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.

12 comments:

  1. Is a match of 6.1 cM on the x chromosome enough to verify some type of match or just a possible false match? I also match on three other chromosomes with this particular person for a total of 84 cM. We are both females.

    ReplyDelete
    Replies
    1. Sounds like it is a real match but that doesn't mean that the X match is not a false positive segment. 6.1 cM is very small, especially when comparing the X of two females.

      Delete
  2. Hi, there! I just started trying out the tools on GEDmatch and found that I have a 60-cM X match (that's 60 total as well as "largest segment=60"). That seems significant! 60/196 is a large chunk. Strangely, we share 0 cM of autosomal DNA. Does this mean the X match is a false positive? I have dozens of matches at 20+ cM of X but 0 autosomal. How can this be?

    ReplyDelete
    Replies
    1. Hi Jessica, that is unusual. The X behaves somewhat differently to autosomal DNA and large segments of X can be passed down for many generations without breaking up into smaller chunks. It could be a false positive or it could be a true match but from very far back in the distant past (hence no atDNA).

      Delete
  3. I have a male who has a 37.84cM match with a female. There isn't any other chromosome match listed. It's from 23andme and the female hasn't tested at any other site.
    Should I be looking in the 2x/3x maternal grandparent for the common ancestor? I have found that there is a bit of relative marrying relative in the early/mid 1800's

    thanks
    **shiela
    tadjie@gmail.com

    ReplyDelete
  4. I am trying to identify my paternal family. I have a match on 23andme who shares 17.6 cM and 2170 SNPs on chromosome 1, 15.4 cM and 1683 SNPs on chromosome 15, and 19.5 and 84.5 cM, 1370 and 7614 SNPs respectively on chromosome X. Is it possible to determine whether I am related to her on her mother's or father's side? Any the prediction is that we are second to third cousins, which I was very excited to learn, however, it seems that that might not be an accurate prediction given that the majority of the DNA we share is X DNA. Any help would be wonderful so I know which path to follow from here. I'm so confused.

    ReplyDelete
    Replies
    1. Hi Rebecca, when comparing two women, it is difficult to tell whether the connection is on your paternal or maternal side because you get X DNA from both sides. If you were comparing two men, then the X-DNA can only be maternal in origin.

      Delete
  5. Can anyone tell me what this means? I am trying to figure out who my biological father is. My 1/2 sister ML and I share a high CM value of X-DNA of 68.5 cm's and I share 34.0 cm's with our maternal aunt but my sister only shares 5.0 with her. Could my Aunt and I have the same fathers??? Note, my sister and I share the same mother, and this Aunt is my mom's half sister which share the same mother.

    Thanks so much! I am just getting started with all this DNA stuff and am confused! The closest relatives I have matched with are in the 4-6 cousins range.



    ReplyDelete
    Replies
    1. Hi MG, if you and your aunt shared the same father, you would both have received his single X chromosome in it's entirety (196 cM). And so, because you only share 234 cM with your aunt, you cannot have shared the same father.

      It looks like that (just by chance) your half-sister received a much smaller portion of shared DNA with your aunt than you did.

      Delete
  6. Actually according to a different column for our shared 23, X-Chromosone, it looks like my sister and I share 79.5 and my Aunt and I share 34, my sister and my Aunt do not share any cm's???????

    Thanks again

    ReplyDelete
  7. I am very confused concerning the X-DNA shared with a female parental 2nd cousin,we share 64.5 cMs...also with a male maternal 2nd cousin we share over 100 cMs together..I have tried to figure it out..the male cousin is my great grandfather's grandson..his mom and my grandmother are 1/2 siblings....please help if you can.

    thank you
    aka on gedmatch Butterfly Diva
    email: ggmama.vj@gmail.com

    ReplyDelete
  8. I have a third cousin on my fathers side (we are both females) who I share 7.1 cm of x DNA. Can you explain this in simple terms? Our fathers are first cousins

    ReplyDelete