Tag Archives: X DNA

X Chromosome Master Class

Posted on by
13

The X chromosome can be especially useful to genetic genealogists because it has a unique inheritance path. Thanks to that characteristic, some of the work of identifying your common ancestor is done just by simply HAVING an X match.

Unfortunately, X-DNA and X matching is both underutilized and somewhat misunderstood – in part because not all vendors utilize the X chromosome for matching.

The X chromosome has the capability of reaching further back in time and breaking down brick walls that might fall no other way.

Hopefully, you will read this article, follow along with your own DNA results and make important discoveries.

Let’s get started!

Who Uses the X Chromosome?

The X chromosome is autosomal in nature, meaning it recombines under some circumstances, but you only inherit your X chromosome from certain ancestors.

It’s important to understand why, and how to utilize the X chromosome for matching. In this article, I’ve presented this information in a variety of ways, including case studies, because people learn differently.

Of the four major testing vendors, only two provide X-DNA match results.

  • FamilyTreeDNA – provides X chromosome results and advanced matching capabilities including filtered X matching
  • 23andMe – provides X chromosome results, but not filtered X matching without downloading your results in spreadsheet format
  • Ancestry and MyHeritage do not provide X-DNA results but do include the X in your raw DNA file so you can upload to vendors who do provide X matching
  • GEDmatch – not a DNA testing vendor but a third-party matching database that provides X matching in addition to other tools

It’s worth noting at this point that X-DNA and mitochondrial DNA is not the same thing. I wrote about that, here. The source of this confusion is that the X chromosome and mitochondrial DNA are both associated in some way with descent from females – but they are very different and so is their inheritance path.

So, what is X-DNA and how does it work?

What is X-DNA?

Everyone inherits two copies of each of chromosomes 1-22, one copy of each chromosome from each of your parents.

That’s why DNA matching works and each match can be identified as “maternal” or “paternal,” depending on how your match is related to you. Each valid match (excluding identical by chance matches) will be related either maternally, or paternally, or sometimes, both.

Your 23rd chromosome is your sex determination chromosome and is inherited differently. Chromosome 23 is comprised of X and Y DNA.

Everyone inherits one copy of chromosome 23 from each parent.

  • Males inherit a Y chromosome from their father, which is what makes males male. They do not inherit an X chromosome from their father.
  • Males always inherit an X chromosome from their mother.
  • Females inherit an X chromosome from both parents, which is what makes them female. Females have two X chromosomes, and no Y chromosome.
Chromosome 23 Father Contributes Mother Contributes
Male Child Y chromosome X chromosome
Female Child X chromosome X chromosome

X-DNA and mitochondrial DNA are often confused, but they are not the same thing. In fact, they are completely different.

Mitochondrial DNA, in BOTH males and females is always inherited from only the mother and only descends from the direct matrilineal line, so only the mother’s mother’s mother’s direct line. X DNA can be inherited from a number of ancestors based on a specific inheritance path.

Everyone has both X-DNA AND mitochondrial DNA.

Because males don’t inherit an X chromosome from their father, X chromosome matching has a unique and specific pattern of descent which allows testers who match to immediately eliminate some potential common ancestors.

  • Males only inherit an X chromosome from their mother, which means they can only have legitimate X matches on their mother’s side of their tree.
  • Females, on the other hand, inherit an X chromosome from both their mother and father. Their father only has one X chromosome to contribute, so his daughter receives her paternal grandmother’s X chromosome intact.
  • Both males and females inherit their mother’s X chromosome just like any of the other 22 autosomes. I wrote about chromosomes, here.

However, the unique X chromosome inheritance path provides us with a fourth very useful type of DNA for genealogy, in addition to Y-DNA, mitochondrial and autosomal DNA.

For the vendors who provide X-matching, it’s included with your autosomal test and does not need to be purchased separately.

The Unique X Chromosome

The X chromosome, even though it is autosomal in nature, meaning it does recombine and divide in certain circumstances, is really its own distinct tool that is not equivalent to autosomal matching in the way we’re accustomed. We just need to learn about the message it’s delivering and how to interpret X matches.

