That Unruly X….Chromosome That Is


Something is wrong with the X chromosome.  More specifically, something is amiss with trying to use it, the way we normally use recombinant chromosomes for genealogy.  In short, there’s a problem.

If you don’t understand how the X chromosome recombines and is passed from generation to generation, now would be a good time to read my article, “X Marks the Spot” about how this works.  You’ll need this basic information to understand what I’m about to discuss.

The first hint of this “problem” is apparent in Jim Owston’s “Phasing the X Chromosome” article.  Jim’s interest in phasing his X, or figuring out where it came from genealogically, was spurred by his lack of X matches with his brothers.  This is noteworthy, because men don’t inherit any X from their father, so Jim’s failure to share much of his X with his brothers meant that he had inherited most of his X from just one of his mother’s parents, and his brothers inherited theirs from the other parent.  Utilizing cousins, Jim was able to further phase his X, meaning to attribute portions to the various grandparents from whence it came.  After doing this work, Jim said the following”

“Since I can only confirm the originating grandparent of 51% my X-DNA, I tend to believe (but cannot confirm at the present) that my X-chromosome may be an exact copy of my mother’s inherited X from her mother. If this is the case, I would not have inherited any X-DNA from my grandfather. This would also indicate that my brother Chuck’s X-DNA is 97% from our grandfather and only 3% from our grandmother. My brother John would then have 77% of his X-DNA from our grandfather and 23% from our grandmother.”

As a genetic genealogist, at the time Jim wrote this piece, I was most interested in the fact that he had phased or attributed the pieces of the X to specific ancestors and the process he used to do that.  I found the very skewed inheritance “interesting” but basically attributed it to an anomaly.  It now appears that this is not an anomaly.  It was, instead the tip of the iceberg and we didn’t recognize it as such.  Let’s look at what we would normally expect.


The X chromosome does recombine when it can, or at least has the capacity to do so.  This means that a female who receives an X from both her father and mother receives a recombined X from her mother, but receives an X that is not recombined from her father.  That is because her father only receives one X, from his mother, so he has nothing to recombine with.  In the mother, the X recombines “in the normal way” meaning that parts of both her mother’s and her father’s X are given to her children, or at least that opportunity exists.  If you’re beginning to see some “weasel words” here or “hedge betting,” that’s because we’ve discovered that things aren’t always what they seem or could be.

The 50% Rule

In the statistical world of DNA, on the average, we believe that each generation receives roughly half of the DNA of the generations before them.  We know that each child absolutely receives 50% of the DNA of both parents, but how the grandparents DNA is divided up into that 50% that goes to each offspring differs.  It may not be 50%.  I am in the process of doing a generational inheritance study, which I will publish soon, which discusses this as a whole.

However, let’s use the 50% rule here, because it’s all we have and it’s what we’ve been working with forever.

In a normal autosomal, meaning non-X, situation, every generation provides to the current generation the following approximate % of DNA:

Autosomal % chart

Please note Blaine Bettinger’s X maternal inheritance chart percentages from his “More X-Chromosome Charts” article, and used with his kind permission in the X Marks the Spot article.

Blaine's maternal X %

I’m enlarging the inheritance percentage portion so you can see it better.

Blaine's maternal X % cropped

Taking a look at these percentages, it becomes evident that we cannot utilize the normal predictive methods of saying that if we share a certain percentage of DNA with an individual, then we are most likely a specific relationship.  This is because the percentage of X chromosome inherited varies based on the inheritance path, since men don’t receive an X from their fathers.  Not only does this mean that you receive no X from many ancestors, you receive a different percentage of the X from your maternal grandmother, 25%, because your mother inherited an X from both of her parents, versus from your paternal grandmother, 50%, because your father inherited an X from only his mother.

The Genetic Kinship chart, below, from the ISOGG wiki, is the “Bible” that we use in terms of estimating relationships.  It doesn’t work for the X.

Mapping cousin chart

Let’s look at the normal autosomal inheritance model as compared to the maternal X chart fan chart percentages, above, and similar calculations for the paternal side.  Remember, the Maternal Only column applies only to men, because in the very first generation, men’s and women’s inheritance percentages diverge.  Men receive 100% of their X from their mothers, while women receive 50% from each parent.

