Wednesday 7 August 2019

A New Genetic Family is Born - Lineage VIII (North Tipperary)

Back in April this year, some new Y-DNA-37 results recently came back from the lab and I've been meaning to blog about them since then! The results were reviewed by me and our new Co-Administrator Lisa Little, and here is a brief summary of what they tell us.

The new member (MG-9273) had 11 matches (comparing his 37 marker results to everyone else in the database) and one of them was an ungrouped Gleeson who was already in our project (PG-7861). The Genetic Distance (GD) between them was 3/37 indicating 3 steps away from an exact match. And this would predict that they share a common ancestor some time within the last 14 generations (i.e. after 1530) and probably closer to 6 generations ago (about 1770). And as a result of this match, we were able to identify a new genetic family, which we have called Lineage VIII.

Judging by the other people these two project members match, this group appears to have come from North Tipperary. The names Meara, O’Mara, Leahy, and Carrell appear among their matches and all have strong North Tipperary connections. You can see where they sit in relation to each other on the “Tree of Mankind” here and in the diagram below.

The new genetic family (Lineage VIII) sits somewhere in this region of the Tree of Mankind

The names Kennedy & Carrell / Carroll (in the diagram above) are also strong North Tipperary names.

A SNP Progression is the series of SNPs that characterise each branching point in the Tree of Mankind from a relatively upstream ancient SNP marker down to where you sit on the Tree of Mankind. And the SNP Progressions associated with the O’Meara & Leahy branches are:
  • R-P312/S116 > Z290 > L21/S145 > DF13 > DF21/S192 > FGC3213 > Z16532 > Z16526 > Z16524 > Z16534 > Z16533 > Z16538 >Z16525 > Z16523 … 
  • then > BY61171 > Y142760 (Meara) … 
  • or > FGC14748 (Leahy)
Many of these SNP markers can be seen in the diagram above and also among the Y-DNA matches of the two members of the new Lineage. This all suggests that this particular Gleeson branch sits somewhere in the same area of the Tree of Mankind as the O’Meara’s and Leahy's.

The new group (Lineage VIII) is one of several North Tipperary groups of Gleeson’s (the others being the large Lineage II and the smaller Lineage VII). It could be that if we went back far enough along the father’s father’s father’s line of these two men that eventually we would see the name change to O’Meara or Leahy, but that could have been 400 years ago or more. The only way to be sure would be to do the Big-Y-700 test which would give very fine-scale detail about the position of this new Lineage on the Tree of Mankind.

But before that there are several things that can be done that would provide us with some useful additional information:
  1. Both project members could update the information on their MDKA (Most Distant Known Ancestor) - this will optimise the chances of making connections with other genetic cousins. See here for instructions ...
  2. Joining the relevant Geographic & Haplogroup DNA Projects could provide some additional interpretation from the Project Administrators, and its all free. To do so, simply click on JOIN in the photo on the following webpages:
    1. Ireland yDNA
    2. Munster Irish
    3. R1b & subclades
    4. R-L21
    5. R-DF21
    6. R-Z16526
  3. The members of the new group could contact each other and share information about their family trees. If they are lucky, they might even be able to identify where they connect.

Maurice Gleeson
April 2019

Uploading your New Big Y 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 and we will look at these results in a subsequent post.

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.

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

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 the particular portion of the Big Tree. Here you will see 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. Gleeson Lineage II members are surrounded by O'Carroll's (from nearby Offaly), McMahon's (from neighbouring Clare), McCarthy's (from North Cork), and Treacy's (from Galway). You can see these neighbouring branches in this portion of the Big Tree here.

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 Gleeson'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.

Maurice Gleeson
Aug 2019

Thursday 24 January 2019

What's in a name?

