Tuesday, 8 December 2015

Surname Projects - Understanding what you See

Anyone who has recently taken a Y-DNA test will be encouraged to check out the FamilyTreeDNA website and see if there is a Surname Project running for their own particular surname. And if there is, they should join up. But for people who have never seen a Surname Project before, it can be a bit confusing to understand what they are actually looking at.

Below is a blog post I wrote for my Gleeson DNA Project (of which I am co-administrator). It helps to illustrate what you see, what it means, and how you can use the information to help move your own research forwards.


Maurice Gleeson
Dec 2015



The Gleason/Gleeson DNA Project has a number of different resources to help you trace your Gleason/Gleeson ancestry. If you are new to the Project, or even if you are an old hand, here is a useful summary of all the wonderful places you can visit and what each of them has to offer you.

But before we even get to the Project resources, the starting place for most people will be their own DNA results page on FamilyTreeDNA and here is my Dad's results page below as an example.



If you click on Matches under Y-DNA, that will show you what matches you have at different levels of comparison. The picture below shows that my Dad has 2 matches at 111 markers. But I could adjust the number of markers compared by clicking on the dropdown list beside the heading "Markers" (indicated by the red arrow) and choose 67 markers or 37 markers, etc. This will allow me to compare my Dad's results with other people within the FTDNA database who have tested to this particular marker level.

In the first column, the heading is Genetic Distance (GD), and my Dad has a GD of 6 and 9 for his two matches. As we are comparing at the 111 marker level, this can be written as 6/111 and 9/111. Genetic Distance refers to how close or how far away your marker values are when compared to another person. A Genetic Distance of zero means that the values for all of the markers are exactly the same - this is called an exact match.


Who qualifies as a match to you? Anyone whose marker values are sufficiently similar that they meet the criteria set by FTDNA to be declared "a match". And here are those criteria:
The ISOGG Wiki has a very nice summary of Genetic Distance and the criteria for matching.

However, your own webpage only shows you your own matches - it does not show you other people's matches. And it does not show you matches that fall outside of FTDNA's matching criteria but which may still be relevant to you. For that, you need to visit the Gleason/Gleeson DNA Project website.

Click to enlarge

And the most useful page is probably the Results page because this is where you can compare your results to everyone else in the project. Above is a screenshot of the results page.

Explaining the Columns

Reading from left to right across the table ...
  • the first column has the Identification Number assigned to each new member as they join the DNA project
  • the second column lists their kit number
  • the third column records the spelling of their surname (there are several common variants and a few probable NPE's - Non Paternity Events)
  • the fourth column list the Earliest Known Ancestor (also known as the Most Distant Known Ancestor) for each member - this could be written as EKA aka MDKA ... don't you just love acronyms!
  • the next column records the Haplogroup for each member using both the older "long-form" terminology along with the "terminal SNP" terminology (a Haplogroup is simply a collection of people with a broadly similar genetic signature)
  • and thereafter are the values for each marker, one by one, going all the way up to 111 markers (although only the first 37 markers are shown here)

Explaining the Rows

  • The first row contains the headers for the columns. Below that is the "Modal Haplotype" for Haplogroup R1b1 which is the Haplogroup to which all three R1b1 Lineages belong. The Modal Haplotype is simply the marker values that occur most frequently within that particular group.
  • Below that, is the Modal Haplotype for the group Lineage I. You can see that it differs from the R1b1 Modal Haplotype on a number of markers, indicated by the coloured columns (i.e. orange for marker 391, purple for marker 458, orange again for 447, etc). This in turn differs from the Modal Haplotype for Lineage II, further down the table. The colouring of the differences from the R1b1 Modal Haplotype helps distinguish the unique patterns for each Lineage.
  • Each of the subsequent rows contains the details for an individual member - it's as if the Y chromosomes for all of the members are stacked up on top of each other. This makes it easy to compare the values for each of the DNA markers to see if the members in a group match on a particular marker or have a different value. Any differences are again highlighted by coloured squares.

As Project Admins, Judy and I will allocate you to specific groups within the DNA project depending on who you match. So far there are four distinct groups or 'Lineages' within the project. Lineage I members are descended from Thomas Gleson of Cockfield, Suffolk, England (Judy's ancestor), whereas Lineages II & III are Irish groups with origins in Tipperary and Clare respectively. Lineage IV is a small group of people whose origins currently lie within the US. My own particular Gleeson branch belongs to Lineage II.