Generational X %s

Recombination – The Next Problem

The genetic genealogy community has been hounding Family Tree DNA incessantly to add the X chromosome matching into their Family Finder matching calculations.

On January 2, 2014, they did exactly that.  What’s that old saying, “Be careful what you ask for….”  Well, we got it, but “it” doesn’t seem to be providing us with exactly what we expected.

First, there were many reports of women having many more matches than men.  That’s to be expected at some level because women have so many more ancestors in the “mix,” especially when matching other women.

23andMe takes this unique mixture into consideration, or at least attempts to compensate for it at some level.  I’m not sure if this is a good or bad thing or if it’s useful, truthfully.  While their normal autosomal SNP matching threshold is 7cM and 700 matching SNPs within that segment, for X, their thresholds are:

  • Male matched to male – 1cM/200 SNPs
  • Male matched to female – 6cM/600 SNPs
  • Female matched to female – 6cM/1200 SNPs

Family Tree DNA does not use the X exclusively for matching.  This means that if you match someone utilizing their normal autosomal matching criteria of approximately 7.7cM and 500 SNPs, and you match them on the X chromosome, they will report your X as matching.  If you don’t match someone on any chromosome except the X, you will not be reported as a match.

The X matching criteria at Family Tree DNA is:

  • 1cM/500 SNPs

However, matching isn’t all of the story.

The X appears to not recombine normally.  By normally, I don’t mean something is medically wrong, I mean that it’s not what we are expecting to see in terms of the 50% rule.  In essence, we would expect to see approximately half of the X of each parent, grandfather and grandmother, passed on to the child from the mother in the maternal line where recombination is a possibility.  That appears to not be happening reliably.  Not only is this not happening in the nice neat 50% number, the X chromosome seems to be often not recombining at all.  If you think the percentages in the chart above threw a monkey wrench into genetic genealogy predictions, this information, if it holds up in a much larger test, in essence throws our predictive capability, at least as we know it today, out the window.

The X Doesn’t Recombine as Expected

In my generational study, I noticed that the X seemed not to be recombining.  Then I remembered something that Matt Dexter said at the Family Tree DNA Conference in November 2013 in Houston.  Matt has the benefit of having a full 3 generation pedigree chart where everyone has been tested, and he has 5 children, so he can clearly see who got the DNA from which of their grandparents.

I contacted Matt, and he provided me with his X chromosomal information about his family, giving me permission to share it with you.  I have taken the liberty of reformatting it in a spreadsheet so that we can view various aspects of this data.

Dexter table

First, note that I have sorted these by grandchild.  There are two females, who have the opportunity to inherit from 3 grandparents.  The females inherited one copy of the X from their mother, who had two copies herself, and one copy of the X from her father who only had his mother’s copy.  Therefore, the paternal grandfather is listed above, but with the note “cannot inherit.”  This distinguishes this event from the circumstance with Grandson 1 where he could inherit some part of his maternal grandfather’s X, but did not.

For the three grandsons, I have listed all 4 grandparents and noted the paternal grandmother and grandfather as “cannot inherit.”  This is of course because the grandsons don’t inherit an X from their father.  Instead they inherit the Y, which is what makes them male.

According to the Rule of 50%, each child should receive approximately half of the DNA of each maternal grandparent that they can inherit from.  I added the columns, % Inherited cM and % Inherited SNP to illustrate whether or not this number comes close to the 50% we would expect.  The child MUST have a complete X chromosome which is comprised of 18092 SNPs and is 195.93cM in length, barring anomalies like read errors and such, which do periodically occur.  In these columns, 1=100%, so in the Granddaughter 1 column of % Inherited cM, we see 85% for the maternal grandfather and about 15% for the maternal grandmother.  That is hardly 50-50, and worse yet, it’s no place close to 50%.

Granddaughter 1 and 2 must inherit their paternal grandmother’s X intact, because there is nothing to recombine with.

Granddaughter 2 inherited even more unevenly, with about 90% and 10%, but in favor of the other grandparent.  So, statistically speaking, it’s about 50% for each grandparent between the two grandchildren, but it is widely variant when looking at them individually.

