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.

51 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
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    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).

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  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.

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    2. My full brother and I on FT-DNA autosomal are an X-Match but on autosomal test that would not necessarily be the case (true?) since one of us could have an X from her mother, the other an X from her father, theoretically.

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  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.

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  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

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  7. Please advise if there is a chart that shows the amount of shared cms on the x chromosome only. Examplw niece/aunt share 138cm on x with largest segment being 78..total cm 1347 and trying to verify full versus half relationship.
    Thanks

    ReplyDelete
    Replies
    1. I'm not aware of any but you might ask Blaine Bettinger and see what he says. He runs the Shared cM Project at https://thegeneticgenealogist.com/2017/08/26/august-2017-update-to-the-shared-cm-project/

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  8. Hello all. I have been trying to solve a mystery for 3 years. I hoped x would help. I was adopted. I found my birth mother many years ago. I am trying to determine who is my birth father since she did not tell me. I have my closest match on family tree DNA either 1/2 first cousin or first cousin once removed. Total cm. 485. We share no x. I am trying to determine which side of her family I match her on. Is it possible that I could match to her father's side if she and I do not share any x? Or do I have to match her on her mother's side? Please help me solve this. It would help so much. I do have a male match 9 cm. on x who has family names from my female matches father's side on his grandmother's line. Unfortunately it is a very common Jewish name - Cohen and difficult to be sure. Thank you so much.

    ReplyDelete
    Replies
    1. Either scenario (half-1st cousin or 1C1R) could be associated with no X match.

      Delete
  9. When trying to determine relationships with a father and daughter who you share 150cm X each with, would the large X match help? Example: I share 694 autosomal and 150 x cm with someone who is either my half uncle or 1cousin 1x. It can go either way but would the large x push it towards half uncle? His daughter and I share 150 cm on the X also. His half niece and I share 380 cm and 60 x cm

    ReplyDelete
    Replies
    1. The X can be passed down in very large chunks indeed, some times with no recombination for several generations, so I don't think the size of the chunk points in a particular direction.
      Obviously the father passed his entire X chromosome on intact to his daughter. And the connection is on his mother's side (hence his half-neice's X match).

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    2. Thank you. I’m adopted and trying to determine if the large X match could point in the direction of paternal grandmother. My daughter also shares large X chromosome shares as well ie)112cm with the same descendants I share 150cm on. I was hoping that would help

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    3. Blaine Bettinger has written an excellent post on the topic (see link below) but whilst a large segment may point you in a certain direction, it will never be 100% definite ... https://thegeneticgenealogist.com/2009/01/12/more-x-chromosome-charts/

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  10. Also, I read on DNA Detectives cm chart that you should add the x to the autosomal if you tested with Ancestry and uploaded to gedmatch. Is this accurate? If true, then the shared cm would be much higher for the above DNA matches right?

    ReplyDelete
    Replies
    1. Check with the Shared cM Project, or the DNA Painter tool to see the probability for the different possible relationships.

      Delete
  11. You mentioned a male with an x match having only a common ancestor on the maternal side with the caveat of weak X and thus eliminating paternal side
    My son is a 47 XXY male and would throw a monkey wrench into your elimination of paternal ancestors in common as Klinefelter syndrome results from either the mother's XX joining the father's Y or from the father's XY joining the mother's X
    there are other genetic chromosome issues that can influence your X matches so I would add this as another "caveat"
    On a totally unrelated matter- were you related to Marg Farrell Thompson?
    cheers

    ReplyDelete
    Replies
    1. Good point. The various sex chromosome abnormalities can alter the situation quite considerably. In addition, women who are XXY can test their Y chromosome.
      I have not heard of Marg Farrell Thompson.
      Best, Maurice

      Delete
  12. Shared autosomal is 1313.8 largest cM 113 and x dna total cM is 32.7 and largest cM is 26.5! What does this mean to me? Please!!

    ReplyDelete
    Replies
    1. According to the Shared cM Project (via DNA Painter at https://dnapainter.com/tools/sharedcmv4), the data suggests a 56% probability that the relationship is a half-sibling, Aunt / Uncle, Niece / Nephew, or Grandparent Grandchild; and a 43% probability that it is 1C, Great-Grandparent, Great-Aunt / Uncle, Half Aunt / Uncle, Half Niece / Nephew, Great-Niece / Nephew, or Great-Grandchild.