Click to enlarge

Another important page on the website is the Patriarchs Page. This is where we post the pedigree of each project member and as you can see in the screenshot above for Lineage I, it potentially helps in the reconstruction of the family tree of the Common Ancestor associated with each Lineage. All members are encouraged to submit their pedigrees for inclusion on this page. Have a look through it - you may discover your own ancestor there!

The other major resources associated with the Project include this blog and the Gleeson Genealogy Forum on Facebook. This currently boasts 178 members and is a great place for socialising with the other members of the project, sharing information, and making new friends.



And anyone who joins will get a brief "report" of their results courtesy of myself or Judy. This will include an analysis of haplogroup origins, interpretation of matches, what additional projects would be worth joining, and what further DNA testing might prove fruitful for their particular situation.

So do explore the website, this blog, and the Facebook group - there is lots to discover about your Gleason/Gleeson heritage. And come back to this blog often - it will be a repository of knowledge and a log of our ongoing discoveries.

Maurice Gleeson
16th July 2015



Thursday, 15 May 2014

Presentations & Slides available for download

Now you can see all the videos of presentations I have given all in one place. The new Presentations & Downloads page has a selection of videos that deal with a variety of different DNA-related topics including:

  • The basics of DNA testing
  • How to take your own DNA sample via a cheek swab
  • The three main types of DNA test and what each one can do for you
  • How DNA can help you break through Brick Walls in your own family tree research
  • One-Name Studies run by the GOONS (Guild of One-Name Studies) and how DNA can be used to help further surname research 
  • How to set up a DNA study as part of a One-Name Surname Study
  • Using DNA for Caribbean genealogical research
  • Using DNA for Northern Irish genealogical research
  • A step-by-step approach to analysing your matches on autosomal DNA
Many more topics will be included in the future, and handout notes of the slides will be available to accompany the presentations.












Friday, 17 May 2013

Step 3.5 - other techniques to eliminate non-contenders

This will include:

  • mitochondrial DNA
  • Y-DNA

Step 3.4 - Using phasing to eliminate grandparental lines

This is a very complicated and time-intensive approach and requires testing multiple people to identify what parts of your DNA were inherited from which of your 4 grandparents. Testing might include at least 1 parent, 3 siblings, and several cousins.

The value of this approach is that it will potentially eliminate 3 of your 4 grandparental lines and in so doing reduce the number of possible contenders for Common Ancestor to a mere 25%. Taken in conjunction with the other techniques described in this blog, this can considerably narrow down the number of possible candidates for Common Ancestor.

The ISOGG wiki has a summary of phasing and how to do it. It also has some useful references at the end.

Monday, 13 May 2013

Step 3.3 - eliminating lines of unlikely ethnicity or nationality

Can you rule out certain ancestral lines on the basis of ethnicity or nationality?

This technique is not as foolproof as the ones previously discussed but it can certainly help you further narrow down your list of possible candidates for Common Ancestor. It works particularly well if you or your match have ancestors from a variety of different countries. For example, in my own family tree, all my ancestors are Irish (as far as I know). There is the possibility that if I went further back I might find some English, Welsh or Scottish ancestors too, but it is far less likely that I will discover Chinese or African ancestors within the last several hundred years.

Having said that, my ethnic admixture results from 23andMe reveal that I am 99.8% European and 0.1% Sub-Saharan African so this suggests that perhaps 1 of my 1000 or so ancestors (at the level of my 8x great grandparents, born about 1600) was African. So you can never be sure what awaits you in the unknown generations further back from where you have currently managed to extend your tree!

Nevertheless, I can be reasonably certain in suggesting to all my matches that any Common Ancestor that I share with them is likely to be Irish. As a result, they can focus their attention on any Irish lines in their own family tree. I'm not confident enough to say to them that they can eliminate any non-Irish lines from further consideration, but I can certainly say that the "balance of probabilities" sways more towards the Irish lines and more away from the non-Irish lines in their tree.

This could be given further credence by demonstrating that the segment of DNA on which we match is more likely to be Irish / European, rather than Asian or African (for example).

In her blog entitled X Marks the Spot, Roberta Estes uses an example from her own family to demonstrate the practical application of X-chromosome inheritance in combination with ethnicity and nationality analysis to narrow down the number of potential ancestral lines on which the Common Ancestor sits.