I am delighted to introduce this guest blog post by Lisa Little, a member of the Lineage II Gleeson's of North Tipperary. Lisa has done some excellent research on her own particular direct male line which has taken her on an exciting adventure into the past, full of twists and turns. Lisa started out as a Little but ended up as a Gleason! And this is not an uncommon situation - many of us will find a surname or DNA switch (SDS or NPE) somewhere along our direct male line. Lisa used an ingenious approach (combining Y-DNA and autosomal DNA data) to elaborate this family mystery and discover where the surname switch occurred.

Thank you, Lisa, for sharing this wonderful story with us.
Maurice Gleeson
Jan 2019

What's in a name? that which we call a Gleason
By any other name would still be a Gleason . . .

The Story of Finding my Gleason Ancestry
By Lisa M Little

Benjamin J Little (1889-1989)

My maiden name is Little.  As a child, the name made me an easy target for a bully’s joke. Despite this, I have proudly kept this surname throughout my adult life.  Until 2006, I knew almost nothing of my Little ancestry.  My grandfather, Ben Little, was born in late 19thcentury San Francisco, California.  The documentary record of his early life was largely destroyed in the 1906 San Francisco earthquake and fire.  There was a vague family story of Ben’s father abandoning him as a toddler, never to be heard of again.  In the pre-home computer age of the 1970s, my hunt for my Little great grandfather, turned up only a single document (Ben Little’s Baptismal Certificate from Our Lady of Guadalupe Church on Broadway in San Francisco) bearing my great grandfather’s name:  Eugenio Little.

Figure 1   Author's documented paternal lineage 
at start of research 
(Eugenio is a Spanish variant of Eugene)

Thirty years later, in 2006, I was living in Georgia, USA, far from my family in California when I got the news that my father was in the hospital following a heart attack.  Being so far away, and feeling the need to connect, I returned to my search for my Little ancestry.  Genealogy had changed in the meantime, resources were now online and DNA analysis was opening doors to the past.  I decided to have my father do a Family Tree DNA (FTDNA) Y-25 test in hopes that we would find a match among those who had tested and were participating in the Little Surname DNA Project.  Much to my disappointment, the results identified my father as R1b haplogroup but did not match a single Little in the project.  Despite this disappointment, with the help of the project administrator, the late Leo Little, we hit the genealogical jackpot.  Leo was able to connect my Eugenio with his Little lineage by finding a reference to him in Descendants of George Little, who came to Newbury, Massachusetts, in 1640 by George Thomas Little1.  All of a sudden, I had generations of Littles to become acquainted with --- Littles who were early colonists in North America, Littles who fought in the Revolutionary War, even Littles who had participated in the Salem Witch Trials.  Following the paper trail to George Little now occupied my time and the DNA test slipped from my memory.

Figure 2   Cover of George Little genealogy 
which includes reference to Eugene M Little

Then, in November of 2013, I received an email from a FTDNA project administrator who, having reviewed my father’s Y-DNA results, suggested that he was likely to have the Z255 mutation, associated with the Irish Sea Haplotype.  By this time, I was teaching basic genetic structure and function to community college students in Southern California and thought testing for the mutation might prove useful as a teaching aid.  So, I ordered the Z255 SNP test from FTDNA. The test came back positive!  With these results in hand, I decided it was time to revisit the Little Surname DNA Project results page.  Surely, after so many years another descendant of George Little must have tested and joined the project.  Alas, still no match!  I asked myself how this could be the case.  The published George Little genealogy was over 600 pages long and included more than 6,400 descendants.  Surely, there was a living descendant apart from my father who had done a DNA test.

It was obviously time to put some real energy into figuring out what the DNA results were telling me.  Reviewing my father’s Y-25 DNA matches didn’t make any sense – not a single Little among all those genetic matches.  In fact, five of his 25 matches had the last name Gleason/Gleeson.  Only two other surnames had multiple matches:  Fennessy with two matches and Salisbury with three matches.  My head was spinning!  Obviously, I had more work to do to understand the results.  

