Who Tests the X Chromosome?

Recently, someone asked which of the major DNA testing companies test the X chromosome and which ones use the X in matching. How does this difference influence the quality of our matches?

Vendor X in Download File Uses X in Matching X Included in Total cM Count
23andMe Yes Yes Yes
Family Tree DNA Yes Yes (if have a match on another chromosome) No
Ancestry Yes *No No
MyHeritage Yes No No
GedMatch N/A Separately No

*If Ancestry did utilize the X in matching, it wouldn’t benefit customers because Ancestry does not show segment information by chromosome.  In other words, no chromosome browser.

Family Tree DNA includes any size X match IF and only if the two people already match on a different chromosome.

GedMatch, of course, isn’t a vendor who does DNA testing, so they don’t provide download files.  They are solely on the receiving end.

X CentiMorgan Counts

Due to variations in the way vendors calculate matches and total cM counts, your mileage may vary a bit.

In other words, the 23andMe cM total, if an X match is involved, may be slightly more than a match between the same two people at Family Tree DNA, where the X match cM is not included in the cM total.

Conversely, you won’t show an X match with someone at Family Tree DNA if there isn’t also another segment on a different chromosome that matches.

In general, due to the thin spread of SNPs on the X chromosome, you will need, on average, a cM match that is twice as large as on other chromosomes to be considered of equal weight.

In other words, a 10 cM match on the X chromosome would only be genealogically equivalent to approximately a 5 cM match on any other chromosome.

X matches really can’t be evaluated by the same rules as other chromosomes due both to their SNP paucity and their inheritance path, which is why most vendors don’t include those segments in the total cM count.

X Matches

While including the X chromosome cM count is problematic, X matching can be a huge benefit because of the unique inheritance path of the X chromosome.

In the article, X Marks the Spot, we discussed the inheritance path of the X chromosome for both males and females. Females inherit an X chromosome from both father and mother, which recombines just like chromosomes 1-22.  However, men only inherit an X from their mother, because they inherit a Y from their father instead of the X.  Therefore, males will only inherit an X from their mother, and females will only inherit their father’s mother’s X chromosome.

Charting Companion software works with your genealogy software of choice to produce a lovely fan chart where the contributors of my X chromosome are charted in color, above. You can read more about Charting Companion here.

The great news is that if you and a match share a significant portion of the X chromosome, meaning more than 15 cM which reduces the likelihood of an identical by chance match, the common ancestor (on that segment) has to come from an ancestor in your direct X path.

I’m always excited to see with whom I share an X.  That piece of information alone helps me focus my ancestor detective efforts on a specific portion of my tree.

Some X segments can remain intact for generations and may be very old.  So don’t be surprised if the common ancestor of the X segment and another matching segment may not be the same ancestor.

Sorting by X

I wasn’t able to find a way to sort by X chromosome matches at 23andMe, but you can sort by the X at both Family Tree DNA and GedMatch.

At GedMatch, X matching shows on the one-to-many match page.  You can sort by either Total X cM or Largest X cM by using the up and down arrows, at right, below, in the X DNA columns.

After you identify an X match, be sure to run the X one-to-one match option to verify.

My GedMatch matches cause me to wonder if 23andMe is using a different reporting threshold for the X chromosome, because one of my matches at GedMatch is a close family member with no X match at 23andMe, but a total of 32 X cM and with a longest segment of 14 X cM at GedMatch.

That same individual matches me with the largest X segment of 14 cM at Family Tree DNA as well.

Family Tree DNA X Match Phasing

At Family Tree DNA, on your Family Finder matches page, just click on the X-Match header (at right, below) to bring all of your X matches to the top of your list.

If you have linked any kits of relatives to your tree, you will see numbers of phased kits on the maternal and paternal tabs with the red and blue male and female icons. In the example above, I have 3313 matches total, with 744 being paternal, 586 being maternal.

Next, click on the maternal or paternal tab to see only the people with X matches who match you on the  your maternal and paternal lines. Matches are automatically sorted into maternal and paternal “buckets” for you. Remember to check the size of the X match before deciding about relevance.

Who is your largest X match that you don’t already know?  Maybe you can find your common ancestor today.

Have fun!!!

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Using X and Mitochondrial DNA Charts by Charting Companion

Charting Companion by Progeny Genealogy interfaces with many genealogy software programs to produce lovely charts and graphs not available within the genealogy software applications themselves. I first installed Charting Companion when I used PAF and was very glad to see that it interfaces with RootsMagic too, the software I switched to when PAF was no longer supported. RIP PAF😦

Over the past couple years, Charting Companion has implemented DNA focused reports. I covered their first report, the X Ancestor Chart when it was first introduced, but they have since added mtDNA charts, and most recently X Descendant Charts. I love these reports and how useful they are to the genealogist.