Grandson 1, as mentioned, inherited his entire X from his maternal grandmother with absolutely no recombination.

Grandsons 2 and 3 fall much closer to the expected 50%.

The problem for most of us is that you need 3 or 4 consecutive generations to really see this happening, and most of us simply don’t have data that deep or robust.

A recent discussion on the DNA Genealogy Rootsweb mailing list revealed several more of these documented occurrences, among them, two separate examples where the X chromosome was unrecombined for 4 generations.

Robert Paine, a long-time genetic genealogy contributor and project administrator reported that in his family medical/history project, at 23andMe, 25% of his participants show no recombination on the X chromosome.  That’s a staggering percentage.  His project consists of  21 people in with 2 blood lines tested 5 generations deep and 2 bloodlines tested at 4 generations

One woman’s X matches her great-great-grandmother’s X exactly.  That’s 4 separate inheritance events in a row where the X was not recombined at all.

The graphic below, provided by Robert,  shows the chromosome browser at 23andMe where you can see the X matches exactly for all three participants being compared.

The screen shot is of the gg-granddaughter Evelyn being compared to her gg-grandmother, Shevy, Evelyn’s g-grandfather Rich and Evelyn’s grandmother Cyndi. 23andme only lets you compare 3 individuals at a time so Robert did not include Evelyn’s mother Shay, who is an exact match with Evelyn.

Paine X

Where Are We?

So what does this mean to genetic genealogy?  It certainly does not mean we should throw the baby out with the bath water.  What it is, is an iceberg warning that there is more lurking beneath the surface.  What and how big?  I can’t tell you.  I simply don’t know.

Here’s what I can tell you.

  • The X chromosome matching can tell you that you do share a common ancestor someplace back in time.
  • The amount of DNA shared is not a reliable predictor of how long ago you shared that ancestor.
  • The amount of DNA shared cannot predict your relationship with your match.  In fact, even a very large match can be many generations removed.
  • The absence of an X match, even with someone closely related whom you should match does not disprove a descendant relationship/common ancestor.
  • The X appears to not recombine at a higher rate than previously thought, the previous expectation being that this would almost never happen.
  • The X, when it does recombine appears to do so in a manner not governed by the 50% rule.  In fact, the 50% rule may not apply at all except as an average in large population studies, but may well be entirely irrelevant or even misleading to the understanding of X chromosome inheritance in genetic genealogy.

The X is still useful to genetic genealogists, just not in the same way that other autosomal data is utilized.  The X is more of an auxiliary chromosome that can provide information in addition to your other matches because of its unique inheritance pattern.

Unfortunately, this discovery leaves us with more questions than answers.  I found it incomprehensible that this phenomenon has never been studied in humans, or in animals, for that matter, at least not that I could find.  What few references I did find indicated that the X seems to recombine with the same frequency as the other autosomes, which we are finding to be untrue.

What is needed is a comprehensive study of hundreds of X transmission events at least 3 generations deep.

As it turns out, we’re not the only ones confused by the behavior of the X chromosome.  Just yesterday, the New York Times had an article about Seeing the X Chromosome in a New Light.  It seems that either one copy of the X, or the other, is disabled cell by cell in the human body.  If you are interested in this aspect of science, it’s a very interesting read.  Indeed, our DNA continues to both amaze and amuse us.

A special thank you to Jim Owston, Matt Dexter, Blaine Bettinger and Robert Paine for sharing their information.

Additional sources:

Polymorphic Variation in Human Meiotic
Recombination (2007)
Vivian G. Cheung
University of Pennsylvania

A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome, Science October 2005, Myers et al
Supplemental Material

147 thoughts on “That Unruly X….Chromosome That Is

  1. Hello Roberta, I have a a X chromosome situation going on here :-). My mother, her brother, me and my son all have share a considerable amount of X DNA with another family but no autosomal DNA. My daughter does not share any X DNA with the other family, Have you come across anyone sharing so much XDNA (50.4 cM) and no autosomal DNA.