A few months later, I was reading a post on the ISOGG website by Fannie Barnes Linder, entitled The Shock of Our Lives!  Ms. Linder told the story of receiving her brother’s DNA results only to find the top 16 matches all shared the same surname, not the surname of her brother, nor their father.  What she had discovered was a non-paternity event (NPE) in her paternal lineage.  According to ISOGG wiki, a non-paternity event is “any event which has caused a break in the link between an hereditary surname and the Y-chromosome in a son using a different surname from that of his biological father.”2  Suddenly, everything fell into place!  The lightbulb went off in my head!  No Little surname matches, but five Gleason/Gleeson matches!  My father was not a genetic Descendant of George Little.  Rather, he was the genetic descendant of some unknown Gleason.  No!  As a genetic genealogy novice, I didn’t trust my reading of the results.  So I turned to my friend, David Lyttle, who was at the time the DNA test consultant for Clan Little North America.  After reviewing my assembled data, he agreed I must be onto something.

Armed with this new NPE hypothesis, my research had three initial goals:  1) do more advanced testing, 2) reach out to close genetic matches in order to identify the North American Gleason lineage to which I belong and 3) explore the timing of the non-paternity event.

Still doubting the validity of my Gleason hypothesis, in the spring of 2014 I ordered a Y-67 DNA test.  Results were posted on June 6th:  of 23 matches, four were Gleason/Gleesons, with Genetic Distance (GD) values of 2 to 7.  The following day, June 7th, another Gleason match appeared, with GD 1.
TABLE 1:  FTDNA Y-67 Matches on June 7, 2014
# matches
Doty, Johnston, Myrick, Tripp
Anthony, Daley, Fennessy, Fitzpatrick, Gleason, Hogan-Wilbur, McCarthy, McCloughan, Myrick (2), Phelps (3), Whitmore (2), Wyght

have come to realize that Hestia, the Greek goddess of the hearth and family, is surely smiling upon me and guiding the search for my ancestry.  The two closest matches (or rather the administrators of the matches’ DNA kits) turned out to be genealogy experts who would become my teachers and partners in the search for our shared origins.  The closest match was Herbert L Gleason Jr (HLG/G55), the father and father-in-law of a couple who own Heirlines Family History & Genealogy in Salt Lake City, Mary Gleason Petty & James Petty .  The second closest match was father of none other than our Gleason/Gleeson DNA Project co-administrator and professional genetic genealogist, Dr. Maurice Gleeson. I again hit the genealogy jackpot! Thank you, Hestia!  On June 6th I sent my first email to Maurice and on the 8th received a message from Mary Gleason Petty.  In a matter of days, I discovered that my (genetic) paternal ancestors were Irish and that I fit somewhere into a North American Gleason lineage whose patriarch was James Gleason (1775-1805) of Dorchester, Massachusetts (See Figure 3).

Figure 3   Mary Gleason Petty's Paternal Lineage

Over the next year Y-111, Big Y, and Family Finder genetic tests were completed on my father.  With each new set of results, the evidence of my Gleason ancestry grew stronger (See Table 2).  And, yes, I became more and more addicted to genetic testing.

TABLE 2:  FTDNA Y-111 Matches on September 16, 2014
Surname (Kit #/Project ID)
Gleason (338070/G55/HLG)
Gleeson (N74958/G21)
Gleeson (334030/G54)
Gleason (N101540/G39)

Analysis of my father’s Y-111 STR mutations placed our paternal ancestors within Lineage II – Gleesons of North Tipperary, Ireland.  This evidence, coupled with Big Y SNP mutations, narrowed his position within Lineage II to Branch B (See Figure 4).  The details of this placement within the Gleason/Gleeson Mutation History Tree have been described in Maurice’s blog post dated 8 July 2018, A Closer Look at Branch B - New Y-DNA Results.

