see some of the results so far on their Coverage Page here (and if you like you can search for kits by surname, including your own).

1) to create a link to your VCF file, right click on the green Download VCF button, and then click on "Copy link" from the drop-down menu. You will later paste this link into the the "Download URL" box on the Submission Form.

Alternatively you can simply (left) click on the green Download VCF button and this downloads a 10 MB file to your computer. This can then be directly uploaded via the Submission Form below. However it is preferable (and less problematic) to generate a link instead.

2) to create a link to your BAM file, click on the green Generate BAM button. You will then get a message that "Your Big Y BAM file is currently being generated" (see below). This generates a very large BAM file ... but it takes several days to prepare so you will have to come back to this page in a few days time! Put a reminder in your diary / calendar!

Uploading your VCF file

Having created the first link (to your VCF file) and copied it, click here to go to the Y-DNA Data Warehouse and fill in the form with your standard information - email, kit number, surname of your paternal MDKA (Most Distant Known Ancestor), and (most importantly) the link to your file - you do this by pasting the link you copied earlier into the "Download URL" box underneath the heading "Raw Data Upload" at the bottom of the page.

If you want to upload the actual file itself (rather than a link), click on the blue Direct tab under "Raw Data Upload" and then click on the "Choose File" button and attach the file from where you downloaded it onto your computer (on my laptop, the "Choose File" button appears to be slightly hidden under some text but it works if you click on the start of the text). 

Don't forget to tick the checkbox to confirm you agree with the Data Policy and then click the blue Submit button.

Uploading your BAM file

Several days later, come back to this same place to get a link to your newly generated BAM file. So, navigate to your Big Y Results page, and after clicking on the blue Download Raw Data button, you will find that the BAM file has been generated. DO NOT DOWNLOAD IT - you don't need to and it is way too big. Instead, click on the green Share BAM button and then the green Copy button in order to copy a link to your BAM file. You will share this link in the next step.

Then go to the Y-DNA Data Warehouse and fill in the same form as before BUT ...

1. select Other for the Testing Lab
2. enter your Kit ID Number 
3. leave everything else on its default setting
4. paste the link to the BAM file in the "Download URL" box underneath the heading "Raw Data Upload"
5. tick the checkbox to confirm you agree with the Data Policy and then click the blue Submit button

Maurice Gleeson

Aug 2019

Birth of a new Genetic Family - Group 10

A new project member recently joined the Ryan DNA Project (CR-5799). He does not have any Ryan's among his list of matches but he does match another Ryan within the project (SR-3236) at a Genetic Distance of 7/37 (i.e. 7 steps away from an exact match). These two people also share a number of STR marker values in common, creating a relatively Unique STR Pattern (USP) compared to other project members. And on this basis I have decided to group them together.

Arrows indicate the Unique STR Pattern for this group

How old is the new group?
Even though they are genetically related to each other (probably within the last 1000 years or so), their common ancestor could have lived back in the 1600s or earlier (i.e. it is a distant connection). The TiP Report predicts an approximate 50% probability that they share a common ancestor within the last 14 generations (i.e. born about 1530 AD) and an approximate 95% probability within the last 24 generations (i.e. about 1230 AD). More accurate predictions could be achieved by testing to a higher number of STR markers (e.g. Y-DNA-111) but there would still be a range of about +/- 300 years on either side of the midpoint estimate. In other words, these estimates will always be crude (from a genealogical perspective).

However, given that the connection is so far back, and they both carry the same Ryan surname, this group could represent a relatively ancient Ryan subgroup, that has been around for many hundred years, but which does not have many surviving descendants.

Where did they come from?
There is no information available about the MDKA (Most Distant Known Ancestor) for either project member so there are no clues from either individual's genealogical data. We may find clues among the surnames of their matches, or from the terminal SNP markers of their matches.

Matches' Surnames
CR-5799 has 16 matches (at the 37 marker level of comparison) and they have the following surnames: Burns, Coleman, Coulson (x2), Ford, Hagan, Healy, Jackson, Johnson, Lewis, Mason Minett, Pemberton, Potteet, Smith, Williams

SR-3236 has 13 matches (at the 37 marker level of comparison) and they have the following surnames: Creswick (x3), Eason (x3), Easton, Evans, Hayes, Hobson, Paige, Pelsue, Ratcliffe

There are both English & Irish names among these matches so this suggests an origin in either Britain or Ireland within the last 1000 years (our timeframe of interest).