    This is my mother’s shared XDNA with someone from the other family
    Chr Start Location End Location Centimorgans (cM) SNPs
    X 1982358 30249248 50.4 3921

    This my mother’s brother with the same person of the other family
    Chr Start Location End Location Centimorgans (cM) SNPs
    X 1982358 30232847 50.4 3242
    Largest segment = 50.4 cM
    Total of segments > 7 cM = 50.4 cM Actual.

    This is me with the same person of the family
    Chr Start Location End Location Centimorgans (cM) SNPs
    X 22803814 30230136 9.3 922
    Largest segment = 9.3 cM
    Total of segments > 7 cM = 9.3 cM Actual.

    This is my son with the same person of the other family
    Chr Start Location End Location Centimorgans (cM) SNPs
    X 22906823 30230136 8.7 897
    Largest segment = 8.7 cM
    Total of segments > 7 cM = 8.7 cM Actual.

    • The X is sometimes passed intact from one ancestor. In other words, your daughter may have received one of your X chromosomes from one ancestor and none from the other. To sort through this would take some map-drawing and maybe some additional relatives.

  2. I found out through that I have 3 % British ancestry in me but my family comes from eastern Europe (Germany, Poland, Austria, Slovakia) How would I know where this gene came from and from what generation? Where would I look to find out the family that contributed that gene.

  3. I am wondering what impact on my X Chromosome does it make where my mother’s father’s mother’s mother (g-g-grandmother) is the same person as my father’s mother’s mother’s mother (g-g-grandmother). The chart shows I would get 12.5% from each one due to their position but does it increase the % that I would get from her? Or increase the likelihood of getting more?

      • So let’s say that on FTDNA, Katie matches me at 29cm on my X chromosome (and she also matches me on other various chromosomes at a level making her around a 2nd cousin something or other). I downloaded the full chromosome browser spreadsheet, and found all of the people who overlap with Katie on the X. However, when I did a Matrix Match with them on Katie, then they don’t match autosomally. So although they overlap on the X with Katie, they don’t appear to be genetically related to Katie. Is that correct?

      • By the way, I have already matched and Matrix Matched the autosomal matches (we need less ambiguous terminology) with Katie, so I know who her true matches (lol – IBD) are. I’m trying to make sense out of the X-overlap people with Katie but who don’t match her autosomally.

      • Keep in mind that the matrix only looks at people who match above the threshold of total 20cM and a largest segment of 7cM. When you download your matching segments, you get much smaller ones than that too.

  4. Roberta, I enjoyed your article very much and learned a lot from it, but I want to make sure I am seeing typos and not assertions of fact in two places. In your first two column spreadsheet it looks like you missed the 3G-GP generation and that threw off your percentages. Please confirm. Secondly in both spreadsheets you use 12% as the contribution of GP’s, which I believe (from other numbers in the article) should actually be 12.5%. Please confirm. Otherwise, well done, thanks.

  5. Hi Roberta, on Gedmatch, I have a female match of X CM only of 30.6, no Autosomal match. In comparison, I share 35.7 X CM with my 1/2 sister. (of course I also share Autosomal). When I compared her Gedmatch list to mine, we have 22 common names. Can you tell me if I am related to this X match?

  6. I am hoping you can shed some light on a mystery. I have recently connected to a young man that could be as closely related as my first cousin. Neither he nor I know who our biological fathers are but do know our mothers. We have not found a link between the families yet but clearly there is one between the two of us. Can you give me your impression of what the results could mean? After doing an x-dna comparison this is the result:

    Chr St loc. End loc. cM. SNPs
    X. 488604. 133841337. 150.5. 13818

  7. Hi Roberta–
    Thanks for this posting. I am curious about your heading that the “X chromosome doesn’t recombine as expected”–isn’t this outcome a result of the fact that the X chromosome is only one chromosome, 180 centiMorgans long, while the autosomes are both more numerous and represent many times more opportunities for recombination? So, one could apply the same reasoning to any individual chromosome, it is just that the math of the autosomes works out so that the inheritance looks more evenly distributed. Wouldn’t you see a similar pattern if you were focused on a particularly large segment on a single autosome? I just wanted to clarify this for my own understanding.