A Worked Example

Using the previous example of my aunt JH and MB, we were able to shortlist the potential ancestral lines to those marked with a red X (because JH & MB match each other on the X-chromosome). However, it is clear from MB's Bow Tie chart that her 3 specific ancestors 29, 30 & 31 are English, and therefore, while it is not possible to rule out these ancestral lines completely, it certainly points us away from these lines as potential candidates and draws our focus onto the other shortlisted ancestral lines (26, 27, and 21, 22, & 23).



Links, Reources, & Further Reading

Roberta Estes combines a variety of the techniques we are discussing to narrow down the list of potential candidates for her Common Ancestor in Revealing American Indian and Minority Heritage Using Y-line, Mitochondrial, Autosomal and X-Chromosomal Testing Data Combined with Pedigree Analysis. This article was published in JOGG (the Journal of Genetic Genealogy) Fall 2010, Vol. 6, Number 1, pp1-37.





Wednesday, 8 May 2013

Step 3.2 - a match on the X?


Do you match each other on the X-chromosome?

In order to answer this question it is best if you upload your raw DNA data to Gedmatch.com, as this is the best way currently available to assess if there is a match on the X-chromosome. Instructions on how to upload your results can be found here. 23andMe have an X-chromosome browser which can also be useful, and FTDNA is planning to introduce one at some point in 2013.

A match on the X chromosome helps to limit the possible ancestral lines down which the DNA you share with your match could have passed. The X chromosome can only be passed down certain ancestral lines.  Daughters receive one X-chromosome from each parent, sons receive an X only from their mother, but a Y from their father. For this reason, as you go back along your ancestral lines, anytime you hit a male ancestor, the X line cannot continue back through that male ancestor's father – it can only continue through his mother.

The diagram below shows the X chromosome inheritance pathways - orange arrows indicate the path of the X chromosome, blue arrows the path of the Y chromosome.  The X chromosome in the man at the bottom of the diagram is inherited only from his mother (orange arrow), who in turn could have got it from either her father or her mother, but her father could only have got it from his mother. Thus, as you trace the line of X-inheritance back, as soon as you hit a male, the line of X-inheritance can only continue back through his mother’s side. This effectively excludes all the ancestors on the paternal side of each male encountered as you go back through the family tree. Fabulous!



The X-inheritance pathways for men and women are illustrated in the Ancestor Fan Charts below, using me and my maternal aunt as examples. The only ancestors from whom the X could have been inherited are contained within the boundaries of the red lines.

There are several unique characteristics of X-chromosome inheritance including the following:

  •  If a male matches someone on his X-chromosome, this means that the common ancestor can only be on his maternal side. All the ancestors on his paternal side are immediately eliminated from consideration as possible candidates. (Caveat: the only possible exception would be if the match on the X-chromosome was a weak match - in other words, if only a very small portion of DNA on the X was shared between the two matching individuals. In such circumstances, the chances of the match being a “false positive” could be quite high. False positive matches are discussed further in the section on IBS vs IBD.)
  • The further back you go in your ancestral tree, the smaller the percentage of ancestors that could have passed you your X chromosome. This is illustrated in the tables below the charts.
  • Fathers pass on their X-chromosome unchanged to their daughters (i.e. it has not undergone recombination – click here for an explanation). Therefore, it is identical to the X-chromosome that he got from his own mother.  In other words, girls inherit one unchanged (albeit recombined) X-chromosome from their father’s mother.
  • On the other hand, a mother passes on an X-chromosome that has undergone recombination (and therefore represents a mixture of her two X-chromosomes, the one she got from her father and the one she got from her own mother). It follows therefore, that there is less recombination of the X on those ancestral lines that have more males, and more recombination on those lines that have more females. As a result, the amount of X-DNA that is passed down from any given ancestor is greater for those ancestors who sit on ancestral lines with more males, and lower for those ancestors who sit on ancestral lines with more females. (In the charts below, the “male heavy” ancestral lines are toward the left hand side of the enclosed red area, while the “female heavy” ancestral lines are towards the right hand side of the enclosed red area). The final chart below illustrates the average percentage of X-DNA inherited from each ancestor.


