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.

Step 3.1 Maternal or Paternal ancestor?


Can you tell if the match is on your maternal or paternal side?

There are several ways to determine this:

  1. If you are a male, and you match someone on the X chromosome, the common ancestor has to be on your mother’s side. (For females, a match on the X does not narrow it down to either maternal or paternal side). This is a particularly useful technique if you have only tested yourself and no other family member (e.g. adoptees). X-matches are detailed further in Step 3.2.
    .
  2. If you have tested another family member (e.g. parent, aunt, cousin) then anyone who matches both of you has to share a common ancestor with you on that particular side of the family.

    For example, if you have tested a family member on your mother’s side (e.g. mother, mother’s sister, maternal 1st cousin, etc), and you both match the same match, then the common ancestor is on your mother’s side. Similarly if you have tested a family member on your father’s side, a match with both you and your paternal relative confirms a match on the paternal side.

    The reverse is 
    also true where parental matches are concerned – if a match matches you but not your mother, then the common ancestor is on your father’s side. Similarly, if a match matches you, but not your father, then the common ancestor is on your mother’s side.

Have other members of your family been tested? If so, check to see if they also match your match.

Below is a diagram of my family and the members who have been tested (highlighted in yellow) – me (MJG), my siblings (KJG & ED), my father (MHG), my maternal aunt (JH), and my father’s 2nd cousin (ALH). 

  • If I have a match who also matches my maternal aunt (JH), then I know that the common ancestor is on my mother’s side, and I can immediately rule out all the ancestors on my father's side. 
  • If I have a match who also matches my Dad (MHG), then I know that the common ancestor is on my father’s side, and I can immediately rule out all the ancestors on my mother's side. 
  • If in addition they match my Dad’s 2nd cousin (ALH), then I know that the shared DNA has to have passed through my 2x great grandparents JG & AG and the common ancestor is  somewhere in the tree above these two individuals, perhaps one of  their parents, grandparents, and so on...



A Worked Example 

FTDNA’s FF results indicate a match between MB and 3 of the 6 members of my family that have been tested. MB matches ED, KJG & JH. ED & KJG are my sibs (sister and brother), JH is my maternal aunt. This indicates that the match is on my mother's side, and not my father's. This is confirmed by the fact that MB does not match MHG (my Dad) or ALH (my Dad’s 2nd cousin via his father’s father’s father).

These matches are indicated in the diagram above by the green arrows. The yellow squares are those members of my family who have been tested. The fact that MB does not match me (MJG) is pure chance due to the random recombination of genetic material as it is passed down from our common ancestor. To learn more about the science behind the transmission of autosomal DNA have a look at this brief video from SMGF.

MB has persuaded some of her cousins to test and this will tell us whether the match is on her maternal or paternal side. I have asked some of my cousins to test and this will tell us whether the match is on JH’s maternal or paternal side. This will substantially reduce the number of candidates for our Common Ancestor.