Figure 4   Detail of Lineage II Branch B Relationships. 
RTL = G57, HLG = G55

The Family Finder (FF) test, completed in July of 2015, identified Mary Gleason Petty’s father (HLG/G55) as my father’s (RTL/G57) 3rd to 5th cousin, with 40 shared centiMorgans (cM).  Assuming the two men were of the same generation, due to their similar ages, the FF results suggested that they shared a 2nd great grandfather to 4th great grandfather.  James Gleason of Dorchester, MA (1772-1805) would be their 3rd great grandfather. James had two sons and six grandsons. I simply didn’t have enough genetic data to narrow down where my paternal lineage fit into Mary’s family tree. The best I could do is try to find a geographic overlap between Mary’s Gleasons and my Littles.  One possible overlap became evident:  James Gleason (1772-1805) had a grandson, James Henry Gleason, who had settled in Monterey, California in 1846 and married a Californiobeauty.  While James Henry Gleason died 28 years before my grandfather was born, he did have four sons who might be worth a closer look.

I decided to focus some effort on the timing question:  When did the Gleason Y-DNA enter my Little lineage?    My first working hypothesis was:  My father (RTL/G57) was the first genetic Gleason and, thus, would not be a Y-chromosome match to his brothers.  (Forgive me Grandma Little for ever considering such a thing!)  As both of my paternal uncles passed away prior to my DNA discovery, I turned to one of their sons (G64 in Figure 4) for a Y-DNA test.  In May of 2015 my cousin’s Y-37 results were published:  a perfect match (GD = 0) to my father.  With my initial hypothesis rejected, I moved onto the prior generation. This is where I hit a brick wall. My grandfather, Ben Little, had no full male siblings.  There were half-brothers from his mother’s second marriage, but they would not share the same Y-DNA.  I moved back to Eugene Little’s generation in search of another living male descendant. Unfortunately, Eugene and his younger brother, Arthur Little, never had any male children that could be traced in the genealogical record.  My search for a living descendant of George Little continued generation by generation and took me from California to Maine, spanning 240 years.  Finally, a single living descendant was identified.  Then came time for that dreaded exchange, “Hello, I am a distant cousin.  Would you be willing to do a DNA test for me?”  This is a question that always leaves me feeling uneasy.  However, in this case, the answer was, ‘Yes’.  No hesitation.  In October of 2015, the FTNDA Y-37 results told us that my father and the Little 4th cousin are not a genetic match. These results pinpointed a 100-year period during which the Gleason Y-DNA could have been introduced into my paternal ancestry.  The problem remained that my exhaustive research of the Little family tree had failed to identify another living direct male descendant whom I could approach for DNA testing.  I began to create fanciful storylines with the genealogical evidence that was available:  Eugene Little’s grandmother got pregnant after an encounter with a Gleason man and was hurriedly married off to her first cousin. Ok, I’ll admit I have an over active imagination.  It’s just more fun to imagine a romance story than to admit I had hit the brick wall and saw few strategies to surmount it.

While in 2015 this Little “4th cousin” did not have a Y-DNA match to another male within the Little DNA Project, who claims descent from George Little of Newbury, MA, in January of 2019 a GD 1/37 match was made.  The two men share George Little’s oldest son as their most recent common ancestor, making them 8th cousins.  Taken together, the Y-DNA results for the two men have now established a genetic profile for their Little lineage to which future descendants of George Little can be matched.

Figure 5   Possible locations of the Surname / DNA Switch (SDS a.k.a. NPE)
The switch happened somewhere on the Little Direct Male Line ... but where?
FF suggests a connection to HLG / G55 via common 2x to 4x great grandparents (red bracket on left)
Y-DNA of Little cousins rules out switch prior to Benjamin Little 1802-1907 & after Benjamin Little 1889-1989
Green indicates Gleason Lineage II Y-DNA, Orange indicates Little Y-DNA
(click to enlarge)

Faced with a seeming insurmountable challenge, during the Spring of 2016 I was excited to hear that Maurice Gleeson was visiting Southern California.  At last, after two years of email exchanges with my mentor, I had the opportunity to meet him in person and discuss future research strategies.  During a delightful lunch, that included Mary Gleason Petty’s sister, Martha (a mini Gleason family reunion), Maurice suggested that I do the autosomal DNA test on my father.  Perhaps, wading into another database would prove helpful.  

