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Let's Talk About X, Baby

Among my favorite DNA cases are the ones where I can put the X chromosome to good use to answer a question. Lately, I've been fielding quite a few X related questions, and I figured now would be a good opportunity to discuss how I have used X in my research.

Let me begin with a brief rundown of the X. We each have 23 pairs of chromosome. 22 pairs are autosomes (hence autosomal DNA), which are tested by all the major commercial testing sites. Both male and female can take these tests, and we use the results to determine relationships between people. The 23rd pair is the sex chromosomes. Mothers pass on an X chromosome to their daughters and fathers pass on either their X or Y chromosome, which determines the sex of the child.

23 pairs of chromosomes

23andme and FamilyTreeDNA (FTDNA) both include X in their chromosome browsers. Neither AncestryDNA nor MyHeritage include X in their totals, but you are able to download your raw data and upload to a third-party site like GEDMatch to analyze the X.

So how might I use the X chromosome? Here are a few examples:

1. Often I may use it to determine whether two females share a father. Paternal half sisters (or full sisters as well) always share a complete X chromosome, which is around 196cMs give or take a few centimorgans. This scenario usually arises when two females share around 1300-2300cMs of autosomal DNA and want to determine how they are related exactly. At this range, options could include paternal or maternal half siblings, aunt/niece, grandmother/granddaughter, or double first cousin. In my personal experience, the answer is usually between aunt/niece and paternal half siblings (when females are surprised that their father is not biological).

A complete X chromosome at 23andme.

When you have access to a chromosome browser, this complete X can be easily viewed. On a site like Ancestry, however, raw DNA must be downloaded and transferred to a site like GEDMatch. There we can run a One-to-One X comparison to determine whether the women could be paternal half-sisters.

Where to find the One-to-One X-DNA Comparison on GEDMatch.

If the X is not complete, they are NOT paternal half-sisters. If it is complete, they are most likely paternal half-sisters, but the other options would still need to be ruled out, since it is possible, albeit unlikely, for maternal half-sisters and aunt/niece to share a complete X. The chance two siblings share a complete X from their mother is about 1%, so although unlikely, still possible. Paternal grandmothers ALWAYS share a complete X with their granddaughters because their sons only have the one X to pass along and it comes from them (although age usually rules out this option).

According to GEDMatch, these two matches share two segments of X, but couldn't be paternal half-sisters,

2. X can sometimes be used to determine on which side someone is related. As men only inherit any X they have from their mothers, an X match always belongs to that side of the family. But be warned! FTDNA may tell you that there's an X-match, and if you're male, you might be really excited to be able to place the match on your mother's side. However, X-matches on FTDNA are commonly false positives because they include segments as low as 1cM. It's not uncommon to have an X match, but then the match is actually on the other side of the family, especially if you are dealing with endogamy. Most experts agree that 10cM should be the minimum amount for serious X consideration, some adopting even higher thresholds.

A recently discovered 2c1r listed as an X-Match on FTDNA.

Our shared X-DNA. All segments are less than 10cMs. We're also only related through my paternal grandfather's family!

3. Many of the cases I handle involve surprise Ashkenazi Jewish ancestry. When someone learns this on 23andme, I'm ecstatic because I can usually tell you which parent or grandparent was the surprise source. How you may ask?

23andme provides a beautiful chromosome painting, including the X chromosome. Ashkenazi Jewish shows up in green.

My chromosome painting is a sea of (Ashkenazi) green.

When a male shows up as around 50% Ashkenazi, I can look at his X and tell him fairly definitively if his mother or father was ethnically Jewish. He only inherits one X chromosome, so if it's from a Jewish mother, it's fully green. If it's not, then it's dad. Unfortunately, I can't do the same for women because they can inherit the Ashkenazi X from either parent.

This male is 50% Ashkenazi. Because there is no Ashkenazi on his X, we can conclude it's through his father.

In cases of around 25% Ashkenazi, X is also valuable. In women, Ashkenazi on the X means we aren't looking at a paternal grandfather (since fathers don't pass an X to their sons). In surprise cases like these it's also usually a grandfather who is the mystery source of Jewish DNA, so then the first place I would look is the maternal grandfather.

An example: I was assisting someone in finding her biological father, and she had a completely Ashkenazi X chromosome. This indicated to me that her paternal grandmother was fully Ashkenazi, and it helped narrow our search, leading to a happy reunion with her birth father.

Here we have one Ashkenazi X, one non-Ashkenazi. We know the mother isn't Ashkenazi, so it is the paternal grandmother's.

Another case I just recently worked showed no Ashkenazi on the X, which helped a woman determine that biological paternal grandfather was ethnically Jewish, while the paternal grandmother was not.

No Ashkenazi on an X for a male who is around one-quarter Ashkenazi Jewish usually means that the source is his paternal side. For a female, it usually means it was her paternal grandfather. I have an unknown male match like this and coupled with a fairly common Jewish paternal haplogroup that I know belonged to my maternal grandmother's father, I suspect he may be a half-first cousin to my mother through their shared grandfather.

However, I should caution that there are exceptions. For example, I assisted a man who is about one-quarter Ashkenazi and has no Ashkenazi on his X. This led me down the path of focusing on his paternal grandfather as the source of his Jewish heritage. When the client and I spoke further, it was determined that the likely source was in fact his maternal grandfather.

What happened? When a mother passes on her X chromosome, there's usually a process called recombination between her two X chromosomes to make a new one. That way the child usually inherits some X DNA from both maternal grandparents. However, 14% of the time recombination doesn't happen, and the mother passes along a complete X from either one grandparent or the other. This appears to be what happened in this case. The mother passed along her non-Jewish mother's complete X chromosome, which led to a false conclusion.

It's also important to note that absence of X when looking at shared matches doesn't necessarily mean anything. If there is no X shared, it doesn't automatically mean you can determine which side a match is on. For example, if a male doesn't share X with even a 1st cousin match, it doesn't mean the match is definitely on his father's side. It simply means you need to use other tools to solve the mystery.

A match on my husband's maternal side. Absence of X doesn't mean anything.

There are several more potential uses for X-DNA, and these are just the tip of the X-berg. If you're interested in learning more about X-DNA, there are several resources. For X-DNA beginners, I would recommend The Family Tree Guide to DNA Testing and Genetic Genealogy by Dr. Blaine Bettinger and Genetic Genealogy in Practice by Bettinger and Debbie Parker Wayne. For more advanced users, there's a great chapter on X-DNA titled, "X-DNA Techniques and Limitations" by Dr. Kathryn J. Johnston in Wayne's Advanced Genetic Genealogy: Techniques and Case Studies as well as several blogs on the subject that require a simple Google search.

I just finished the X-DNA chapter in this book. Highly recommended!

If you have your DNA at 23andme, FTDNA, or GEDMatch, check out the X. You might learn something new from your matches that could break down your next brickwall.


Contact me at if you're interesting in exploring your family history. Free initial consultations.

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