Friday, 13 July 2018

Goodbye NPE, Hello SDS - some causes of Surname or DNA Switches

The term NPE stands for Non-Paternity Event, or Non-Parental Event, or alternatively Not the Parent Expected - a much more descriptive and accurate term coined by Emily Aulicino. It refers to the break in transmission either of the surname or of the DNA from parent to child. The break in transmission can occur from father to child, or from mother to child, or both. For fathers, the break in transmission can involve either the surname or the DNA; for mothers, the break in transmission involves only the DNA.

In relation to surname research, an NPE refers to a break in transmission of either Y-DNA or the family surname from the father to the son, along the direct male line (the father's father's father's line). Either the surname is switched for another one, or the father's Y-DNA is switched for some other man's Y-DNA. For this reason, I prefer to use the term Surname or DNA Switch (SDS), because it is much more descriptive and easier to understand than the term NPE which is somewhat obscure.



Surname or DNA Switches are important because they can mislead your family tree research, especially if you are using Y-DNA to research your surname, which should have passed down your father's father's father's line hand in hand with your Y-DNA ... but that is not always the case. 

In Ireland (as in many European cultures) where a system of hereditary surnames has been in existence for almost 1000 years, the chances of having an SDS on any one of your ancestral lines is about 50%. Here's the reason why:
  • According to several different studies, the average incidence of SDSs seems to be about 1-2% per generation.
  • So, if we allow 25 years per generation and hence 4 generations in 100 yrs, that will give us 40 generations in 1000 years.
  • multiply that by 1-2% per generation and that gives us a 33-55% chance of an SDS on any ancestral line going back 40 generations [for these corrected calculations see the first comment in the Comments section below]
  • If we go back along the father's father's father's line, then there is a 33-55% chance that your Y-DNA does not go back to the person who originated that surname.
  • If we allow 33 years per generation (and hence 3 generations per 100 years), then the chances of an SDS in the past 1000 years is 28-49% on each ancestral line [for these corrected calculations see the first comment in the Comments section below]
  • Whether you choose the 33-55% option or the 28-49% option, about half of us will not share the same DNA as the man who first held our surname … but half of us will.

There are many causes for SDSs and in relation to Irish family history, there are some unusual Irish-specific reasons for SDSs.

Allegiance to the Lord or Chieftain of the Clan (Sept, or Tuath)
It was not unusual for the servants, soldiers, vassals, tenants, or slaves of a clan to take (or be given) the name of their chief. This was a sign of respect for the chief but may also have conferred protection on the bearers of the surname. As a result, one would expect surnames that were associated with powerful clans to have many different Y-DNA signatures. And conversely, surnames that were associated with non-powerful clans and septs would have relatively few Y-DNA signatures. Surnames that might demonstrate this kind of pattern of multiple Y-DNA signatures associated with a single surname might include: O'Brien, Kennedy, O'Neill, O'Donnell, etc

This is an example of a surname-switch SDS. It means that the father who is doing the child-rearing will raise a son with the same Y-DNA as himself but with a different surname.

The Past was a different country - different customs, different reasons for Surname  or DNA Switches (SDS)

A similar situation arose with the Trans-Atlantic Slave Trade, where many enslaved people were given the surname of the Plantation Owner. Thus many African Americans today will carry the name of the slave owner of their ancestors (i.e. SDS present), and some will carry the Y-DNA of that slave owner (i.e. no SDS present), or his family (possible SDS), or the overseers he employed on his plantation (SDS present).

Adoption / Fostering / Guardianship
Modern adoptions are an obvious cause of surname switches. The adopted child takes on the surname of the adoptive father but carries the Y-DNA of his birth father. In times past, orphans or waifs would take on the surname of their guardians. These examples result in the child-rearing father having a son with the same surname as himself but with different Y-DNA.

Fostering on the other hand, did not frequently result in a surname switch. Under the Brehon Law of fosterage, children were brought up by relatives who were usually within the 5th degree of kinship (e.g. great uncle, 1st cousin once removed). However, the child did not adopt the family name of his foster family. Instead he retained his own family name and thus there would have been no SDS as a result.

Similarly, with modern-day fostering, the child in question does not usually take on the name of the foster family i.e. there is no SDS.

Young widow remarries
It would not be unusual for the young children of a woman recently remarried, to adopt the surname of her new husband. This results in the child-rearing father (i.e. the second husband) having a son (i.e. stepson) with the same surname as himself but with different Y-DNA (i.e. from the first husband).

"Widowed and fatherless"

Legal Condition of Marriage / Inheritance
Sometimes it was stipulated that a man would have to change his name in order to marry the daughter of a wealthy man to ensure that the family name was carried on. A good example is the Pennington family of Muncaster. There are two recent generations where the husband had to change his surname to Pennington as a condition of marriage. Thus, there have been two successive switches in the DNA associated with the Pennington surname along the same direct male line of descent.

A similar condition arises where the prospective heir has to change his name as a condition of inheritance - "You won't inherit a penny, my boy, unless you change your surname to Sidebottom".

