Ghosts of DNA Past: Irish Kings

   In 2006, Laoise T. Moore and the folks at Trinity College in Dublin published a paper famous for identifying the modal haplotype of Irish High King Niall of the Nine Hostages.  In their work, they used seventeen Y-DNA STR markers.  While time to most recent common ancestor (TMRCA) calculations have accuracy issues, having only 17 markers gives a common ancestor over 2,000 years ago.   What the Trinity folks really accomplished was the identification of Niall’s paternal ancestor from over 400 years earlier.  The media in 2006 had a field day in their interpretation that most of Ireland is descended from Niall.  “Niall may be the most prolific male in Irish history.”  Also at 17 markers, there is a very high probability of convergence.  Through normal mutations, haplotypes can change over time to appear similar or identical to other haplotypes.  The lower the number of markers, the higher the chance of convergence.  At that time only high level SNPs were tested to determine haplogroup.  Without terminal SNPs it would have been impossible to recognize convergence, if it existed in the samples.

   In my research on the Kings of Ireland, I have used 67 markers to reduce the chance of convergence and to calculate the age of common ancestors on the descendant side of the target rather than the ancestor side.  I will demonstrate traditional median-joining networks and novel “tribal” markers for the identification of four historic Kings of Ireland.  Did Trinity get Niall’s haplotype correct with the limited data they had at the time?

Ghost:  a manifestation of a dead person

Modal haplotype:  a derived haplotype based on the DNA tests of a group of people

   A modal haplotype is a ghost of a person.  When we look at multiple DNA test results and calculate the mode, by definition we are just taking the values that appear most often.  There is no way to determine if the modal haplotype is the actual haplotype of the historic individual we are researching (short of historic samples).  While the modal is not perfect, it will be close enough at 67 markers for us to determine the genetic “ghost”.

   The septs of Ireland provide us an opportunity to develop genetic genealogy techniques and processes.  Irish surnames are typically patronymic.  The surnames generally take the form of Mac Cárthaigh (McCarthy), meaning son of Cárthaigh or Ui Néill (O’Neill), meaning grandson / descendant of Néill.  Irish septs serve as a collective of related families with shared ancestry and patronymic surnames.  Multiple septs then belong to larger dynasties such as the Eóganachta and the Dál gCais.

   If septs are patrilineal, then Y-DNA haplotypes should be consistent across sept surnames.  Research on the Uí Néill haplotype started with a geographical selection and then a subsequent reduction by sept surnames (Moore et al 2006).  For each target sept, affiliated surnames were identified.  In the case of Uí Néill, the following surnames and associated Y-DNA STR records were accessed from Family Tree DNA projects: O’Neill, Gallagher, Doherty and O’Donnell.  The selection includes 600 records and 5 common European haplogroups.

   Median-joining networks have been in use for over a decade for the visualization of genetic relationships.  The use of them at 67 STR markers has been rare, but it should be the norm.  This first image has the central cluster of a median joining network based on 25 STR markers from the Uí Néill group.  It is just a single cluster with no differentiation.

Figure 1 - Using only 25 STR markers, the Uí Néill network collapses to a single cluster.

When we look at the same group using 67 markers, we get four distinct clusters, each with their own SNP.  The cluster at the far right is predominantly R-L159 and the cluster at the lower right has R-P311/R-L151 nodes.  The cluster at the left contains all of the Uí Néill dynastic surnames, has the majority of nodes and is SNP R-M222, which is consistent with earlier studies.

Figure 2 - View of the Uí Néill network torso showing four distinct clusters.  Three groups on the right are O’Neill only.

As a double check to make sure that I wasn’t seeing some other phenomena, I analyzed three random Irish surnames; Duffy, Kelly and McCormick.  The random sample produced over ten unique clusters with no surname overlap.  This comparison shows that septs are patrilineal and that Y-DNA haplotypes are consistent across sept surnames. 

Figure 3 - Median-joining network of yDNA sampled from three random Irish surnames; Duffy, Kelly and McCormick.  