FamilyTreeDNA is one of two vendors who utilizes X chromosome matching, along with 23andMe, which is another good reason to encourage your matches at other vendors to upload their DNA file to FamilyTreeDNA for free matching.

The four major vendors do include X-DNA results in their raw DNA download file, even if they don’t provide X-matching themselves. This means you can upload the results to either FamilyTreeDNA or GEDmatch where you can obtain X matches. I provided step-by-step download/upload instructions for each vendor here.

Let’s look how X matching is both different, and beneficial.

My X Chromosome Family Tree

We are going to build a simple case study. A case study truly is worth 1000 descriptions.

This fan chart of my family tree colorizes the X chromosome inheritance path. In this chart, males are colored blue and females pink, but the salient point is that I can inherit some portion of (or all of) a copy of my X chromosome from the colorized ancestors, and only those ancestors.

Because males don’t inherit an X chromosome from their father, they CANNOT inherit any portion of an X chromosome from their father’s ancestors.

Looking at my father’s half of the chart, at left, you see that I inherited an X chromosome from both of my parents, but my father only inherited an X chromosome from his mother, Ollie Bolton. His father’s portion of the tree is uncolored, so no X chromosome could have descended from his paternal ancestors to him. Therefore he could not pass any X chromosome segments to me from his paternal side – because he doesn’t have X DNA from his father.

Hence, I didn’t inherit an X chromosome from any of the people whose positions in the chart are uncolored, meaning I can only inherit an X chromosome from the pink or blue people.

Essentially any generational male to male, meaning father/son relationship is an X-DNA blocker.

I know positively that I inherited my paternal grandmother, Ollie Bolton’s entire X chromosome, because hers is the only X chromosome my father, in the fan chart above, had to give me. His entire paternal side of the fan chart is uncolored.

Men only ever inherit their X chromosome from their mother. The only exception to this is if a male has the rare genetic condition of Klinefelter Syndrome, also known as XXY. If you are an adult male, it’s likely that you’ll already know if you have Klinefelters, so that’s probably the last possibility you should consider if you appear to have paternal X matches, not the first.

Sometimes, men appear to have X matches on their father’s side, but (barring Klinefelter’s) this is impossible. Those matches must either be identical by chance, or somehow related in an unknown way on their mother’s side.

Everyone inherits an X chromosome from their mother that is some combination of the X from her father and mother. It’s possible to inherit all of your maternal grandmother or maternal grandfather’s X chromosome, meaning they did not recombine during meiosis.

Using DNA Painter as an X Tool

I use DNAPainter to track my matches and correlate segments with ancestors.

I paint my DNA segments for all my chromosomes at DNAPainter which provides me with a central tracking mechanism that is visual in nature and allows me to combine matches from multiple vendors who provide segment information. I provide step-by-step instructions for using DNAPainter, here.

This is my maternal X chromosome with my matches painted. I’ve omitted my matches’ names for privacy.

On the left side of the shaded grey column, those matches are from my maternal grandmother’s ancestors. On the right side, those matches are from my maternal grandfather’s ancestors.

The person in the grey column descends from unknown ancestors. In other words, I can tell that they descend from my maternal line, but I can’t (yet) determine through which of my two maternal grandparents.

There’s also an area to the right of the grey column where there are no matches painted, so I don’t know yet whether I inherited this portion of my X chromosome from my maternal grandmother or maternal grandfather.

The small darker pink columnar band is simply marking the centromere of the chromosome and does not concern us for this discussion.

Click on any image to enlarge

In this summary view of my paternal X chromosome, above, it appears that I may well have inherited my entire X chromosome from my paternal great-grandmother. We know, based on our inheritance rules that I clearly received my paternal grandmother’s X chromosome, because that’s all my father had to give me.

However, by painting my matches based on their ancestors, and selecting the summary view, you can see that most of my paternal X chromosome can be accounted for, with the exception of rather small regions with the red arrows.