"Sidebottom, grandfather? ... Seriously?!"

Taking wife’s name upon marriage (because of her higher social status)
In times past, it was not unusual for a man, upon marriage, to take the name of his wife if she was considered to be of higher social status. A famous example is that of Oliver Cromwell. His real name (perhaps we could say his maiden name) was Oliver Williams. His great-great-grandfather, Morgan Williams, married Katherine Cromwell in 1497. She was sister of Thomas Cromwell, Henry VIII’s chief minister, who was famously promoted to the earldom of Essex but later executed in 1540 when he fell from the King’s favour.

Morgan and Katherine’s three sons took the surname Cromwell in honour of their famous maternal uncle. This practice was repeated by many of their descendants, who also occasionally used the surname Williams-alias-Cromwell. Or at least they did until the Restoration, when some members of the family reverted to the surname Williams temporarily to distance themselves from any links to Oliver.

Morgan Williams and Katherine Cromwell’s eldest son Richard had two sons, Henry and Francis, both of whom also used the surname Cromwell. Henry was knighted and one of the youngest of his eleven children (Robert) was Oliver's father.

Thus the Cromwell surname became associated with Williams DNA.

Oliver Williams

Customary coupling with Dignatories
In ancient Celtic culture, apparently it was customary to offer one's wife to visiting dignitaries for "entertainment". This custom of guest-friendship-prostitution is still practiced in certain cultures today and is somewhat similar to the droit de seigneur or jus prime noctis that was apparently practiced in some places. Thus the dignitary's Y-DNA would become associated with any offspring of the union, but the child could be raised with the surname of the woman's husband.

Why was such a custom practiced? A child by a powerful man would give protection to a family and also had rights to succession under Brehon Law. A good example is that of Mathew (Fear Dorcha) O'Neill (1520-1558), the illegitimate son of Conn O'Neill. He was accepted by Conn as his natural son and was made his heir. However, Shane (Mathew's half-brother) contested his right of inheritance and Shane's men eventually killed Mathew, but not before Mathew had a son, Hugh O'Neill, who later went on to become The Great Earl and Clan Chief of the O'Neill. On this occasion the Y-DNA and surname remained intact (no SDS) but in other cases, the surname of the father who reared the dignitary's child may have been retained (i.e. SDS present).

There was also an associated custom of “Naming” children on a wife’s deathbed (i.e. she would reveal which of her children were the offspring of famous people). Apparently, as she lay dying, the wife would call her husband into the bedroom and something like the following conversation would ensue:
WIFE:           Husband dear, I need to have a word with you.
HUSBAND:   My dearest wife, what do you want?
WIFE:            Well ... you know our eldest child?
HUSBAND:     Of course I do ... sure isn't he my son?!
WIFE:              Well ... that's what I want to talk to you about ...
This sort of conversation does not happen very often today (or does it??), but it was relatively commonplace 500+ years ago.

Infidelity - a different thing under Brehon Law
In many ways, the old Brehon Law system practised by the mediaeval Irish, as well as their social attitudes, were more advanced and less restrictive than the laws we have today, especially in relation to the rights of women. There was a completely different concept of infidelity under Brehon Law. And such thinking is quite foreign to our modern ears.

How common infidelity was in medieval society is open to question. But if it was commonplace, and in addition married couples practiced regular sexual relations, then it must have been very difficult for a man to know which children were his and which were someone else's. Maybe they played guessing games at medieaval cocktail parties.

Attitudes to infidelity have varied with time and place. In Shakespearean times, "cuckolding" was the subject of derision and the cuckolded husband would be mocked. In Victorian and more modern times, infidelity carried a stigma and was taboo. As a result, it would probably be kept secret and remain undetected. Husbands would be blissfully unaware that their child carried another man's DNA.

Infidelity usually goes undetected, but sometimes there may be clues in the genealogical records. I came across a note written by the parish priest in the margin of an 1890 baptism record which read: this is not the husband's child - he has been working on the docks in Liverpool for 18 months.

"Not tonight, Joseph"

Illegitimacy - another different thing under Brehon Law
There was a completely different concept of illegitimacy under Brehon Law and it was not unusual for men to have concubines. In addition, sex with servants was commonplace.

There was also apparently a custom whereby a woman could decide which man she wanted to sire her child and which she wanted to raise him. So Dim Dave may have been in demand for his awesome good looks, whilst Four-Eyed Stan was lumped with child-rearing because he was an excellent Dad (despite the limp and halitosis).

In more recent times, and certainly since the introduction of Victorian morality, the illegitimate offspring of any "out of wedlock" encounter would usually be given the maiden name of the mother. However, this was not always the case and I have seen illegitimate children christened with their biological father's surname (in which case, no SDS is present).

Girl Power under Brehon Law

Anglicisation of surname
It was common for surnames to be anglicised in Ireland. And as a result there are some unlikely genetic associations between different surnames. The surname Green was at times an anglicised version of Hooney or Fahy, both of which are derived for an Irish word for the colour green.