It’s important to understand that both your mitochondrial DNA and the X chromosome have special inheritance paths and therefore, special uses for genetic genealogy research. I wrote about the X chromosome here and here.

The article 4 Kinds of DNA for Genetic Genealogy is a brief description of the various kinds of DNA testing available to genetic genealogists, and who can test for which kind.

X Chromosome Inheritance Path

In males, the X chromosome is only inherited from the mother, because the father gives the male a Y chromosome, which is what makes the male, male. In females, the father contributes his X chromosome to his daughter, as does her mother. However, the father only received an X from his mother – so you can see that the inheritance pattern for the X chromosome is not the same as other chromosomes where all children receive 50% of their inherited DNA from each parent.

Because of this unusual inheritance pattern, you can easily tell whether an autosomal match that shares an X chromosome could descend from the ancestor you think they might. If you’re a male and you think an X match comes through your father or one of his ancestors – think again, because it can’t.

Here’s my hand-drawn chart of the ancestors that portions of my X chromosome could have descended from.

X Chart0001

Now that I have charting companion, I no longer have to hand draw this chart. Charting Companion does it quickly and easily for me. And it’s much, MUCH neater!

x fan

The X chromosome is tested as part of an autosomal DNA test, but not all vendors report X matches. Ancestry does not provide information about the chromosomes where you match anyone, so at Ancestry, there is no way to know if you match someone on the X chromosome. Family Tree DNA’s Family Finder test does test for and report X chromosome matching and so does GedMatch if you upload your raw data files from any vendor.

Mitochondrial DNA Inheritance Path

Mitochondrial DNA is not passed to the children from males. Females pass their mitochondrial DNA to both genders of their children, but only females pass it on.

This pedigree chart below shows the Y and mitochondrial DNA inheritance path for a brother and sister. Both siblings received their mother’s mtDNA, which reaches back in time directly up the matrilineal line ONLY.

Y and mito

The great news is that since the mitochondrial DNA is never admixed with the father’s DNA, it’s a direct pipeline that informs us about the matrilineal line for hundreds and thousands of years back in time.

The bad news is that in order to find out about the mitochondrial DNA of another ancestor in your tree – meaning all of your ancestors that don’t have red circles in the chart above, you must find someone descended from a female through all females to the current generation, which can be a male. Testing for mitochondrial DNA is available through Family Tree DNA.

Let’s say you want to find out about the mitochondrial DNA of your father’s mother to fill in one of the haplogroups in your DNA pedigree chart. You would need to locate an individual to test who carries your father’s mother’s mitochondrial DNA. Your father can test, if he’s living and willing. If your father is deceased, and he had no siblings, and his mother is deceased with no siblings, you’re going to have to go on back up that tree until you find someone with living descendants who descend through only females to the current generation, which can include males.

Charting companion makes finding those descendants easy.

Getting Started

You can purchase Charting Companion at this link. And for those of you wondering, no, I don’t have any financial interest in Charting Companion or Progeny Genelaogy, nor is this a paid article, nor do I receive any commission or kickback or anything like that if you purchase this product, nor am I related to or know the owner. I don’t accept or write any articles for pay from anyone or any company, ever, and never have. I did, however, receive a free update to the Charting Companion software I had already purchased, but you will too if you have already purchased version 6.

After installing Charting Companion, which is painless (I had to install the latest upgrade for this article), Charting Companion opens the file you indicate, which is typically your production file for your genealogy software. You’ll select the person you want to be reflected as the source or center of your charts or reports in the yellow Name field, shown below. In my case, I selected Barbara Dreschel to be the person around whom the reports will center.

In case you’re wondering, “Babbit” was her nickname and J1c2f is her mitochondrial DNA haplogroup.  The only effective way I’ve discovered to maintain haplogroup information is as a middle name, so that’s what you’re seeing.

chart-drechsel

Next, you’ll select the type of report that you want to create.

You’ll want to click on the “Charts and Reports” tab and for the X chromosome charts, you’ll want to select either the Ancestor Charts, or the Descendant Charts.

chart companion

Net, you’ll select the X version, which is located under “color” because the proper people are colorized in pink and blue.