It’s not terribly unusual for either a male or female to inherit their entire maternal X chromosome from one grandparent, or in this case, great-grandparent.

Of course, a male doesn’t inherit an X chromosome from their father, but a female can inherit her paternal X chromosome from either or both paternal grandparents.

Does Size Matter?

Generally speaking, an X match needs to be larger than a match on the other chromosomes to be considered genealogically equivalent in the same timeframe as other autosomal matches. This is due to:

  • The unique inheritance pattern, meaning fewer recombination events occurred.
  • The fact that X-DNA is NOT inherited from several lines.
  • The X chromosome has lower SNP density, meaning it contains fewer SNPs, so there are fewer possible locations to match when compared to the other chromosomes.

I know this equivalency requirement sounds negative, but it’s actually not. It means 7 cM (centimorgans) of DNA on the X chromosome will reach back further in time, so you may carry the DNA of an ancestor on the X chromosome that you no longer carry on other chromosomes. It may also mean that older segments remain larger. It’s actually a golden opportunity.

It sounds much more positive to say that a 16 cM X match for a female, or a 13 cM X match for a male is about the same as a 7 cM match for any other autosomal match in the same generation.

Of course, if the 7 cM match gets divided in the following generation, it has slipped below the matching threshold. If a 16 or 13 cM X match gets divided, it’s still a match. Plus, in some generations, if passed from father to daughter, it’s not divided or recombined. So a 7 cM X match may well be descended from ancestors further back in time.

X Chromosome Differences are Important!

Working with our great-great grandparent’s generation, we have 16 direct ancestors as illustrated in the earlier fan chart.

Given that females inherit from 8 X-chromosome ancestors in total, they are going to inherit an average of 45.25 cM of X-DNA from each of those ancestors. Females have two X chromosomes for a total length of 362 cM of X-DNA from both parents.

A male only has one X chromosome, 181 cM in length, so he will receive an average of 36.2 cM from each of 5 ancestors, and it’s all from his mother’s side.

In this chart, I’ve shown the total number of cMs for all of the autosomes, meaning chromosomes 1-22 and, separately, the X for males and females.

  • The average total cM for chromosomes 1-22 individually is 304 cM. (Yes, each chromosome is a different length, but that doesn’t matter for averages.)
  • That 304 cM can be inherited from any of 16 ancestors (in your great-grandparent’s generation)
  • The total number of cM on the X chromosomes for both parents for females totals 362
  • The total cM of X-DNA for males is 181 cM
  • The calculated average cM inherited for the X chromosome in the same generation is significantly different, shown in the bottom row.

The actual average for males and females for any ancestor on any random non-X chromosome (in the gg-grandparent generation) is still 19 cM. Due to the inheritance pattern of the X chromosome, the female X-chromosome average inheritance is 45.25 cM and the male average is 36.2 cM, significantly higher than the average of 19 cM that genetic genealogists have come to expect at this relationship distance on the other chromosomes, combined.

How Do I Interpret an X Match?

It’s important to remember when looking at X matching that you’re only looking at the amount of DNA from one chromosome. When you’re looking at any other matching amount, you’re looking at a total match across all chromosomes, as reported by that vendor. Vendors report total matching DNA differently.

  • The total amount of matching autosomal DNA does not include the X chromosome cMs at FamilyTreeDNA. X-DNA matching cMs are reported separately.
  • The total amount of matching autosomal DNA does include the X chromosome cMs in the total cM match at 23andMe
  • X-DNA is not used for matching or included in the match amount at either MyHeritage or Ancestry, but is included in the raw DNA data download files for all four vendors.
  • The total match amount shows the total for 22 (or 23) chromosomes, NOT just the X chromosome(s). That’s not apples to apples.

Therefore, an X match of 45 cM for a female or 36 for a male is NOT (necessarily) equivalent to a 19 cM non-X match. That 19 cM is the total for 22 chromosomes, while the X match amount is just for one chromosome.