    • Jonathan, you are correct that any chromosome can be inherited in an all-or-none fashion from a grandparent. Look at generation 2 in Figure 2 of Graham Coop’s blog:

      I have a case in my own family where the entire length of chromosome 4 has been inherited intact through at least five and maybe six transmission events.

      I suspect there’s a bit of ascertainment bias going on here: if you notice something that strikes you as “odd,” you are more likely to notice if it happens again, and other people will chime in if they’ve seen the same thing. AFAIK, no one has collected a *random* sample looking at the X chromosome to see if it behaves any differently than other chromosomes of a similar size.

  8. Thanks for a facinating article Roberta!

    I happen to be so lucky that I was able to test both of my grandmothers (paternal and maternal) and thus with my parents tested I have been able to determine many very interesting things about my personal autosomal DNA and how much of it I did inherit from which grandparent.

    But my point is that as your article points out X chromosome does not seem to recombine “normally” – I myself have inherited my X chromosome completely from my maternal grandmother (I am a male, thus I have only one X chromosome) with nothing from my grandfather.

    So I have been able to determine I have inherited 21,6% from my paternal grandfather, 28,4% from my paternal grandmother, 20,5% from my maternal grandfather and 29,5,% from my maternal grandmother.

  9. X inactivation is a fascinating topic, but I don’t know of any research to show that it affects recombination. The inactivated chromosome uncoils during replication for cell division and recombination. Roberta posted another blog just yesterday, where she demonstrates that the all-or-nothing inheritance of a grandparental chromosome happens on the autosomes as well. As I mentioned above, I suspect there was a bit of ascertainment bias in reports of this happening on the X. People just noticed (and thus reported) it more.

  10. Pingback: DNAeXplain Archives – Intermediate DNA Articles | DNAeXplained – Genetic Genealogy

  11. Phased data from Gedmatch
    X chromosome
    1/2 brothers-same mother
    Comparing Kit PF404852M1 (Michael)(M) and PFN80425M1 (D R )(M)
    Minimum threshold size to be included in total = 700 SNPs
    Mismatch-bunching Limit = 350 SNPs
    Minimum segment cM to be included in total = 7.0 cM

    Chr Start Location End Location Centimorgans (cM) SNPs
    X 2,710,157 10,013,642 23.5 1,086
    X 128,787,527 149,034,194 37.2 2,701
    1/2 sibs, same mother
    Comparing Kit PF404852M1 (Michael )(M) and PF204898M1 (cynthia)(F)

    Minimum threshold size to be included in total = 700 SNPs
    Mismatch-bunching Limit = 350 SNPs
    Minimum segment cM to be included in total = 7.0 cM

    Chr Start Location End Location Centimorgans (cM) SNPs
    X 2,710,157 9,225,116 19.9 908
    X 148,374,123 154,551,755 14.2 943
    full sibs
    Comparing Kit PFN80425M1 (D R)(M) and PF204898M1 (cynthia)(F)
    Chr Start Location End Location Centimorgans (cM) SNPs
    X 2,710,157 9,225,116 19.9 957
    X 9,921,481 129,060,072 123.2 12,612

  12. X chromosome
    Comparing Kit PF404852M1 (Michael)(M) and PFN80425M1 (D R)(M)
    1/2 brothers-same mother
    Comparing Kit PF404852M1 (Michael Schlegel)(M) and PFN80425M1 (D R Smith)(M)
    Minimum threshold size to be included in total = 700 SNPs
    Mismatch-bunching Limit = 350 SNPs
    Minimum segment cM to be included in total = 7.0 cM
    Chr Start Location End Location Centimorgans (cM) SNPs
    X 2,710,157 10,013,642 23.5 1,086
    X 128,787,527 149,034,194 37.2 2,701
    1/2 sibs, same mother
    Comparing Kit PF404852M1 (Michael)(M) and PF204898M1 (cynthia)(F)