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  13. Why do I share 159.6 cms of x DNA with my maternal grandmother, but my sister only shares 59?

    ReplyDelete
    Replies
    1. The luck of the genetic draw.

      Delete
    2. But does it seem that maybe my mothers x that she got from my grandmother didn’t recombine? Or, I got a segment that is identical to the x DNA that my mother got from my grandmother? I wish I understood this better

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    3. No recombination would result in a shared segment of about 196cM match on the X.
      Lack of recombination is not uncommon.
      And segments can be passed on in their entirety.

      Delete
    4. Thank you. So, from what I understand, I just got a larger matching segment than my sister?

      Delete
  14. When you look at DNA matches do you add autosomal and X together and the total cm is the amount you consider or autosomal only?

    ReplyDelete
  15. Was wondering if a woman that came up as close relation on ancestry is my half aunt. We share 983cm and 123 x dna. Could she be my fathers half sister?

    ReplyDelete
    Replies
    1. I know she is related on my fathers side through cousins related to me and her on my dads side.

      Delete
    2. Yes that is definitely a possibility. Have you determined the relationship yet? Could be more than one possible relationship such as first cousin as well as a half aunt.

      Delete
  16. Hello,
    I am trying to trace my father. I have a 3rd-4th cousin match on Gedmatch and Ancestry. I know she is on my paternal side. We have 0 match on the X chromosone. Can this give me any clues to which of her ancestors is my common ancestor?
    Thank you

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  17. Hello, trying to figure out why 23andme is telling me my cousin is my half sister we share 18.2% DNA across 34 segments? Has anyone heard of a number of shared dna between cousins that high before? Thank You, Dale



    ReplyDelete
    Replies
    1. I have a similar question. I am hoping to be notified of any answers to your question. I've got 26.9% shared DNA across 29 segments. (higher % but less segments) Largest segment 184.5 cM.

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    2. what is your question exactly? or what exactly are you looking for? are you using 23andme? if so, you can find the total cm value by comparing your dna on the website - or to get a close approximation, you can multiply the total percentage times 68, so 26.9 x 68 = 1829.2 - you can then plug those numbers into a relationship estimator (http://relationshipestimator.azurewebsites.net/index.htm) to get probable outcomes. so for you - it says Half Sibling/Grandparent/Grandchild/Uncle/Aunt/Niece/Nephew/Double First Cousins or you can go to dnapainter and plug in the total cms and it says: 100.00% Grandparent/Aunt/Uncle/Half Sibling/Niece/Nephew/Grandchild

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    3. daleymom - 23andme is going to give you it's best prediction - that's not set in stone. however, those numbers are a bit off. can you get more info, as in the total cm and the largest segment. i can get an approximation of your total cms (1237.6) - but that along with the number of segments doesn't add up. the percentage of dna is too high for cousin. but its a bit too low for half sibling. its kind of around the range for double first cousin? did siblings from two different families marry? like two siblings from one family married two siblings from another family? having the true total cm value and largest segment would really help. and don't get me wrong, cousin COULD be possible... just the numbers aren't usually that high.

      Delete
    4. Hello Virginia Rose, sorry just saw your reply. Thank you, we share 1353cm and we share 27,709 SNPs on the 12th chromosome. Thanks again, Dale

      Delete
  18. My biological father is one of two brothers. Brother A is alive and had no children. Brother B is deceased, but had a daughter and a son. This daughter, who could be either my half sibling or my first cousin has a son who I am DNA matched with on Ancestry and GEDmatch. We share 589 cm on Ancestry, and 640 on GEDmatch. My X-DNA match with this young man is: total segments 94.1 and largest segment 77.4. Our overall DNA one to one match shows largest segment 82.2 with 25 segments and an estimated MRCA of 2.2 Which brother is more likely to have fathered me? Is this young man my half-nephew or my 1C1xr? His average DNA match to me seems too low or too high respectively. I am 65 and Brother B is 88 years old. I need to decide whether contacting Brother B about my paternity is merited. Thanks Sam

    ReplyDelete
    Replies
    1. How old is Brother A? If he was only 10 or 11 when you were conceived, then it is more likely to be Brother B.