Surname change to match the prevailing social circumstances 
Sometimes people would change their name to suit their circumstances. A lot of Jewish immigrants to the US changed their name to make it sound more "English" and thus avoid discrimination. Similarly Catholics living in a predominantly Protestant community might change their name to "fit in".

There is a popular belief that a lot of surnames were misspelt or assigned as people entered the US via Ellis Island but this has been contested for a variety of reasons. Firstly, passenger lists were not created in Ellis Island but at the port of departure of the immigrant i.e. in his or her native country, probably by a native speaker of the immigrant's language. The inspector at Ellis Island did not write down the immigrant's name - he worked from the passenger list.


Abandonment by husband
In cases where the husband deserted his family, the children sometimes took name of their mother out of respect for her and perhaps to distance themselves from their wayward father.

Legal Name Change after an important ancestor
Some people changed the family's name to reflect the family's ambition to achieve higher social status.

Babies switched at Birth
Occasionally we hear stories of babies being swapped at the hospital and the mother going home with the wrong baby. Several recent cases have come to light with the help of DNA testing.

More modern causes
In more modern times, the nature of SDSs is subtly changing with the introduction of new causes such as surrogacy, sperm donation, mitochondrial donation, and three parent families (one parent donates the egg, another the sperm, and a third the mitochondria).



Other causes
This is not an exhaustive list of the causes of Surname or DNA Switches, so if you can think of other examples (and I am sure there will be many), please leave a comment below.


But hopefully it will be abundantly clear from the above, why you only have a roughly 50:50 chance that your Y-DNA goes all the way back to the person who originated your surname some 1000 years ago (or thereabouts). And why, as you go back along each ancestral line in your family tree, there are likely to be 3-parent and 4-parent families. In other words, one particular family may consist of a genetic father as well as a genealogical one. And some families (e.g. where an adoption has taken place) will consist of two genetic parents and two genealogical parents.

As a result, we all have two types of family tree superimposed on each other - one purely genetic, one purely genealogical. But both equally valid in terms of our family history. Both types of ancestor (genetic & genealogical) have contributed to who their offspring became ... and who we are today.

Maurice Gleeson
July 2018






Tuesday, 3 July 2018

New guide to Irish Family Tree Research

I recently wrote a supplement for the magazine Tracing Your Ancestors that deals with my strategic approach to Irish genealogical research. The guide is entitled "Irish Research - a practical approach" and is available either as a hard copy print edition or as a pdf edition with hyperlinks to specific websites. You can purchase the guide online via Your Genealogy History Store.

The new guide to Irish genealogical research

There has been a huge effort to digitise Irish records in recent years which has enabled Irish genealogical research to be conducted from the comfort of your own home in front of your computer. Many of these resources have been made freely available by the Irish government via its website www.IrishGenealogy.ie, including all civil registration birth marriage and death records from 1845 up to the present day (with a 100 year restriction for births, 75 years for marriages and 50 years for deaths). In addition, the majority of all available church records are now available via two websites - www.IrishGenealogy.ie and www.RootsIreland.ie (subscription-based). This makes Irish research a lot more feasible than previously.

The contents of the guide

The guide includes a section on how to strategically approach Irish records. It helps you identify which record sets are worth consulting for each time period (from the 1900s back into the 1700s). This saves you time by directing you to the correct records for research.

The guide covers the main record sets but also the less common ones that can be particularly useful in certain circumstances. Many record sets are still being built, notably gravestone records and newspaper collections. These are invaluable sources of genealogical information.

The section on DNA discusses how best to use this additional tool to break through Brick Walls in your research.

The guide costs US$8.50 for the pdf edition and US$9.95 for the print edition and is available from Your Genealogy History Store.

Maurice Gleeson
July 2018








Tuesday, 26 June 2018

Please Grant Admins Access

This post is for anyone who is a member of any of my DNA projects, including surname projects researching the following surnames: Boylan, Caldwell, Carruthers, Farrell, Gleeson, Glisson, Maloney, Molloy, O’Malley, Ryan, Spearin, among others. However the same principles can be applied to anyone in a surname project who wants to grant limited access to the Admin managing that specific surname project.

FamilyTreeDNA have changed a few things on their website (due to the introduction of GDPR - the new European data protection law) and this includes how much access Project Administrators (like myself) have to your data. You can read all about it on this FTDNA Learning Centre page here.

In order to run my various DNA projects efficiently, if you are a member of any of my projects, I need you to grant me "Limited Access" to your data. This will allow me to see your matches and offer you advice. Most of you will already have "Limited Access" assigned automatically but here is how you can double-check.


First, sign in to FTDNA, hover over your name in the top right, and click on Privacy & Sharing ...




Next, click on the Project Preferences tab ...




Next, scroll down to the relevant DNA Project and click on the orange Edit button ...




From the drop-down menu, select Grant Limited Access in the box beside my name ...




Once you have done this, click on the green Accept button ...




Then click on the green Confirm button ...