You might consider a 20 cM match on the regular autosomes significant, but a 20 cM X-only match *could* be only roughly equivalent to a 10ish cM match on chromosomes 1-22 in the same generation. That’s the dog-leg inheritance pattern at work.

This is why FamilyTreeDNA does not report an X-only match if there is no other autosomal match. A 19 cM X match is not equivalent to a 19cM match on chromosomes 1-22. Not to mention, calculating relationships based on cM ranges becomes more difficult when the X is included.

However, the flip side is that because of the inheritance pattern of the X chromosome, that 19 cM match, if valid and not IBC, may well reach significantly further back in time than a regular autosomal matches. This can be particularly important for people seeking either Native or enslaved African ancestors for whom traditional records are elusive if they exist at all.

Critical Take-Away Messages

Here are the critical take-away messages:

  1. Because there are fewer ancestral lineages contributing to the tester’s X chromosome, the amount of X chromosomal DNA that a tester inherits from the ancestors who contribute to their X chromosome is increased substantially.
  2. The DNA of the contributing ancestors is more likely to be inherited, because there are fewer other possible contributing ancestors, meaning fewer recombination events or DNA divisions/recombinations.
  3. X-DNA is also more likely to be inherited because when passed from mother to son, it’s passed intact and not admixed with the DNA of the father.
  4. X matches cannot be compared equally to either percentages or cM amounts on any of the other chromosomes, or autosomal DNA in total, because X matching only reports the amount on one single chromosome, while your total cM match amount reports the amount of DNA that matches from all chromosomes (which includes the X at 23andMe).
  5. If you have X matches at 23andMe and/or FamilyTreeDNA, you can expect your total matching to be higher at 23andMe because they include the X matching cM in the total amount of shared DNA. FamilyTreeDNA provides the amount of X matching DNA separately, but not included in the total. MyHeritage and Ancestry do not include X matching DNA.

For clarity, at FamilyTreeDNA, you can see my shared DNA match with my mother. Of course, I match her on the total length of all my chromosomes, which is 3563 cM, the total Shared DNA for chromosomes 1-22. This includes all chromosomes except for the X chromosome which is reported separately at 181 cM. The longest contiguous block of shared DNA is 284 cM, the entire length of chromosome 1, the longest chromosome.

Because I’m a female, I match both parents on the full length of all 23 chromosomes, including 181 cM on both X chromosomes, respectively. Males will only match their mother on their X chromosome, meaning their total autosomal DNA match to their father, because the X is excluded, is 181 cM less than to their mother.

This difference in the amount of shared DNA with each parent, plus the differences in how DNA totals are reported by various vendors is also challenging for tools like DNAPainter’s Shared cM Tool which is based on the crowd sourced Shared cM Project that averages shared DNA numbers for known relationships at various vendors and translates those numbers into possible relationships for unknown matches.

Not all vendors report their total amount of shared DNA the same way. This is true for both X-DNA and half identical (HIR) versus fully identical (FIR) segments at 23andMe. This isn’t to say either approach is right or wrong, just to alert you to the differences.

Said Another Way

Let’s look at this another way.

If the average on any individual chromosome is 19 cMs for a relationship that’s 5 generations back in time. The average X-DNA for the same distance relationship is substantially more, which means that:

  • The X-DNA probably reaches further back in time than an equivalent relationship on any other autosome.
  • The X-DNA will have (probably) divided fewer times, and more DNA will descend from individual ancestors.
  • The inheritance path, meaning potential ancestors who contributed the X chromosomal DNA, is reduced significantly.

It’s challenging to draw equivalences when comparing X-DNA matching to the other chromosomes due to several variables that make interpretation difficult.

Based on the X-match size in comparison to the expected 19 cM single chromosome match at this genealogical distance, what is the comparable X-DNA segment size to the minimum 7 cM size generally accepted as valid on other chromosomes? What would be equal to a 7 cM segment on any other single random autosomal match, even though we know the inheritance probabilities are different and this isn’t apples to apples? Let’s pretend that it is.