Re-evaluating the Uí Néill data also shows that Trinity was correct in their identification of a 17-marker Uí Néill haplotype.  New data and new techniques allow us to produce a 67-marker haplotype.

Figure 4 - Sixty-seven STR Uí Néill Modal Haplotype (Niall of the Nine Hostages).

   A different technique that I’d like to illustrate involves the fact that not all STR markers are created equal.  This method takes advantage of “slow” mutating STR markers.  Each marker has its own mutation rate.  By selecting the 15 “slowest” markers with an average mutation rate of 0.00024, a virtual tribal haplotype is created that would be stable within the last 2,000 years (90% probability of 80 generations).  This is an order of magnitude lower than the average rate of 0.0029 used as a constant in typical TMRCA calculations.  The “tribal” markers isolated are DYS426, DYS388, DYS392, DYS455, DYS454, DYS578, DYS590, DYS641, DYS472, DYS594, DYS436, DYS490, DYS450 and DYS640.

   To manipulate the “tribal” haplotype of 15 microsatellites faster the resulting values are concatenated into a string – ex. 12121411119168108101212811.  The “tribal” haplotypes are summarized per surname and plotted to illustrate majority and affinity.

Figure 5 - Uí Néill dynastic haplotypes converted into 15 marker “tribal” haplotypes and summarized.

   The Uí Néill dataset resolved into 37 unique “tribal” haplotypes.  Figure 5 shows that haplotype 12121411119168108101212811 is the most dominant across the Uí Néill surnames.  As with the median-joining network analysis, this “tribal” haplotype is consistent with SNP R-M222. 

   I repeated these two techniques for the Uí Briúin sept using the following surnames and associated Y-DNA records: O’Brien, Hogan, Kennedy and McMahon.  The selection includes 615 records.  The Mac Cárthaigh dataset has the following surnames: McCarthy, Callaghan, Donovan and Sullivan.  The selection includes 319 records.  The Ua Conchobhair data has the following surnames: O’Connor, McManus, Reilly and Rourke.  The selection includes 352 records.

For more details, see my paper at Academia.edu.

Figure 6 - Sixty-seven STR Uí Briúin Modal Haplotype (Brian Boru).

Figure 7 - Sixty-seven STR Mac Cárthaigh Modal Haplotype (McCarthy Eoganachta Kings).

Figure 8 - Sixty-seven STR Ua Conchobhair Modal Haplotype (Last High King Roderick O'Connor).

   Here are a couple of interesting insights from my research.  Niall Noígíallach was High King of Ireland around 378 CE and founder of the Uí Néill dynasty.  Historically, his half-brother Brión, was one of the founders on the Connachta dynasty and an ancestor of the last High King of Ireland, Ruaidrí Ua Conchobair.  If their genealogies are correct, the evidence is in their descendant’s DNA.  The data shows that Uí Néill and Ua Conchobair share the same SNP, R-M222.  The Uí Néill and Ua Conchobair modals are a 6-step match at 67 markers.  There is a 99% probability of a relationship not further than 1,260 years ago.  The results make a strong case for the validity of this historic genealogy.

   Brian Boru, High King of Ireland in 1002 CE, belonged to the Dál gCais dynasty and Tadhg Mac Cárthaigh, the first King of Desmond, belonged to the Eóganachta dynasty.  Ancient genealogies have the Eóganachta and Dál gCais dynasties descended from Ailill Aulom, the son-in-law of legendary king Conn of the Hundred Battles.  The Mac Cárthaighs and Uí Briúins do not share the same SNP (R-L226 vs. R-CTS4466), but by descent they would share a common R-DF13 ancestor.  The Mac Cárthaigh and Uí Briúin modals are an 11-step match at 67 markers.  There is a 99% probability of a relationship not further than 1,920 years ago.  This puts a Mac Cárthaigh-Uí Briúin common ancestor as a contemporary of the legendary Conn.

   New and improved genetic genealogy techniques are invaluable for the identification of historic individuals and the reconstruction of distant family trees at the macro level.

