Wednesday, 21 August 2019

Grace O'Malley and her DNA

One of the great aspects of Ireland’s heritage is the fact that we have the oldest genealogies in Europe. [1] These relate to the ancient Irish clans (septs) and their colourful chieftains, kings and queens.

Not all of these genealogies are 100% accurate – some times they were modified for political reasons or social climbing – but with the advent of genetic genealogy, the exciting possibility has emerged that the truth or otherwise of these ancient genealogies can be confirmed through Y-DNA testing. And a direct offshoot of this is the possibility to link your DNA with that of famous Irish medieval royalty, such as Brian Boru, or our very own Grace O’Malley, the Pirate Queen (1530-1603). The link to Brian Boru is well-established. But the question is: can we do something similar for Grace and the wider O'Malley clan?

Grace O’Malley meeting Queen Elizabeth I in 1593

Let's look at the case of Brian Boru and see what lessons it can teach us.

Identifying the DNA Signature of the Dal gCais

Brian Boru was first High King of Ireland and was famously killed at the Battle of Clontarf in 1014.  The Ancient Annals are historical texts that recorded the genealogies of many Irish tribes/clans. They tell us that Brian Boru belonged to the clan of the Dal gCais (pronounced Doll Gosh) which was a tribe/sept that descended from a man called Cas (born 347 AD) whose 5x times great grandfather was Oilioll Olum, King of Munster (and therefore born about 150 AD). This sept rose to prominence in the south of Ireland and was centred around Clare, Limerick & northern Tipperary. As the clan evolved over time, it gave rise to many distinct branches each with their own surname. These Dalcassian surnames included: O'Brien, Casey, McGrath, Hogan, and many more. But they all had the same root - the clan of the Dal gCais. And therefore (if the Annals are true) they should all share a similar genetic signature.

Fast forward to 2006 and Ken Nordtvedt, an intrepid genetic genealogist, notices that a particular Y-DNA signature seems to be emerging for people with ancestry in southwest Ireland. Y-DNA is most informative for this research as (like the surname) it follows the direct male line. Another genetic genealogist, Dennis Wright, then decides to investigate this further. Dennis runs the R-L226 (Irish Type III) DNA Project and is co-administrator of the O’Brien DNA project. [2,3]

Dennis took the Irish Type III signature and searched the available databases for people with this Y-DNA signature. He identified 191 people with this signature and subjected them to further analysis. You can read his paper detailing the analysis here. [4] Most of the sample had Irish surnames, supporting an Irish origin for this particular genetic signature. Of those that had genealogical information available, most had MDKAs (Most Distant Known Ancestors) that had origins in the area around Clare, Tipperary & Limerick (the ancestral homeland of the Dal gCais).

He then assessed the ancient genealogy of the Dal gCais (from O’Hart’s version, which is readily available online) to identify modern-day surnames that supposedly arose from the Dal gCais (so-called Dalcassian surnames). [5] He then asked two very specific questions:
  1. what proportion of people with the DNA signature have Dalcassian surnames?
  2. what proportion of people with Dalcassian surnames have the signature?


Dalcassian surnames identified by Dennis & placed in a "family tree"

How many with the Signature have the Surname?
Dennis found that a significant proportion (29%) of the 191 men with the DNA signature had Dalcassian surnames. Conversely, 71% of the sample did not have Dalcassian surnames. A certain discordance is to be expected due to the occurrence of Surname or DNA Switches (SDS, aka NPEs) over the course of time. People often cite adoption & illegitimacy as obvious examples of how Y-DNA can be switched or become dis-associated with a particular surname, but there are many other causes including switching one’s surname to that of the Clan Chief as a sign of allegiance to him – a custom practiced throughout the time of the Irish clans. [6] Dennis cites a perfect example of another frequently overlooked cause. Morgan O’Brien married Eleanor Butler in 1690 and changed his surname to Butler, probably to ensure his and his wife’s right to inherit Butler lands near Bansha in Co. Tipperary. Thus any sons born to the couple would have carried the Butler name but O’Brien Y-DNA. [4]

How many with the Surname have the Signature?
Dennis also explored the potential association from the other way around – what proportion of people with the surname have the signature? He again searched the available databases to see what proportion of the surnames identified in his original sample (191) were associated with the DNA signature. Of 271 people with Dalcassian surnames, 57 had the signature (21%). And of 371 men with non-Dalcassian surnames, only 37 had the signature (10%). This difference (21% vs 10%) is statistically significant, further supporting the association of the specific DNA signature with the Dal gCais.