      As far as the atDNA is concerned, DNAPainter predicts that 589cM has a 78% probability of being a 1C1R (=> your father is Brother A) and a 20% probability of half-nephew (=> your father is Brother B), whereas 640 equates to probabilities of 57% & 42% respectively. So the atDNA favours 1C1R (=Brother A) ... but it is a bit close to call.

      If it was Brother A, then he would have received (let's say) 200 units of shuffled DNA from his mother. His brother (B) would have also received shuffled DNA from their mother, but (on average) the shuffling would mean that he only gets 50% of the X DNA that his brother got from his mother, so that would be a 100 unit match. He would have passed this on intact to his daughter, so she has 100 units. And she would have shuffled this and would have roughly passed on half of it = 50 units to her son (your 1C1R).

      It it was Brother B, then he would have passed on 200 units intact to both you and your half-sister, who would have shuffled this and passed on 50% to your half-nephew (100 units). So the X-DNA is suggesting the half-nephew option (Brother B). But the X is notoriously difficult to predict ...

      So the best way to solve the mystery is to test Brother B's daughter ... or Brother A.

      Delete
  19. Thanks. Brother A is 88, same age as my mother would be if she were alive. Deceased brother B was 12 years older. Both were in age range to have fathered me. Your answer is helpful. I will follow through and contact Brother A. After all, he may have been out of town during month of my conception (he was in the Navy in 1948 - how long?) or he might have had a long term romantic relationship with my mother and he remembers her. Finally there is the possibility that he already knows, or that she told him. Thanks!

    ReplyDelete
  20. My grandmother was adopted. We had my aunt, her daughter do her DNA. From that, I have been able to create a massive Mirror tree through Ancestry. There are two family lines in contention which my grandmother is definitely connected to. Because nobody that I can see from either sides of these families match within each other, at this point it seems apparent, that one family group could be my grandmother's Bio Father line, and the other my grandmother's Bio mother. All that being said here is my question
    I have two people who share X DNA with my aunt as learned on DNA. They are a mother and a son. Based on my Mirror tree, it would appear the mother is a 2C to my aunt, while the son is a 2C1R. The mother shares the following X DNA per GED Match, Start @ 93,089,054 / End @ 129,242,314 cM 39.9 and SNP 3412. Meanwhile her son matches my aunt on X DNA Start @ 93,068,292 / End @ 04,571,747 cM 38.7 SNP 2,918. Would it be possible to figure out based on these two, if they are related to my grandmother's Paternal or Maternal side of the family. I do know that the 2C's grandfather is a possible, Sibling to one of my grandmother's bio parent, or possibly he is the parent. Her mother is his child. Also the 2C total cM against my Aunt is 222 across 12 line segments. Based on this and my research, she is either a true 2nd C or 1/2-1C or most unlikely 1/2 Great Aunt, or Niece.

    ReplyDelete
  21. sorry the son's X DNA SHARE ends at 127,571,747

    ReplyDelete
    Replies
    1. You would need to draw out all the possible connections and see which ones are impossible for the X to travel down. For example, if your aunt and her female match are 2nd cousins, the route to the common ancestral couple (CAP) on your aunt's side (YA) is one of the following:
      YA < Mother (M) < M < CAP
      YA < M < F (Father) < CAP
      ... the X DNA could have passed down to your aunt along either path.
      On your female match's side (FM), the route to the CAP is one of the following:
      FM < F < F < CAP (impossible route for X transmission from the CAP to your match)
      FM < F < M < CAP
      FM < M < F < CAP
      FM < M < M < CAP
      ... so it could be any of the last 3 pathways.
      You would need to repeat this exercise for the other possible pathways associated with 1/2 1C or 1/2 Great Aunt/Niece.
      Using the amount of DNA is unlikely to be helpful because X-DNA transmission is highly variable. All that we can say is that there is a good strong X-DNA match between your aunt and her female match, and this indicates that they are connected on an X pathway ... but which one?

      Delete