Matches' Terminal SNPs

Here is a list of the most relevant Terminal SNPs of the matches of each of the members. This information may help place them on the Tree of Mankind and this in turn may allow us to identify a likely origin for this particular group.

At the 37-marker level of comparison: CR-5799 ... L21; SR-3236 ... U106, S25007

At the 25-marker level of comparison (most frequent SNPs only - numbers in brackets are number of times each SNP appears):

• CR-5799 (570 matches) ... L20 (3), L21 (2), L48 (5), L513 (2), U106 (3), U152 (4), U198 (2), Y34483 (4), Z156 (2), Z16532 (3), Z18 (2), Z195 (2), Z9 (2)
• SR-3236 (191 matches) ... BY32442 (3), BY34891 (2), L21 (2), S25007 (2), S7432 (2), U106 (2)

Below are the SNP Progressions for these most frequent SNP markers. A SNP Progression is simply the sequence of SNP markers that characterise each branching point on the Tree of Mankind, starting at the level of the Haplogroup (R in this case) and progressing all the way "downstream" to the Terminal SNP.  Comparing SNP Progressions helps us see exactly where each terminal SNP sits on the Tree of Mankind relative to all the other SNPs:

• L21 (2) ... ... R-P312/S116 > Z290 > L21
• L513 (2) ... .. R- P312/S116 > Z290 > L21 > DF13 > L513
• Z16532 (3) ... R-P312/S116 > Z290 > L21/S145 > DF13 > DF21/S192 > FGC3213 > Z16532
• Y34483 (4) ... R-P312/S116 > Z290 > L21 S145 > DF13 > DF21/S192 > FGC3213 > Z16532 > Y34485 > Y34483
• BY34891 (2) ... R-P312/S116 > Z290 > L21 S145 > DF13 > FGC11134 > A353 > Z16250 > A114 > CTS4466/S1136 > S1115 > A541 > S1121 > Z16251 > A159 > Z17981 > A923 > BY21614 > BY30545 > BY34891
• L20 (3) ...  R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > Z367/S255 > L20/S144
• U152 (4) ... R-P312/S116 > Z40481 > ZZ11 > U152
• Z195 (2) ...  R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > Z195/S355
• S7432 (2) ... R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > ZZ12 > ZZ41 > S7432
• U106 (3) ... R-U106/S21
• S25007 (2) ... R-U106/S21 > ...
• Z18 (2) ... ...   R-U106/S21 > Z2265 > Z18
• Z156 (2) ... ...  R-U106/S21 > Z2265 > Z381/S263 > S264/Z156
• U198 (2) ... ...  R-U106/S21 > Z2265 > Z381/S263 > Z301/S499 > S1688 > U198
• L48 (5) ... ... ... R-U106/S21 > Z2265 > Z381/S263 > Z301/S499 > L48
• Z9 (2) ... ... ... .. R-U106/S21 > Z2265 > Z381/S263 > Z301/S499 > L48 > Z9
• BY32442 (3) ... R-U106/S21 > Z2265 > Z381 S263 > Z301/S499 > L48 > Z9 > Z30/S271 > Z2 > ~22277095-G-A > S16218 > b38:7436045AT>A > BY32442

Simply ordering the SNP Progressions in this way allows us to see that the matches of these two group members sit on very distinct branches of the Tree of Mankind (some separated by tens of thousands of years) indicating that a lot of them are "chance matches" that just happen to have similar STR genetic signatures. Thus we cannot reliably predict on which branch of the Tree of Mankind this group is likely to sit. In order to clarify this, one or both group members would need to undertake the Big Y test.

Conclusions

Even though the two members of this group are not close matches to each other (GD 7/37), their Unique STR Pattern suggests that they can be appropriately grouped together and that they share a common ancestor some time in the past several hundred years (probably pre-1600s). For now, we are none the wiser as to where this particular genetic group originated, but hopefully, as more people join the project and are a match to this new group, their origins will become more clear.