And that's it - your project preferences will have been saved. You can go back in and change these at any time.





A complete list of what is and what is not viewable by Project Administrators for each of the three different access levels can be found on a separate FTDNA Learning Centre page here. In relation to my various Surname DNA Projects, I need to look at your Y-DNA data primarily, but also your autosomal DNA data (i.e. Family Finder). If you do not grant me "Limited Access", I won't be able to do the following:

  • I won't be able to see what tests you have done
  • I won't be able to see any of your personal pages (the ones you see when you sign in)
  • I won't be able to see your Y-DNA matches
  • I won't be able to see your SNP marker results
  • I won't be able to see your Family Finder matches
  • I won't be able to assist you with product upgrades
  • I won't be able to assist you with some of the technical aspects of the website
  • I won't be able to assist you in managing your results or webpage

So to help me to run my projects most efficiently, and to give you the level of help I would like to, please change your Project Preferences access settings to "Limited Access".

As always, please email me if you have any questions or need any help.

Maurice Gleeson
June 2018



Saturday, 12 May 2018

Lecture Tour of Australia & New Zealand

Tomorrow I hop on a plane to Brisbane where I start a 4-week tour of Australia and New Zealand. Along the way I hope to take in the sights and sounds of these two fabulous countries, as well as visit cousins, DNA matches, project members, and genetic genealogists who share the same passion for DNA and genealogy that I do.

Several of my wider family ended up in Australia. Ruby Kathleen Gleeson left Tipperary in 1885. We found her 1893 wedding memento (from Thargomindah) among my great grandfather's papers, but we had no idea who she was. After several years of research, and a DNA test, we established that she was the sister of my great grandfather.

Ruby Kathleen Gleeson ended up in Thargomindah (red dot)

Many of my Spearin relatives travelled to Australia, some as prisoners on the Mangles. Their many descendants today have contributed to the Spearin DNA Project, which traces our ancestors back to a group of brothers in Limerick in the late 1600s. Apparently they came from London where they were goldsmiths, and before that from Belgium, where they were merchants or bookbinders.

I look forward to meeting many of the descendants of both these lines of my family during my visit.

Here is the schedule of talks and workshops I will be giving. If you are in the neighbourhood, drop in and say hello!

Saturday 19th May 2018 - Brisbane
Queensland Family History Society
Queensland Baptist Centre, 53 Prospect Road, Gaythorne Qld 4051
09.00 - Managing your Matches - a step-by-step approach to interpreting your DNA matches
11.00 - Marrying DNA and Irish Family Tree Research

Saturday 2nd June 2018 - Christchurch
New Zealand Genealogical Society, Annual Conference
Christchurch Boys' High School, 71 Straven Road, Christchurch
12.00 - DNA: A Beginner’s Guide to the Three Main Tests
14.00 - Identifying Missing Soldiers of WWI – What Role Does DNA Play?  Fromelles as an Example

Sunday 3rd June 2018 - Christchurch
New Zealand Society of Genealogists, Annual Conference
Christchurch Boys' High School, 71 Straven Road, Christchurch
15.30 - Advanced Surname Project Management using DNA

Monday 4th June 2018 - Christchurch
New Zealand Society of Genealogists, Annual Conference
Christchurch Boys' High School, 71 Straven Road, Christchurch
09.00 - Ireland and the Trans-Atlantic Slave Trade: from Indentured Servants to Slave Masters to Abolitionists

Tuesday 5th June 2018 - Christchurch
New Zealand Society of Genealogists, Annual Conference
Christchurch Boys' High School, 71 Straven Road, Christchurch
09.00 - Using your DNA results in practice - focus on autosomal DNA (3-hour workshop)

Thursday 7th June 2018 - Wellington
NZSG Post-Conference Tour
ASB Sports Centre – Matairangi Room, 72 Kemp Street, Kilbirnie, Wellington
13.00 - Using DNA to solve unknown parentage cases
14.30 - Marrying DNA and Irish family tree research

Saturday 9th June 2018 - Auckland
NZSG Post-Conference Tour
St Andrew's Church Hall, corner of Ridge Road and Vincent Street, Howick
13.00 - Using DNA to solve unknown parentage cases
14.30 - Marrying DNA and Irish family tree research

Sunday 10th June 2018 - Te Awamutu
Te Awamutu DNA support group
13.00 - Using DNA to solve unknown parentage cases
14.30 - Marrying DNA and Irish family tree research

Monday 11th June 2018 - Papamoa
NZSG, Papamoa branch
10.00 - Michelle Patient talks on Researching surnames & the Guild of One Name Studies (GOONS)
12.00 - Marrying DNA and Irish family tree research (MG)

Tuesday 12th June 2018 - Papamoa
NZSG, Papamoa DNA Special Interest Group
10.00 - Using DNA to solve unknown parentage cases
12.00 - General Q&A

Saturday 16th June 2018 - Auckland
NZSG, Auckland branch Genealogical Computing Group
St Andrew's Church Hall, corner of Ridge Road and Vincent Street, Howick
14.00 - What's a shrink like me doing in a place like this? (a review of the software and tools that I use in my day to day work)

Maurice Gleeson
May 2018




Monday, 29 January 2018

New publication: "DNA & Your Genealogy"

I've written a 68-page magazine supplement on DNA testing for Your Genealogy Today. It covers all aspects of DNA testing and gives practical advice on how to apply it to your genealogy. Further details can be found here.



