Zeroes aka Deletions – Null DNA Markers

Someone recently asked me about why one of their Y DNA STR marker values was zero, what that means, and how it got to be that way.

Probably the marker most prone to develop this trait is marker 425, the 48th marker that is in the 67 marker panel.  If you haven’t tested beyond 37 markers, then you won’t see a result for marker 425, because it’s in the 67 marker panel which tests markers 38-67.

A null marker result looks like this for Y DNA:

null result

You can see that location DYS425, highlighted in blue, has a zero and a red asterisk.

This means that there is no DNA present at that location, and a deletion has occurred.

Mitochondrial DNA

Deletions also occur in mitochondrial DNA.

If you view your results as CRS values, deletions show as little dash marks.

Mito deletion CRS

In the RSRS results view, below, they are shown with a little d indicating a deletion has replaced the normal value shown before the location number.

Mito deletion RSRS

In the case above in the coding region, an entire contiguous segment has been deleted.  In mitochondrial DNA, these are sometimes haplogroup defining.

While deletions also occur routinely in mitochondrial DNA, we’re going to use Y DNA for our discussion and examples.

What Does This Mean?

A zero in Y DNA as a marker result means that no DNA was detected at this location.  In essence, barring a lab processing error, it means that the DNA that used to be in this location got deleted in the process of replication at some point in time.

Once DNA on the Y chromosome or mitochondrial DNA is gone, it’s gone forever.  This is called a deletion.

Why Did This Happen?

We don’t know exactly why deletions happen, but they do.  If the deletion is in an area that isn’t troublesome to the organism, life goes on normally and the deletion is passed on to the next generation.  If the deletion would interfere with a critical function, typically the organism is never born.

So, if you have a deletion, it’s really nothing to worry about, because, chances are your ancestors, for generations, had this same deletion and you are obviously here. 

When Did This Happen?

Sometimes we can deduce an answer to this question, at least somewhat.

If your DNA value at location 425 is 0 (zero), there are three possibilities.

1.  This mutation happened long ago in your family line – maybe even before the adoption of surnames.  This is usually relatively easy to tell, especially if other men from your direct line have tested.  If they have, you’ll need to determine if their value at location 425 is zero.  If you and they are in a common project, often the easiest way to determine their value is to look within the project page. If you see others with the same surname that match most of your other marker results, and have a value of 0 at 425, then you know that this mutation happened long ago in your family line and has been being passed from father to son ever since – and will be as long as any male who carries that paternal line lives.

You can also check your haplogroup project to see if the people you are grouped, which will have different surnames, with also have a deletion at that location.

In some cases, almost everyone in a particular group has a zero at that location.  In the case of marker 425, the value of 0 is almost universally found in haplogroup E-L117, downstream of E-M35, as you can see in the Jewish haplogroup E project.

Sometimes, if the null marker at that location is not prevalent in the haplogroup itself, or in the larger family group, then the null value may be considered a line marker mutation in your specific family line.

2.  The null value may have happened more recently.  In fact, it’s possible that it happened between you and your father.  It happened between some father and son, someplace in your line.  If you find that you have a null marker value, and no one else if your family surname project has a null value at that marker, I would suggest proceeding in two ways.  First, I would test a second person, slightly upstream.  For example, test another paternal descendant of your grandfather or great-grandfather.  If they too have the null value, then you know that deletion occurred in some generation before your common ancestor.

null family example

If your father is Sterling and his father is Ben, then you’ll want to test one of Ben’s other sons, Hezekiah or Joseph, or one of their sons.

Let’s say that you test Hezekiah Jr. and he too carries a null value at location 425.  This confirms that your common ancestor, Ben Doe, indeed also had a null value because he passed it to both of his sons.  So, the mutation to a null value happened someplace upstream of Ben.

In this next example, let’s say, based on the surname project results, we know that neither John Doe nor James Doe carry the null value mutation, because at least some of their descendants through various sons don’t carry that mutation.  Therefore, it had to happen someplace downstream of Joe and James and between them and you.  The question is where.

Null ancestors inferred

In the original test, you discovered your null value.  In the second test, we discovered Hezekiah Jr.’s null value and by doing so, also discovered the value of that DNA in Sterling, Hezekiah Sr. and Ben, shown in the second test column above.

From previous testing in the family surname project, we know that the progenitor, John Doe and his son James don’t carry that mutation, so that only leaves two generations with an unknown status as to that marker value.  If you can find someone descended through another son born to William or Thomas, you can determine which man had the mutation.

But what if Hezekiah Jr. does not have the null value?

Then, either the mutation happened between you and your father or between your father and his father, which can be confirmed by testing either your father or one of your male siblings, or there was a lab processing error.

3.  In rare cases, the DNA simply does not read in a particular area.  It’s rare, but it does happen.  If you find no other family individuals with a null value, I’d ask the Family Tree DNA lab to take a second look to verify accuracy and to see if they can get a good reading if that is the issue.  They already routinely do multiple reads on null values, so this is rarely an issue.

Does This Really Matter?

It might matter, because in this line, the null value will serve as a line marker mutation for the family lines BELOW the man who had the mutation.  So, in this case, either William or Thomas Doe.  So if you find someone who matches this line, and DOES have a null value, it tells you which line he falls under and where to look.  If he does NOT have the null value, it tells you not to bother looking in the null value line.

Do Other Markers and Haplogroups Have Null Markers Too?

They do indeed.  I’ve written the Personalized DNA Reports for a decade now and I’ve seen null marker values in just about every haplogroup and on many markers, although some instances are very rare and seem to be a one-time occurrence.

In other situations, especially in haplogroup E-M35 (old E1b1b1) and branches, null values are quite common, especially on marker 425.  Marker 425 seems to be more prone to zero or null values in every haplogroup than other markers…and no, we don’t know why.

This has been the explanation of null values for normal air breathing humans.  If you would like the eyes-glazed-over techie version, this presentation was given at the 2009 Family Tree DNA Conference.

5 thoughts on “Zeroes aka Deletions – Null DNA Markers

  1. We ran into this with a cousin’s Y-DNA test. The problem we had was that some surname group administrators counted this as a mismatch by computing the difference between 0 (the test with the deletion) and, say, 27 (a test who matched the first person on most or all markers except for the deletion). So, when computing the predicted common ancestor’s generation it would start with a STR difference of 27 and add to that any further STR differences. So, what’s the better way to do this? ignore the deletion when computing predicted generation? or count it as being off by 1? or ???

  2. Why is DYS425=0 more common? Partly because it is in a palidromic area which rearranges itself more frequently than other regions. During those swapping events one can generate a SNP or rearrange the count of what STR is being moved.

  3. Pingback: DNAeXplain Archives – Basic Education Articles | DNAeXplained – Genetic Genealogy

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