Subsequently, a direct male line descendant of Brian Boru took the Y-DNA test. He has a 30-generation pedigree that goes all the way back to Brian Boru. [7] The results came back revealing that he too shares the Irish Type III signature.

Dennis carried out this work in 2009, using only STR markers. Since then, the Irish Type III signature has become associated with a specific SNP marker (L226+) and a huge body of additional evidence has accumulated that bolsters the conclusions of the original study.

Brian Boru would have tested positive
for the SNP marker L226 (had he lived)

This was one of the earliest examples of how the Y-DNA signature of specific clans (and even specific leaders) could be determined through genetic genealogy. And the same basic methodology applies to any similar research being conducted today, and can equally be applied to help determine the Y-DNA signature of the O'Malley clan of Burrisk, Co. Mayo, which gave rise to Grace O'Malley, the Pirate Queen (1530-1603).

So to summarise the methodology developed by Dennis, the genetic signature of any specific clan can potentially be identified by demonstrating that:
1. Men who carry the specific Y-DNA signature have a higher frequency of MDKA origins in the ancestral clan territory (again, only men have Y-DNA, and this follows the direct male line along with the surname)
2. There is a significant preponderance of the specific DNA signature among men with clan-associated surnames
3. There is a significant surplus of clan-associated surnames bearing that specific DNA signature
4. People with an established genealogy going back to the specific clan also share the same specific Y-DNA signature

Identifying the DNA signature of the Mayo O'Malley's

Currently the O’Malley DNA Project has over 140 members and 70+ Y-DNA samples. [8] Of the 5 genetic groups within the O’Malley DNA Project, one has strong connections with Mayo, the ancestral county of Grace's clan. The Y-DNA signature of this group (Group 3) is therefore a prime candidate for the signature of the Mayo O'Malley clan. However, this group is subdivided into several subgroups - this complicates the analysis as any one of them could represent the signature of the clan. A further complication is the high risk of "chance matches" due to Convergence - a known issue with those people who sit on the M222 branch of the Tree of Mankind.


As a first step, we would need to clarify Grace's direct male line pedigree (back beyond the origins of the O'Malley clan) and put together a list of surnames supposedly associated with it over the passage of time (say, from about 200 AD onwards). This information can be gleaned from online sources, supplemented by data from The Great Book of Irish Genealogies (Leabhar Mór na nGenealach) by Duald Mac Firbis (written in 1650, published in 2004). [5,9]

The genealogy of the direct descendants of Grace is documented in the authoritative biography of Grace O'Malley by Anne Chambers, who runs the Grace O'Malley website. [10] Some lines of descent may extend to the present day. However, the Y-DNA in these situations would belong to Grace's husbands (Donal O'Flaherty & Richard Burke) ... and we could certainly try to identify this but it is not O'Malley Y-DNA. This is because Y-DNA is only passed from father to son ... and Grace (being a woman) would not have had a Y chromosome to pass on to her offspring. She would have passed on autosomal DNA to her children and this would have been chopped up, roughly halved, and passed on to the offspring of each subsequent generation up to the present day. As a result, modern day descendants of Grace would be approximately 11x times great grandchildren and would (on average) have inherited only about 0.05% of their DNA from Grace (less than 1 cM). This is essentially untraceable.