X Inheritance Pathways in Men




Below is the same sort of chart but illustrating the ahnentafel numbers of the ancestors concerned. Boys are in blue, girls are in pink. This is reproduced here with kind permission of Blaine Bettinger who uses these charts in his blog post here.



X Inheritance Pathways in Women


Below is the same kind of chart, but using ahnentafel numbers to illustrate the only ancestors who could have passed on an X. This is again used with kind permission of Blaine Bettinger.




Implications of X inheritance pathways in Men & Women

If you are man, a match on the X substantially reduces the number of ancestors who could have passed down the segments of DNA you share with your match. At the level of your great grandparents, only three out of the eight of them (37.5%) could have passed on any X-DNA to you. And if we go even further back, say to the level of your 5x great grandparents, only 21 out of the whole 128 of them (16.4%) could have passed on any X-DNA to you, thus ...

Generational level
Generation
Possible candidate ancestors - fraction
% ancestors
Relation to match
1
Me
1/1
100%

2
Parents
1/2
50%
Sibling
3
Grandparents
2/4
50%
1st cousin
4
great GP
3/8
37.5%
2nd cousin
5
2x g GP
5/16
31.25%
3rd cousin
6
3x g GP
8/32
25%
4th cousin
7
4x g GP
13/64
20.3%
5th cousin
8
5x g GP
21/128
16.4%
6th cousin

Similarly, if you are a woman, matches on the X also reduce the number of lineages down which the matching DNA could have been passed, although by not quite so much as that seen in males. An X-match thus narrows down the number of potential candidates for common ancestor between the person tested and their match ...

Generational level
Generation
Possible candidate ancestors - fraction
% ancestors
Relation to match
1
Me
1/1
100%

2
Parents
2/2
100%
Sibling
3
Grandparents
3/4
75%
1st cousin
4
G GP
5/8
62.5%
2nd cousin
5
2x g GP
8/16
50%
3rd cousin
6
3x g GP
13/32
40.6%
4th cousin
7
4x g GP
21/64
32.8%
5th cousin
8
5x g GP
34/128
26.5%
6th cousin

Furthermore, because the X-chromosome that a man inherited from his mother is passed on unchanged to his own daughter, any ancestral X-line that contains a lot of men will contain more X-DNA than a line that contains a lot of women. You can se this in the diagram below - look at the line toward the left that goes blue-pink-blue-pink and so on, and compare it to the one on the far right / bottom that is all pink. At the top gnerational level (5x great grandparents), the ancestor in the alternating blue & pink line passes on an average of 12.5% of the total X-DNA, whereas the ancestor in the all-pink line only passes on 1.6% of the total DNA (8 times less).
.


% of X-DNA contributed by different ancestors (in a male)

This chart illustrates the average percentage of X-DNA inherited from each ancestor – this is a population average and can vary considerably from person to person, but nevertheless can be useful in helping to focus attention on the most likely ancestral line on which the common ancestor sits. For example, if the suggested relationship between you and your match is 4th cousin (which implies a  common 3x great grandparent), and the percent of X-DNA you share is 20%, then the most likely of your ancestral lines to house the common ancestor is the most “male heavy” one on the left hand side of the coloured area above.

This chart is used with permission from Blaine Bettinger who used it in his blog here.

A worked example

According to Gedmatch, JH and MB also match each other on the X chromosome, thus:


There are only certain ancestral lines down which the X-chromosome can be passed (marked with a red X in the Bow Tie charts below). Therefore, this match on the X effectively eliminates certain ancestral lines from consideration on both my tree and my matches tree - ancestors without a red X are “highly unlikely” to be candidates for the common ancestor and the ancestral lines on which they lie need not be considered further.




Links, Reources, & Further Reading

Roberta Estes combines a variety of the techniques we are discussing to narrow down the list of potential candidates for her Common Ancestor in Revealing American Indian and Minority Heritage Using Y-line, Mitochondrial, Autosomal and X-Chromosomal Testing Data Combined with Pedigree Analysis. This article was published in JOGG (the Journal of Genetic Genealogy) Fall 2010, Vol. 6, Number 1, pp1-37.

Blaine Bettinger discuses the dynamics of X-chromosome inheritance and its application to genealogy in two blogs from December 2008 and January 2009.

Jim Owston blogs about his experience of Phasing the X chromosome

In her blog entitled X Marks the Spot, Roberta Estes writes about the practical application of X-chromosome inheritance in her own family.