    Minimum threshold size to be included in total = 700 SNPs
    Mismatch-bunching Limit = 350 SNPs
    Minimum segment cM to be included in total = 7.0 cM
    Chr Start Location End Location Centimorgans (cM) SNPs
    X 2,710,157 9,225,116 19.9 908
    X 148,374,123 154,551,755 14.2 943
    full sibs
    Comparing Kit PFN80425M1 (D R )(M) and PF204898M1 (cynthia)(F)
    Chr Start Location End Location Centimorgans (cM) SNPs
    X 2,710,157 9,225,116 19.9 957
    X 9,921,481 129,060,072 123.2 12,612

    Comparing Kit F404852 (Michael)(M) and FN80425 (D R)(M) 1/2 sibs same mother

    Minimum threshold size to be included in total = 700 SNPs
    Mismatch-bunching Limit = 350 SNPs
    Minimum segment cM to be included in total = 7.0 cM
    Chr Start Location End Location Centimorgans (cM) SNPs
    X 2,710,157 10,013,642 23.5 1,092
    X 128,787,527 148,644,876 36.5 2,712
    Comparing Kit F404852 (Michael)(M) and F204898 (cynthia)(F) 1/2 sibs same mother

    Minimum threshold size to be included in total = 700 SNPs
    Mismatch-bunching Limit = 350 SNPs
    Minimum segment cM to be included in total = 7.0 cM
    Chr Start Location End Location Centimorgans (cM) SNPs
    X 2,710,157 9,225,116 19.9 913
    X 148,374,123 154,551,755 14.2 963
    Comparing Kit FN80425 (D R)(M) and F204898 (cynthia)(F) full sibs

    Minimum threshold size to be included in total = 700 SNPs
    Mismatch-bunching Limit = 350 SNPs
    Minimum segment cM to be included in total = 7.0 cM
    Chr Start Location End Location Centimorgans (cM) SNPs
    X 2,710,157 9,225,116 19.9 961
    X 9,921,481 129,060,072 123.2 12,663

  13. Read this blog item again after observing the data I show below which seems to fall perfectly into your discussion. As surrogate for my mother in matching, I’ve been using her only surviving sister – I call her “Aunt Sue” below. I am male, the others are female.

    1. My X chromosome matches Aunt Sue with 129cM total / 69cM longest segment.
    2. My sister Sally matches Aunt Sue with 156 total / 97 longest segment.
    3. My niece Martha – the daughter of another (deceased) sister – matches Aunt Sue (her great aunt) with 195 cM total / 165 longest segment.
    4. I match sister Sally for 137 total / 69 longest segment
    5. I match niece Martha 69 total / 59 longest segment.
    6. Sister Sally matches niece Martha 120 total / 96 longest segment

    My understanding is that the X Chromosome is 197 cMs. If so, since she matches her great aunt with 195 cM, my niece Martha must have inherited almost the exact X Chromosome of her great aunt Sue from Sue’s sister – Martha’s grandmother – who then must have had virtually the identical X Chromosome (of course Martha’s mother must also have had the near-identical X chr). But if I, a male, inherited only my mother’s X Chromosome, should I not match niece Martha for the entire X Chromosome rather than just 69 cM? Where have I gone wrong in my thinking? What else might I infer from these data and how might I use it to best advantage elsewhere?

    • Hi Wallace,
      I am going to make a stab at trying to answer your question. You don’t give a name for your mother. I will call her Jane. Jane and Sue are sisters. They received an X from their mother and one from their father. The X from their father was identical for both of them, as he only has one to give them. But the X that Sue and Jane received from their mother, your maternal grandmother, was most likely not identical. It could, and likely was, an unpredictable mixture of dna from recombination of the X from your maternal grandmother’s mother and father.

      If Martha matches her grandmother, then it appears that for two generations, there was very little recombination of the X in her line. It also seems to indicate that your mother and her sister, Sue, did not inherit identical X chromosomes from their mother. This is why you do not match with Martha more than you do.

      Interestingly, if recombination in the X fails to take place in a fair number of eggs as they are formed, it is possible that there would be instances where two brothers do not share any dna on their X chromosomes! One inherits the mother’s paternal X and the other inherits the mother’s maternal X. That seems like an amazing result and might raise a few eyebrows!

      • Thank you for the clear explanation, Marley! Yes, I failed to account for the recombination, thinking erroneously that the X was passed intact similar to Y-dna.

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