Click here to go to page


An early review of the supplement


Here is an extract of another review written by Leland Meitzler of GenealogyBlog.com:
Published in a saddle-stapled format by Moorshead Magazines, this 66-page guide to DNA research is the one of the most readable and easy-to-understand of all the DNA-related guides that I’ve seen. When I finally got some time to read, I found that I read the entire publication, and understood most of what I was reading!
Written by Dr. Maurice Gleeson MB, the book is written about the science – for those of use who thought we’d just stick with the humanities! I can’t recommend a guide more – especially if you are just getting into using DNA in your research. The guide is inexpensive, while giving you the knowledge that you need to be off and running with your DNA genealogy research.
This 66-page DNA guide is the most easy-to understand DNA Guide published to date. Heavily illustrated, this guide is for the rest of us!

If you have read it and would like to leave a review, please feel free to use the Comments section below. 


Maurice Gleeson
Jan 2018





Wednesday, 13 December 2017

Downstream SNP Prediction using the MTSA method

I covered much of this topic in a presentation I gave at the FTDNA Annual Conference in Houston (Nov 2017) and you can watch it on YouTube here. The relevant section is from 37 minutes 40 seconds onwards.



Let's imagine that the Tree of Mankind (aka Y-Haplotree) starts with "genetic Adam" (some 250,000 years ago) and splits into progressively more downstream branches as the timeline approaches modern day. These downstream branches can be identified by downstream SNP marker testing of your Y chromosome (with tests such as SNP Packs, and in particular the Big Y). This downstream Y-SNP testing helps locate your position on the Tree of Mankind and potentially this can prove very helpful for a variety of reasons:

  • It can help ensure that you have been grouped accurately in a specific "genetic family" (within a Surname Project, for example)
  • It can help determine your ancestral origins - at times the actual country, and potentially even the region or county ... this helps focus your genealogical research
  • It can identify your nearest genetic neighbours and their associated surnames ... which in turn can tie you into the genealogy of a specific 'clan' or sept
  • It can identify branches within a genetic family and which one you sit on (it can also be useful in generating a Mutation History Tree)
  • It can highlight the risk of Chance Matches due to Convergence amongst your list of matches

But ... the Big Y test is expensive. The technique below tells how to predict the Big Y result without doing the test. In that way you can reap the benefits of the Big Y without actually having to do it. 

The technique is called Downstream SNP Prediction because we will be predicting what SNP markers you are likely to test positive for "downstream" i.e. approaching the modern era, say within the last 500-1500 years. And the MTSA in the title stands for Matches Terminal SNP Analysis - in other words, you will be analysing the terminal SNPs of each person on your list of Y-DNA matches generated from the Y-STR test that you have previously done (be it the Y-DNA-37, Y-DNA-67 or Y-DNA-111).

The technique is quite simple. It just takes a little bit of time to complete (about 10 minutes). But there is one major caveat - it does not always work. And once you see the results, you will have to make a judgement call on whether or not you think the result is likely to be reliable. But when it does work, it works well.

Essentially the MTSA method involves collecting the terminal SNPs of all of your Y-STR matches and then seeing where each SNP in turn sits on the Tree of Mankind. 

If they all sit on the same branch, then you probably do too. If they sit on widely different branches, then the results are untrustworthy (in this particular instance), and the method has not been able to predict which downstream SNP you are likely to test positive for. As a consequence, formal SNP testing (Big Y or otherwise) will be necessary to determine your position on the Tree of Mankind.

The Methodology


Here is a list of the steps involved in Downstream SNP Prediction using the MTSA method. We will go through them later in detail one by one:

  1. To start, sign in to your FTDNA account and open your Y-DNA Matches List
  2. Sort your matches list by "Haplogroup"
  3. Note down the terminal SNPs and how often each one occurs - repeat this step for each marker level (111, 67, 37, & 25). 
  4. Plot each SNP in turn on the Haplotree
  5. Assess whether or not the SNPs fall on a single line of descent coming down the Haplotree ...
    1. if they do, there is a good chance that you will also follow this line of descent and end up on the same downstream branch (or a branch very close by)
    2. if they do not fall on the same single line of descent, then the technique has not worked in this instance because Convergence is present
  6. Make a judgement call on how reliable you think the results are

Now let's look at each step in detail.


Step 1 - open your Y-DNA Matches list



Step 2 - sort your matches by Haplogroup ... just click on the title "Y-DNA Haplogroup" and this will arrange your list of matches alphabetically by their Terminal SNP.