Reference:

Maglio, MR (2015) Identifying Y-Chromosome Dynastic Haplotypes: The High Kings of Ireland Revisited (Link)

Genealogy Gold: McCarthy DNA

   Sometimes in genealogy, we go for the gold.  We try to figure out how we are descended from Presidents, royalty or other famous people.  In the US, if your last name were Adams, you might ask if you are related to the second President.  With a surname like Stewart/Stuart you could try to research back to UK royalty.  If you are Irish, some of those royal names are O’Neill, O’Brien or McCarthy.

   The last King in Ireland died in the 1600s.  For many of us it is incredibly difficult to go back beyond the 1800s in our Irish genealogy research.  The lack of paper records makes finding that connection to Irish royalty challenging.

   DNA is the next best answer to the lack of records.  Both regional and surname projects can collect enough genetic samples to build family trees.  Not in the same sense as child - father - grandfather etc., more in a phylogenetic sense.  A phylogenetic tree will show how individuals connect back to common ancestors and in turn, those common ancestors trace further back to another common connection.

   I have McCarthy ancestry and like everyone else I have researched as much as possible about one of my surnames.  Historically the surname comes from Carthaigh or Carthach, an 11th century King of Ireland and ancestor of the McCarthy Kings of Desmond (current day Cork and Kerry).  His son, Muireadhach, was the first to take on the Mac Carthaigh name.  Literally the ‘son of Carthaigh’.  In names like O’Neill or O’Brien, the O’ means grandson or descendant.

   Time to go for the gold.  How am I related to the Kings of Ireland?  Which DNA haplogroup do the McCarthys belong?  First, I found that a surname project existed on Family Tree DNA.  Then I started analyzing the data on the McCarthy Surname Study DNA site.  Nothing is ever simple.  There are six different haplogroup represented in the group, E1b, I1, I2a, I2b, R1a and R1b.  There are also four different R1b subgroups.  The site has R1b divided into Group A (SNP R-L21), Group B (SNP R-P314.2), Group C (SNP R-M222) and Group D (misc. others).  I would expect there to be multiple R1b subgroups as it is the most numerous haplogroup in Western Europe.

   Like the Olympics, there can only be one gold medal winner in this event.  Only one (or none) of these groups can be related to the original Carthaigh.  There are many reasons why there are multiple McCarthy haplogroups.  The Administrator of the McCarthy site, Nigel McCarthy, is well aware that there could be non-paternal events and has posted some possible situations where a McCarthy name could have arisen:

“•Soldiers, serfs, or slaves or hostages taken in battle and who remained with their captives, all under the tutelage of a McCarthy king, chief of chieftain, adopting this surname.
•Rape of McCarthy womenfolk by invading forces.
•Other illegitimacy.
•Adoption (e.g. by a chieftain of a sister’s orphaned children).
•Raiders such as Vikings being absorbed, a century or two after they settled in Ireland,  into the group which became the McCarthy family as they became “gaelicised”.
•Stepsons taking the McCarthy name of their new stepfather (early deaths of husbands or wives, and thus remarriages, were common).
•The sons of Cárthachs other than he who died in 1045 forming their surnames in a similar manner (although there is no explicit evidence of this).”
-source McCarthy Surname Study - Background

   Which genes are the royal McCarthy genes?  Other projects have been able to analyze DNA records and come back with an announcement that they have identified the haplotypes of Genghis Khan or Niall, ancestor of the O’Neill kings.  The same methods should work for the McCarthys.  If we consider the McCarthy DNA records as a random sample representing the larger population, then the groups with the larger number of records are more likely to be part of the royal group.  A wealthier family would have had more resources to provide for larger families, allowing for more descendants.

   Looking at the McCarthy site, haplogroup R1b Groups A and B have the most records.  At first glance, the other haplogroups seem to be ruled out for lack of representation.  An analysis of the haplotypes within these haplogroups gives us additional evidence.  The E1b group shows a clear pattern of migration from Greece through Italy, Germany, England and Scotland before arriving in Ireland.  This is consistent with the Alexandrian origin of E1b and the timing fits with Rome’s incursion into the region.