Eureka! In May of 2016 I opened my father’s newly published DNA results on my computer.  As I scrolled down the list of matches, my reaction was, “You have to be kidding me!”  Many usernames were simple initials.  It was going to take some real time investment to find Gleason matches with only last initials to go by.  My initial panic was unwarranted as among the 3rd cousin matches was an individual with a ‘G’ surname initial and a kit manager with the surname Gleason. Correspondence with the kit manager confirmed that the individual was a descendant of James Henry Gleason (JHG) of Monterey, California.  This match and my father shared 118 centiMorgans over three segments, a considerably closer autosomal match than to Mary’s father of 40 cM.  Could I hope that one of the four sons of JHG could be my genetic great grandfather?

This is where I needed to bring the genealogical record together with the genetic data.  Eugene Little was born in 1853 in Maine.  JHG was born in Plymouth, MA in 1823, making him old enough to have been Eugene’s biological father.  However, JHG’s youth has been well documented and published in a book entitled Beloved Sister:  Letters by James Henry Gleason from California and the Sandwich Islands, 1841-1859.JHG was a continent away when Eugene was conceived and born.  JHG’s four sons were born between 1850 and 1860, making them 39 to 29 at the time my grandfather, Ben Little, was born.  The timing is right for one of James’ sons to be my genetic great grandfather but what other evidence could be brought to bear?  

If one of these four Gleason men was my grandfather’s biological parent, I should also find genetic matches to descendants of their mother’s family.  I mentioned above that she, Mariana Catarina Demetria Watson, was a Californio beauty.  Many early European settlers in California married into prosperous Mexican families prior to US control of the territory.  JHG’s father-in-law, James E Watson, was among this group.  James Watson, an Englishman of Scottish origin, arrived in California in the 1820s and set up a hide and tallow business.  He married Marianna Escamilla in 1830 and in 1850, he purchased the Rancho San Benito in the Salinas Valley.  I began to search my father’s DNA matches for descendants of the Watson and Escamilla families.  

This is where DNA Circles can be a useful aid in exploring hypothesized relationships.  After updating my linked family tree to include JHG and his wife, as well as her Watson/Escamilla parents, a DNA Circle was generated that included several individuals who trace their ancestry to Marianna Escamilla.  Today, that DNA Circle includes 21 members.

Figure 6   Ancestry's DNA Circle
for my (genetic) great great grandmother

Being a genetic match to 20+ descendants of Marianna Escamilla strongly supports the idea that one of her grandsons was the biological father of Ben Little.  The DNA evidence had revealed a NPE and led me to my genetic Gleason family.  The task that lies ahead is figuring out which of the four sons of James Henry Gleason met another Mexican beauty, Ben’s mother Librada Solano, and conceived my grandfather. If I could locate a living grandchild of each of the four brothers, three of them would be 2nd cousins to my father, and one of them would be a half-1st cousin. Autosomal DNA testing of each should distinguish between them: 2nd cousins share on average 220 cM, while half-1st cousins have an average 440 shared centiMorgans.

That part of my journey is for a future blog post.

Figure 7   The current draft of my (genetic) family tree on my father's side

1 Little, G. Thomas. (1882). Descendants of George Little: who came to Newbury, Massachusetts, in 1640. Auburn, ME: George Thomas Little.
International Society of Genetic Genealogy Wiki:  Non-paternity event.  Page last modified 17 July 2018.  Page accessed  21 January 2019.
Californio (plural Californios) = A Spanish-speaking resident of the now US state of California during the period of Spanish and Mexican rule, roughly from the late 17th to mid-19th centuries.
Gleason, James Henry (1978) Beloved Sister: The letters of James Henry Gleason, 1841-1859, from Alta California and the Sandwich Islands, with a brief account of his voyage in 1841 via Cape Horn to Oahu and California. Glendale, CA:  A. H. Clark Co.

Lisa M Little
Jan 2019