This individual has 183 matches at the 25 marker level (top left)


Step 3 - note down the terminal SNPs and how often each one occurs

In the example above, this would produce a list like this:
  • BY3441
  • CTS7030
  • DF13
  • FGC10116
  • FGC10117 (x2)
  • FGC10125 (x2)
  • FGC28987
  • L1065
  • L1335 (x8)
  • etc ...


Notes 
1) I don't bother recording the frequency of single SNPs. Thus, any SNP in the list without a number in brackets has only occurred once in the list.
2) I ignore any known "upstream" SNPs (e.g. M269, L21, etc) as these are too far upstream to be informative.
3) this exercise should be repeated at each marker level (111, 67, 37 & 25). In practice, the 25 marker level appears to be the most informative (currently).


Step 4 - Plot each SNP in turn on the Haplotree

This is the most time-consuming part of the exercise but you will get quicker with practice. To be comprehensive, it is best to identify the SNP Progression for each SNP in turn. The SNP Progression is simply the series of SNPs that characterise each branching point on the line of descent to the "terminal SNP' in question.

Thus the SNP Progressions associated with the list above would be listed as follows:
  • BY3441 ... 
    • R-P312/S116 > Z290 > L21/S145 > DF13 > Z39589 > DF49/S474 > Z2980 > Z2976 > DF23 > Z2961 > FGC6540 > FGC6562 > FGC6545 > BY3442 > BY3437 > BY3441
  • CTS7030 ... equivalent to L1065
  • DF13 ... too far upstream 
  • FGC10116 ... equivalent to FGC10117
  • FGC10117 (x2) ... 
    • R-P312/S116 > Z290 > L21/S145 > DF13 > Z39589 > L1335/S530 > L1065 > FGC10125 > FGC10117
  • FGC10125 (x2) ... 
    • R-P312/S116 > Z290 > L21/S145 > DF13 > Z39589 > L1335/S530 > L1065FGC10125
  • FGC28987 ... 
    • R-P312/S116 > Z290 > L21/S145 > DF13 > Z39589 > L1335/S530 > L1065 > Z16325 > S744 > S764 > FGC28987
  • L1065 ... 
    • R-P312/S116 > Z290 > L21/S145 > DF13 > Z39589 > L1335/S530 > L1065
  • L1335 (x8) ... 
    • R-P312/S116 > Z290 > L21/S145 > DF13 > Z39589 > L1335/S530
  • etc ... 

Notes
1) the easiest way to find the SNP Progression is simply to google "YTREE" and the SNP in question. This will bring you to Alex Williamson's Big Tree, each page of which has the SNP Progression for the particular branch of the Y-Haplotree under discussion (as in the diagram below for the first SNP in the list).


2) Sometimes the google approach will bring you to a branch slightly upstream of the SNP you want and you will have to search the webpage for the more downstream SNP. Do this by clicking cmd+F (ctrl+F on a PC) to FIND the SNP in question.
3) Sometimes the SNP won't be on the Big Tree and you may have to use the FTDNA or YFULL Haplotrees instead in order to find where the particular SNP sits on the tree. 
4) Sometimes you may have to check www.YBROWSE.org to see if the SNP has an alternative name


Step 5 - Do the SNPs fall on a single line of descent?

Comparing the SNP Progressions above, a pattern clearly emerges. The majority of the SNP Progressions are on a single line of descent, at least as far down as L1065. The exception is the first SNP (BY3441), which splits off from the rest, two branches above L1065.

Below L1065, there are at least two branches - one via FGC10125 (5 instances - count carefully - count bullet points 4-6), the other via Z16325 (bullet point 7). So the SNPs do fall on a single line of descent ... up to a point. And beyond that point, there is some disparity ... some discordance ... different SNPs on different (i.e. separate) branches of the Haplotree. 

But a single man cannot sit on two conflicting branches. He can only ever sit on one branch. Beyond a certain point, the predicted branches are contradictory. And this discordance indicates that some of his Y-STR matches are Chance Matches due to Convergence.

Note
Chance Matches could also conceivably be due to an extreme lack of Divergence (i.e. the Y-STR signature / haplotype is passed down unchanged for many thousands of years), but the chances of this being the cause are probably very low.


Step 6 - make a judgement call

So where is this particular individual likely to sit on the Tree of Mankind? Based purely on the (partial) data presented above, he sits ...
  • Probably below Z39589 (estimated probability ... what? say ... 99%? 95%?)
  • Probably below L1335 (estimated probability ... 16 out of 17 instances = about 94%?)
  • Probably below L1065 (estimated probability ... 8 out of 9 instances = about 89%?)
  • Probably below FGC10125 (estimated probability ... 5 out of 7 instances = about 71%?)
  • Probably below Z16325 (estimated probability ... 1 out of 7 instances = about 14%?)
  • Probably below DF49 (estimated probability ... 1 out of 17 instances = about 6%?)

These probabilities are relatively crude, but certainly give a strong impression that the individual in question is highly likely to test positive for L1065, and below that is more likely to test positive for FGC10125 than for any of the other downstream SNPs.