This calculation presumes at the great-great-grandparent level that the 19 cM is in one single segment on a single chromosome. Now let’s divide 19 cM by 7 cM, which is 2.7, then divide the X amounts by the same number for the 7 cM equivalent of 16.75 cM for a female and 13.4 cM for a male.

When people say that you need a “larger X match to be equivalent to a regular autosomal match,” this is the phenomenon being referenced. Clearly a 7 cM X match is less relevant, meaning not equivalent, in the same generation as a 7 cM regular autosomal match.

Still, X matching compared to match amounts shown on the other chromosomes is never exact;u apples to apples because:

  • You’re comparing one X chromosome to the combined DNA amounts of many chromosomes.
  • The limited recombination path.
  • DNA from the other autosomes is less likely to be inherited from a specific ancestor.
  • The X chromosome has a lower SNP density than the other chromosomes, meaning fewer SNPs per cM.
  • The X-DNA may well reach further back in time because it has been divided less frequently.

Bottom Line

The X chromosome is different and holds clues that the other autosomes can’t provide.

Don’t dismiss X matches even if you can’t identify a common ancestor. Given the inheritance path, and the reduced number of divisions, your X-DNA may descend from an ancestor further back in time. I certainly would NOT dismiss X matches with smaller cMs than the 13 and 16 shown above, even though they are considered “equivalent” in the same generation.

X chromosome matching can’t really be equated to matching on the other chromosomes. They are two distinct tools, so they can’t be interpreted identically.

Different vendors treat the X chromosome differently, making comparison challenging.

  • 23andMe includes not only the X chromosome in their cM total, but doubles the Fully Identical Regions (FIR) when people, such as full siblings, share the same DNA from both parents. I wrote about that here.
  • Ancestry does not include the X in their cM match calculations.
  • Neither does MyHeritage.
  • FamilyTreeDNA shows an X match only when it’s accompanied by a match on another chromosome.

The Shared cM Project provides an average of all of the data input by crowdsourcing from all vendors, by relationship, which means that the cM values for some relationships are elevated when compared to the same relationship or even same match were it to be reported from a different vendor.

The Best Part!

The X chromosome inheritance pattern means that you’re much more likely to carry some amount of a contributing ancestor’s X-DNA than on any other chromosome.

  • X-DNA may well be “older” because it’s not nearly as likely to be divided, given that there are fewer opportunities for recombination.
  • When you’re tracking your X-DNA back in your tree, whenever you hit a male, you get an automatic “bump” back a generation to his mother. It’s like the free bingo X-DNA square!
  • You can immediately eliminate many ancestors as your most recent common ancestor (MRCA) with an X-DNA match.
  • Because X-DNA reaches further back in time, sometimes you match people who descend from common ancestors further back in time as well.

If you match someone on multiple segments, if one of those matching segments is X-DNA, that segment is more likely to descend from a different ancestor than the segments on chromosomes 1-22. I’ve found many instances where an X match descends from a different ancestor than matching DNA segments on the autosomes. Always evaluate X matches carefully.

Sometimes X-DNA is exactly what you need to solve a mystery.

Ok, now let’s step through how to use X-DNA in a real-life example.

Using X DNA to Solve a Mystery

Let’s say that I have a 30 cM X match with a male.

  • I know immediately that our most recent common ancestor (MRCA) is on HIS mother’s side.
  • I know, based on my fan chart, which ancestral lines are eliminated in my tree. I’ve immediately narrowed the ancestors from 16 to 5 on his side and 16 to 8 on my side.
  • Two matching males is even easier, because you know immediately that the common ancestor must be on both of their mother’s sides, with only 5 candidate lines each at the great-great-grandparent generation.

Female to female matches are slightly more complex, but there are still several immediately eliminated lines each. That means you’ve already eliminated roughly half of the possible relationships by matching another female on their X chromosome.