   Haplogroup I2b shows a migration from the Danube River region through Germany, England, Scotland and into Northern Ireland.  They appear to have arrived before the Romans.  Haplogroup R1a originated from Eastern Europe and took a different path via Normandy, Devon/Cornwall, into Ireland through Cork.  Their timing fits the Norman invasion of Ireland about 900 years ago.

   If we calculate the time to most recent common ancestor (TMRCA) for Groups A and B, we see that within each group they are closely related.  For each group, their common ancestor lived about 1,000 years ago, which coincides with Carthaigh’s timeframe.  Comparing the two groups against each other shows a common ancestor over 2,800 years ago.  Both groups have the right ancestral timing.  Group A has DNA that is associated with Southern Ireland and an analysis across a larger R1b tribal haplotype indicates that this group entered Ireland over 2,600 years ago.  The same analysis of Group B indicates that they entered Ireland about 500 years later.  Group A has been in Ireland longer and occupy the ancestral region of Desmond.

   So far, we have circumstantial evidence.  We need something more concrete.  We can get a clue from the historic royal genealogies.  The McCarthys were more than just a royal family.  They were a dynasty.  Along with the surname McCarthy, there were also the Sullivans, Callaghans, Keeffes, Donoghues and Donovans that made up the larger related genetic dynasty.  Looking at each group in the context of the larger genetic pool of records and surnames shows that Group A has a close DNA connection to the dynastic surnames and Group B does not.  This method was a key factor in the O’Neill project.

   The evidence points to Group A as the descendants of the royal McCarthys.  The haplotype for Carthaigh is slightly different from the modal for the McCarthy Project Group A.  Considering the dynastic records, makes the values of DYS576=19 and DYS442=13.

   The pedigree of Carthaigh’s ancestors borders on mythology.  Many Irish pedigrees trace back to Milesius of Spain as the father of the Irish people.  Historians found it easy to dispute these claims as these records often are full of conflicting historical information, a lack of dates and obvious attempts to connect back to the Biblical genealogies.  As with most mythology, the Irish origins contain grains of truth.  Haplogroup R1b, which is predominant in Ireland, has its origins in Iberia (modern day Spain and Portugal).  The McCarthy Group A DNA data can be traced backward in time via STR mutations to their Spanish and Portuguese cousins.  Imagine two brothers at a farewell party on the slopes of the Pyrenees 3,000 years ago.  One brother has decided to go north to seek better fortunes and the other decided to stay behind.  The ancestors of each exist today for us to compare.

   The Irish do have ‘Spanish’ origins.  Some elements of that oral history remained intact over 3,000 years as the Iberian tribe migrated and settled in Ireland.  As with any oral tradition, embellishment can occur, especially when developing a royal pedigree to show divine right.

   McCarthy Group A was not the first Iberian tribe to land in Ireland and certainly not the last.  Group B arrived about 500-1,000 after Group A.  Irish mythology suggests that there were at least four previous waves of immigration to Ireland from the mainland.  The E1b McCarthy ancestors begin to show up around 2,000 years ago with the Roman invasion and the R1a McCarthys are associated with the Norman invasion of Ireland about 900 years ago.

   My next steps are to find my male McCarthy cousins and get them tested.  I’ll look for at least two, one from each of my g-granduncle’s surviving lines.  My McCarthys trace back to Kilmichael Parish in County Cork and my gg-grandfather, Florence McCarthy, has one of those names that repeats throughout McCarthy history.   I look forward to finding out which McCarthy DNA group I belong.

   If you are a McCarthy, please consider DNA testing and joining the McCarthy DNA Project.  Your data will help build a better understanding and a better genetic family tree of the McCarthy groups.  Along the way, we can learn more about our ethnicity and our Irish culture.  You may even want to change your surname back to its original Irish spelling, Súilleabháin (Sullivan), Ceallacháin (Callaghan), Donnchadha (Donoghue), Donnabhain (Donovan) or Mac Carthaigh.

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