So while this exercise has not identified a specific downstream SNP with 100% probability, it has  pointed us in a specific direction and has identified a "most likely candidate", namely FGC10125 (about 70% probability) ... or maybe, some SNP below it, possibly FGC10117.

The SNP FGC10125 appears to have arisen some time at least 1150 years ago, so the exercise has potentially moved us down the Haplotree to a branch that arose within the last 1000-1500 years.

In addition, it has identified with even greater confidence (about 90% probability) that the individual sits somewhere below L1065 for which there happens to be a dedicated SNP Pack. So rather than doing an upstream SNP Pack like the R1b-M343&M269 Backbone Panel, this individual may choose to do the more downstream R1b-L1065 SNP Pack ... which (from the above) is likely to be appropriate with 90% probability. I always caution my project members that there is a chance (10% in this instance) that they will be wasting their money. The choice is theirs.

But before doing any downstream SNP Pack test (the R1b-L1065 SNP Pack in this example), it is always advisable to check that the SNP Pack actually contains the "further downstream" SNPs of interest (extracted from the list of matches' terminal SNPs above). And in this instance, the R1b-L1065 SNP Pack contains all the "more downstream" SNPs identified in the list above. So it would be a good choice to make in this instance ... if the individual did not want to spend money on the Big Y.

The Output


Several different types of profile can emerge from this exercise and they broadly fall into the following categories:
  1. all the evidence points to a single downstream branch of the Y-Haplotree (say, within the last 1000 years)
  2. most of the evidence points to a single downstream branch, but there is some minor downstream discordance within the last 2000 years or so, with several "very downstream" branches predicted
  3. most / all of the evidence points to a major subclade branch (say, about 2000-4000 years ago) but, below this, many downstream branches are predicted indicating major downstream discordance
  4. the evidence suggests several conflicting upstream branches of the Y-Haplotree (e.g. L21, U106, M198) and only some or none of the evidence points to a single major subclade. Thus in this case, major upstream discordance is present and accurate Downstream SNP Prediction is not possible

The various degrees of discordance arise due to Convergence  This is when by chance, and over the passage of time, the descendants of one branch of the Haplotree develop a similar set of Y-STR marker values to the descendants of another branch of the Haplotree. Thus the genetic signatures  of the descendants of both branches look similar and thus they match each other i.e. they appear in each other's matches list. This suggests there is a close connection (say, within several hundred years) when in fact the common ancestor is several thousand years ago. They sit on completely different branches of the Haplotree, but their Y-STR signatures suggest they could be close cousins (when in fact they are not).

Here are a few examples of each profile.

Scenario 1 - no discordance, everything points to a single downstream branch

This scenario occurs with Farrell Group 2. Using the MTSA method on many of this group's members and then plotting the terminal SNPs generated onto a diagram of the Haplotree, indicates that they all fall on a single line of descent. And predicts that the members of this group will test positive for the downstream SNP FGC20561.

There is no or little evidence that there is Convergence in this group - all the STR matches appear to be "genuine" "true positive" matches, none of the matches appear to be Chance Matches due to Convergence.

MTSA of many Farrell Group 2 members predicts they will test positive for FGC20561


Scenario 2 - minor downstream discordance

The exercise described above (to illustrate the methodology) indicated that the individual's Y-STR matches all sat on a single line of descent as far down as Z39589. Immediately after that there was some "minor discordance" (one match tested positive for DF49), but the majority of the group continued downstream to L1335 and L1065. Thereafter, there was some more discordance in the group, with 5 going down the path of FGC10125 and one turning down to Z16325. Thus, all the evidence was concordant down to Z39589 (100%), a majority of the available evidence was concordant down to L1065 (89%), and a smaller majority of the available evidence was concordant down to FGC10125 (71%). And from this we can conclude that this individual and his Y-STR matches share a common ancestor on the branch of the tree characterised by Z39589, and probably share another common ancestor further downstream on the branch characterised by L1065, and possibly share another common ancestor on the FGC10125 branch.

This is a fairly typical profile that emerges from this exercise. It takes you so far down the Haplotree but no further. Additional SNP testing will be needed to confirm the predictions.

In this scenario, Convergence is present, but it does not exert an influence until we get quite far downstream. Thus the common ancestor for the group is relatively far downstream, certainly below the major subclade level (about 2000-4000 years ago), and probably within the last 1500 years. In the example above, the major subclade L1065 is at least 1800 years old and the downstream SNP FGC10125 is at least 1150 years old. In the diagram below, the major subclade L226 is at least 1450 years old, and the downstream SNP FGC5628 is at least 1100 years old.

Two Discordant Downstream Branches occurring below major subclade R-L226 


Scenario 3 - major downstream discordance 

In this scenario, the MTSA methodology identifies many Discordant Downstream Branches, frequently with no particular sub-branch predominating. The individual is predicted to sit somewhere below a major subclade branch but there are so many candidates further downstream that no reasonable prediction can be made.