Both members should join the relevant Haplogroup & Geographic Projects and seek further advice from the Admins of those projects. For now, until Big Y data is available, only topline recommendations can be made re potentially relevant projects:

• Ireland Y-DNA Project
• R1b & Subclades

Options for these project members would be to upgrade to Y-DNA-111 and do the Big Y test. This would help confirm that they are appropriately grouped together and would help isolate on which particular branch of the Tree of Mankind they sit. This in turn could give clues as to their origins.

Maurice Gleeson

June 2019

What can Y-DNA Results tell us?

Most people who join surname projects (like the Ryan DNA Project) start off with the Y-DNA-37 marker test. This tests 37 STR markers, and you can later upgrade to 67 or 111 STR markers. Some people also do SNP marker testing, either via a special "SNP Pack" or the Big Y test. So there are two types of DNA markers - STR markers and SNP markers. You can read more about them here.

Each type of marker gives different kinds of information. The SNP markers help define the exact location that someone sits on the Tree of Mankind, whilst the STR markers give an indication of how closely two people are related within the last several hundred years. Both types of marker can provide crucial information that helps the interpretation of the overall data and allows us to draw specific conclusions about each of the genetic groups within the project.

But DNA data is not the only type of data that we analyse. We also analyse the direct male line pedigrees that project members have provided, and in particular the birth location of each MDKA (Most Distant Known Ancestor).

On an individual level, a simple Y-DNA-37 test may help you identify people to whom you are closely related. An exact match at 37 markers (i.e. no mutations; Genetic Distance = 0/37) suggests that you and the other person have a 50% chance of being related on your direct male line within 5 generations and a 95% chance of being related within 8 generations. The probabilities are even stronger for an exact match at 67 markers (50% probability within 3 generations, 95% probability within 5 generations) and 111 markers (3rd cousins or closer). Thus your own individual Y-DNA results can help you with your personal family tree research.

But you get additional value from your Y-DNA results by joining DNA projects - surname projects, haplogroup projects & geographic projects. And at this project level, your Y-DNA results can tell us a lot about the deeper origins of your specific genetic group. Here's how ...

In most projects, distinct genetic groups can be identified from the DNA data. These are groups of people who all share a broadly similar genetic signature, suggesting that they all descended from the same common ancestor some time in the last 1000 years or so (i.e. "within a genealogical timeframe", or "since the advent of surnames"). The key questions that we can ask about any genetic group within a project are:

• Where are they from?
• How old is the group?
• Is the group associated with a specific Irish "clan"?

And as the Y-DNA database has grown, various DNA projects have indeed been able to identify the genetic signatures of specific Irish "clans", thus connecting people with their deeper Irish roots and a history that few may have imagined.

Brian Boru (941-1014), High King of Ireland 

One of the earliest examples of this is the O'Brien DNA Project. The Administrators of this project worked closely with Haplogroup Project Administrators to identify a specific signature for the "tribe" of the Dal gCais (pronounced Doll Gash), one of whose most famous descendants was Brian Boru, 1st High King of Ireland, who was killed at the Battle of Clontarf in 1014. [1] The evidence collected in support of this conclusion (that a specific signature is that of the Dal gCais) includes the following:

• a specific Y-DNA signature (called the Irish Type III STR signature, which is associated with the L226 SNP marker) is in turn associated with: 

1. a surplus of Dal Cassian surnames (e.g. O'Brien, Casey, McGrath, Hogan, etc)
2. the clan territories of the Dal gCais (centred around Clare & Limerick)

• Sir Conor O'Brien shares the same specific signature (he has a 32-generation direct male line pedigree going back to Brian Boru)

Distribution of L226 is strongest in Dal gCais territories

So Y-DNA results can help you identify matches with whom you share a fairly recent common ancestor (on your direct male line) and can link you up to the deeper origins of your surname and where it came from.

We will see in subsequent posts if the deeper origins of the various groups within the Ryan DNA Project are coming close to identifying specific DNA signatures of specific Ryan "clans".

Maurice Gleeson

May 2019

References:

[1] Dennis M Wright, 2009. A Set of Distinctive Marker Values defines a Y-STR Signature for Gaelic Dalcassian families. Journal of Genetic Genealogy, 5(1):1-7. Available at http://www.jogg.info/pages/51/files/Wright.pdf