In this match with a female second cousin, I was able to identify who she was via our common ancestor based on the X chromosome path. In this chart, I’m showing the relevant halves of her chart at left (paternal), and mine (maternal), side by side.

I added blockers on her chart and mine too.

As it turns out, we both inherited most of our X chromosome from our great-grandparents, marked above with the black stars.

Several lines are blocked, and my grandfather’s X chromosome is not a possibility because the common ancestor is my maternal grandmother’s parents. My grandfather is not one of her ancestors.

Having identified this match as my closest relative (other than my mother) to descend on my mother’s maternal side, I was able to map that portion of my X chromosome to my great-grandparents Nora Kirsch and Curtis Benjamin Lore.

My X Chromosome at DNA Painter

Here’s my maternal X chromosome at DNAPainter and how I utilized chromosome painting to push the identification of the ancestors whose X chromosome I inherited back an additional two generations.

Using that initial X chromosome match with my second cousin, shown by the arrow at bottom of the graphic, I mapped a large segment of my maternal X chromosome to my maternal great-grandparents.

By viewing the trees of subsequent X maternal matches, I was then able to push those common segments, shown painted directly above that match with the same color, back another two generations, to Joseph Hill, born in 1790, and Nabby Hall. I was able to do that based on the fact that other matches descend from Joseph and Nabby through different children, meaning we all triangulate on that common segment. I wrote about triangulation at DNAPainter, here.

I received no known X-DNA from my great-grandmother, Nora Kirsch, although a small portion of my X chromosome is still unassigned in yellow as “Uncertain.”

I received a small portion of my maternal X chromosome, in magenta, at left, from my maternal great-great-grandparents, John David Miller and Margaret Lentz.

The X chromosome is a powerful tool and can reach far back in time.

In some cases, the X, and other chromosomes can be inherited intact from one grandparent. I could have inherited my mother’s entire copy of her mother’s, or her father’s X chromosome based on random recombination, or not. As it turns out, I didn’t, and I know that because I’ve mapped my chromosomes to identify my ancestors based on common ancestors with my matches.

X-DNA Advanced Matches at FamilyTreeDNA

At FamilyTreeDNA, the Advanced Matches tab includes the ability to search for X matches, either within the entire database, or within specific projects. I find the project selection to be particularly useful.

For example, within the Claxton project, my father’s maternal grandmother’s line, I recognize my match, Joy, which provides me an important clue as to the possible common ancestor(s) of our shared segments.

Joy’s tree shows that her 4-times great-grandparents are my 3-times great-grandparents, meaning we are 4th cousins once removed and share 17 cM of DNA on our X chromosome across two segments.

Don’t be deceived by the physical appearance of “size” on your chromosomes. The first segment that spans the centromere, or “waist” of the chromosome, above, is 10.29 cM, and the smaller segment at right is 7.02 cM. SNPs are not necessarily evenly distributed along chromosomes.

Remember, an X or other autosomal match doesn’t necessarily mean the entire match is contained in one segment so long as it’s large enough to be divided in two parts and survive the match threshold.

It’s worth noting that Joy and I actually share at least two different, unrelated ancestral lines, so I need to look at Joy’s blocked lines to see if one of those common ancestral lines is not a possibility for our X match. It’s important to evaluate all possible ancestors, plus the inheritance path to eliminate any lineage that involves a father to son inheritance on the X chromosome.

Last but not least, you may match on your X chromosome through a different ancestor than on other chromosomes. Every matching segment has its own individual history. It’s not safe to assume.

Now, take a look at your X chromosome matches at FamilyTreeDNA, 23andMe, and GedMatch. What will you discover?

_____________________________________________________________

Follow DNAexplain on Facebook, here or follow me on Twitter, here.

Share the Love!

You’re always welcome to forward articles or links to friends and share on social media.

If you haven’t already subscribed (it’s free,) you can receive an email whenever I publish by clicking the “follow” button on the main blog page, here.

You Can Help Keep This Blog Free

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Uploads

Genealogy Products and Services

My Book

Genealogy Books

Genealogy Research