However, it remains clear that the individual does fall below a major subclade branch and therefore the associated subclade SNP Pack may be an appropriate test to take (if the individual does not want to purchase the Big Y). The SNP Pack will need to be checked to see if any relevant SNPs are included therein.

In the diagram below, MTSA predicts that the individual will sit on a branch downstream of M222 (a SNP marker known to be associated with significant Convergence . However, there are at least 6 different branches below M222 that the MTSA methodology predicts as possible candidates for the individual's branch. This person went on to do the Big Y test and the confirmed branch he actually sits on turned out to be none of the candidates predicted by MTSA. This illustrates the importance of making a judgement call on the reliability of the predictions.

Several Discordant Downstream Branches indicate major downstream discordance


Scenario 4 - major upstream discordance

In the final scenario, there are multiple Discordant Upstream Branches making it impossible to predict which subclade of the Haplotree the individual belongs to. For example, some matches sit on L21, others on U106, and others on M198 - all upstream SNPs that are thousands of years old. Under these circumstances, actual Big Y testing is the only option for defining where on the haplotree the individual sits.

Note
I generally use the terms Upstream and Downstream in crude approximation to the nearest major subclade, which tends to be in the range of 2000-4000 years ago. Upstream is roughly more than 4000 years ago; and Downstream is roughly less than 2000 years ago. But these are approximations.


Some Final Words


Downstream SNP Prediction using the MTSA method can be surprisingly predictive in many cases.

Currently it works best at the 25 marker level, simply because there are many more matches at this level and therefore many more datapoints. However I always check the higher marker levels first and also check for consistency across the different marker levels. I have rarely explored 12 marker results (because the risk of Convergence at this level is so high) but occasionally they can appear useful (nevertheless, a large grain of salt needs ingestion).

Predicting the "most likely" terminal SNP for an individual allows more targeted "confirmatory" SNP testing (via a SNP Pack or single SNP test) and potentially saves the customer money.

It also helps identify Chance Matches due to Convergence within an individual's match list, and thus gives some indication of the extent of Convergence within the individual's match list. In subsequent blog posts, we will explore how the MTSA methodology can facilitate quantification of the extent of Convergence  not just within an individual's match list, but also for an entire genetic group within a surname project.

I'd like to say a big thank you to Ralph Taylor, James Irvine & Debbie Kennett for helping shape my ideas on this subject.

Maurice Gleeson
Dec 2017






Friday, 17 November 2017

FTDNA Holiday Sale until Dec 31 2017

FamilyTreeDNA have launched their Annual Holiday Sale. This runs from the last day of the Annual FTDNA Conference (Nov 12th 2017) until the end of the year. So now is the time to buy FTDNA tests and take advantage of some of their lowest prices ever. They also make perfect Birthday, Thanksgiving & Christmas gifts for friends and family.

2017 Holiday Sale Discounts

There are discounts on many of their products including upgrades on mtDNA and Y-DNA. The discounts represent approximately a 10-30% reduction from the usual price.


There is a special offer regarding the Big Y test. The usual price is $575 but there is a $100 discount in the sale. Further discounts are possible with the vouchers described below. But everyone who buys a Big Y test will automatically get a FREE upgrade to the Y-DNA-111 test. So if you have only tested your Y-DNA to the 37 marker level, buying the Big Y will get you a free upgrade to 111 markers (which would normally cost you $188).

Even if you haven't done a Y-DNA-37 test yet, you can order it at the Sale Price, and use a voucher for a further discount, and then once it has registered on the system, you can order the Big Y test and get the $100 Sale Price discount, and any additional voucher discount, and a free upgrade to 111 markers. This is a very good deal indeed!
So if you were very lucky, you could get the Y-DNA-37 for $109 (using a $20 voucher) plus the Big Y for $375 (using a $100 voucher) and the free upgrade to 111 markers. This wold normally cost $169 + $575 + $188 = $942 but you would be getting it for $484. This is only 51% of the price you would normally pay.



As mentioned above, you can use Holiday Reward vouchers to lower the sale prices even further. These will be issued every Monday until the end of the Sale but each voucher only lasts for 7 days so you have to use them quickly. In effect, this may reduce the cost of the Family Finder atDNA test to $49 and Y-DNA-37 to $109.

A $20 voucher for the Y-DNA-67 test

To access your voucher, simply log on to your FTDNA account and click on the Holiday Reward icon on your home page. If you make a purchase during the Sale, you frequently get a Bonus Reward as well. This gives further discounts on other tests.



And if you want to use the voucher for yourself, simply click on the Enjoy Rewards button and the product will be added to your Cart and the discount applied. Alternatively you can give the voucher to friends or family by clicking on the Share Rewards button. Each voucher can only be used once, and must be used before the weekly deadline.


A lot of people donate any vouchers they are not using so check the ISOGG Facebook group and Genetic Genealogy Ireland Facebook group for any unused vouchers that you might be able to take advantage of. Be warned, they go fast so you might have to try several before you find one that works.

Enjoy the Sale!

Maurice Gleeson
Nov 2017