Ancestor chart options

Ancestor X Charts

Ancestor charts generally start with you and work their way back in time.   My X version shows which ancestors I inherited my X chromosome from. This can be very helpful when evaluating matches. In some cases, you cannot have a match to a particular person on the X chromosome from the particular line in question.

Ancestor charts come in two flavors, one is a traditional ancestor chart, the fan version shown earlier in this article, and the second version is a pedigree chart.

x pedigree 1

x pedigree 2

These charts make it easy to see who you could have received your X chromosome from – so X matches must be from the pink and blue colored ancestors and cannot be from ancestors whose boxes are not colored.

For example, if I match a descendant of John Y. Estes, located at the top of the pedigree chart, above, on the X chromosome, I know the common ancestor that I received the X DNA from is NOT John Y. Estes, because I couldn’t have inherited any X DNA from him. That’s easy to discern, because there is no coloration in John Y.’s box. So an X match to a descendant of John Y. Estes is not FROM John Y. Estes. It’s either a false match or the matching X chromosome is from another common ancestor. Of course, that doesn’t mean we both aren’t descended from John Y. Estes – it only means that our X match is not from John Y.  I wrote about false matches here.

When I receive an X match to someone and we’re trying to find a common ancestor, I suggest that my match print this same chart for themselves and that will help them determine which ancestors or ancestral lines we might potentially have in common.

Descendant X Charts

Recently Charting Companion announced a new tool, Descendant X Charts. On these charts, the ancestor is the focus and the descendants who inherited their X chromosome are colored either pink or blue. Part of the Descendant X Chart for Barbara Drechsel is shown below. You can click on any graphic to enlarge.

chart-descendant-drechsel

Descendant Charts look a little different than Ancestor Charts. Don’t be confused by the white box between Elnora Kirsch and her daughters. That’s just her husband, Curtis Benjamin Lore. While he contributes an X chromosome (with daughters) or doesn’t (with sons,) it’s not HIS X chromosome we’re tracking in this chart, it’s the X chromosome of Barbara Drechsel. Curtis would be shown either on his own ancestor chart, or you can create a Descendant X Chart for Curtis.

You might notice in this diagram that this family is particularly prone to not having children. Trying to find ANY DNA participants has been very challenging. However, when I do find them (fingers crossed) I’ll know immediately if they (and I) could possibly carry the X chromosome of Barbara Drechsel by looking at these charts. I’m someplace to the left on this chart, but off the edge of the graphic above.

My favorite Charting Companion charts are still the fan charts though, shown below, because they are compact and succinct and you can see everything on one chart on one page.

chart-descendant-fan

Mitochondrial DNA Charts

To find descendants who carry the mitochondrial DNA of any female, select the person whose mtDNA-carrying descendants you want to find. Then click on the Charts and Reports tab and select the Descendant Chart. You’ll then see various options at the top, where you’ll want to click on the Contents tab.

chart-mtdna-menu

Select Mitochondrial DNA. Note that you can also select the Y chromosome DNA, but that’s much more evident if you’re looking for a male, because the surname stays the same, so DNA testing candidates are generally rather obvious.

chart-mtdna-descendants

On the mtDNA Descendants Chart above, the people in pink and blue carry the mtDNA of Barbara Drechsel. The blue people, males, won’t pass it on to their offspring, but the pink people, females, will if they have offspring. You can see that many females in this family did not have children, so there are several dead ends for Barbara’s mtDNA, including one more daughter who is off of the right hand side of the page. On your computer, you can scroll and the printed reports allow you to overlap.

The Mitochondrial DNA Chart is a great tool to find out who carries the mitochondrial DNA of any ancestor.

Summary

I love tools that help people understand their DNA and how it’s useful to their genealogy. The X charts make seeing the X inheritance path so much easier than trying to explain in verbiage (or drawing by hand) – and provides an easy visual to quickly identify whether a particular ancestor could potentially be responsible for an X DNA match.

For mitochondrial DNA, the charting tool makes the task of finding appropriate descendants to test much easier. It can also work in reverse. If you want to know if a particular person is a candidate for testing for a specific ancestor’s mtDNA, it’s easy to see immediately if their box is colored pink or blue.

I especially love tools that are ubiquitous and run with almost any software package and that don’t require special plugins. Furthermore, I’m particularly enamored with vendors who listen to and take suggestions to heart from their customer base. No, this suggestion wasn’t mine, but the X Descendant Chart was implemented within a week of when it was suggested by a customer. Two weeks later, it was in production – and now all Charting Companion customers benefit. A big thank you to Pierre Clouthier at Progeny Genealogy.