However, we have a genealogy for Grace O’Malley that includes a direct male line pedigree of descendants of her first cousin Thomas Roe O’Maille that extends to the present day. Testing male descendants on this direct male line will provide us with Y-DNA that should go all the way back to Grace’s father (if the genealogy is correct and barring any Surname or DNA Switch). And if that Y-DNA signature matches those of project members in one of the Mayo subgroups, then we have probably identified the DNA signature of the O’Malley’s of Mayo.

The analysis will also entail some extensive data gathering and will draw on public data in several Geographic & Haplogroup Projects (including the Ireland Y-DNA Project and the M222 Haplogroup Project). We may need to gather somewhere between 500 and 1000 Y-DNA signatures (to attempt to account for the problem of Convergence).

And thus anyone bearing this signature can claim to be a descendant of the O’Malley clan and a relative of Grace O’Malley.

Hopefully we can start this analysis later in the year. And hopefully it will work! We may only be able to get so far and then reach a roadblock. But it will be an interesting adventure nonetheless.

Watch this space!

Maurice Gleeson
Aug 2019

Sources & Links:

[1] Genealogy. by Kenneth Nicholls in The Heritage of Ireland. The Collins Press, 2000, pp156-161.

[2] R-L226 (Irish Type III) DNA Project … https://www.familytreedna.com/groups/r-l226-project/

[3] O’Brien DNA project … https://www.familytreedna.com/groups/obrien/

[4] 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

[5] O’Hart (1892). Irish Pedigrees, or the Origin and Stem of the Irish nation. Available at … https://www.libraryireland.com/Pedigrees1/index.php

[6] Goodbye NPE, Hello SDS - some causes of Surname or DNA Switches … https://dnaandfamilytreeresearch.blogspot.com/2018/07/goodbye-npe-hello-sds-some-causes-of.html

[7] Sir Conor O’Brien’s direct male line of ascent to Brian Boru … https://en.wikipedia.org/wiki/Conor_O%27Brien,_18th_Baron_Inchiquin

[8] O’Malley DNA Project … https://www.familytreedna.com/groups/omalley/

[9] MacFhirbhisigh, Dubhaltach; Ó Muraíle, Nollaig, editor (2003–2004). Leabhar Genealach. The Great Book of Irish Genealogies. Dublin: DeBurca. (Alternate names by which it may be referenced include Leabhar Mor nGenealach, and Leabhar Mor na nGenealach). It is not available online, but nearest library copies can be found here.

[10] Chambers, Anne (2018). Grace O'Malley : The Biography of Ireland's Pirate Queen 1530-1603. Gill Books, Dublin. More info at http://www.graceomalley.com/index.php/grace-omalley/40th-anniversary-edition




Getting the most from 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. 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), their Terminal SNP is M756 and you will find this branch on the Big Tree here (see screenshot below). The diagram nicely illustrates their placement on the Tree of Mankind and the surnames of the people sitting on neighbouring branches to their 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 (for example) are more closely related to each other 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




Thursday, 1 August 2019

Recent Project Updates all in one place

Over the last 8 weeks or so I have posted a series of updates for each of the 6 genetic groups within the project. Each update concludes with recommendations for Next Steps that group members could undertake to get the most out of their DNA results. The members of each group are encouraged to read the recommendations for their particular group and to ask me for help if there are any questions.

Here is a handy list of these updates with clickable hyperlinks for ease of reference and navigation:

Group 1 - Status Update (May 2019)

Group 2 Update (June 2019)

Group 3 Update (June 2019) - part 1 (subgroups 3b to 3e)

Group 3 Update (June 2019) - part 2 (subgroup 3a)

Group 4 Update (July 2019)

Birth of a New Genetic Family - Group 5

Birth of another new Group (Group 6)


And below is a video of the presentation that I gave at the recent O'Malley Clan Rally (Limerick, 23 June 2019). To watch it on YouTube, just click here.



Maurice Gleeson
Aug 2019




O'Malley Groups 1, 4, 5 & Ungrouped - update 2021

This is the last of the series of articles describing our Project Update 2021. Previous updates dealt with Group 2  (Limerick), the Group 3 ...