Sunday, September 30, 2018

Using the new Family Tree DNA Y-DNA Haplotree

Family Tree DNA has just released new a Y-DNA haplotree that is open to the public. Using the new FTDNA public haplotree can help you decide whether you want to do your own Y-DNA testing and whether you want to recruit others for testing. It can also help you better understand the results you already have. The tree not only includes SNPs from Big Y tests (recently renamed "Big Y-500" tests); it also includes results from FTDNA SNP packs and individual SNP tests. Roberta Estes wrote a good post on how to use this new tree here.

I want to focus on how this new haplotree can help you with interpreting and enhancing your Big Y results. It can also be a good tool for recording your ancestry. Let's start with a Big Y-500 test to see how this process works. 

Your Big Y-500 list of SNP matches

If you took a Big Y-500 test, one of the most confusing parts about your Big Y-500 results is your list of matches. Below we see what many refer to as your step chart. The chart shows the "terminal" SNP which is the most recent SNP that you share with at least one other man. I put the term "terminal" in quotes because this SNP may not actually be your terminal, or most recent, SNP. Your most recent shared SNP can change if you test more closely-related individuals. If you have tested a father and son or two brothers, then you probably do know the real terminal SNP. Note the terminal SNP J-BY45500 and its four upstream branches.

Big Y-500 Step Chart
Step Chart

In the above chart, the most recent shared SNP is BY45500. J-BY45500 is the haplogroup assigned to this person. To the right of the haplogroup is the number 1 indicating that this SNP is shared with only one other man. But the four haplogroups above also seem to show that each of the SNPs is shared with only one other man. When you click on the icon of the male, you will see the name of the match.  In this case the kit belongs to a man named Karns, and his only match at all five levels is a man named Carnes.

Because there is only one match at haplogroup J-Z1295 we could conclude that only two people, Carnes and Karns, have tested within this haplogroup. These results can be very misleading unless you understand that Family Tree DNA is only showing genealogically-relevant matches. Family Tree DNA will not display matches who have more than a 30-SNP difference with you. So the Matches list does not mean that only two people have tested positive for SNPs Z1295, Z631, Z1043, Y98609, and BY45500. 

Using the FTDNA non-public haplotree

To see if there are other people with these SNPs, let's first examine the haplotree that you see within your account. This tree is only available to people who have tested with Family Tree DNA. This is the only haplotree that has been available until the release of the new public haplotree, so it is useful to see the comparison.

To find the haplotree click on myDNA at the top of the screen, then click Y-DNA, then Haplotree & SNPs.

Haplotree SNPs

You will see your position within the human haplotree, and you can see other SNPs associated with your haplogroup by clicking the word "More" next to the haplogroup. You will not see information such as surnames or how many people tested at each level.

FTDNA haplotree

Is there a way to find out how many people have tested at the various levels and maybe even see surnames? Yes, finally there is.

Using the new Family Tree DNA Y-DNA Haplotree

To see the FTDNA public haplotree, you must either log out of your account or open another browser so that you can see your account and the public haplotree at the same time.

If you have logged out of your account, you will be taken to the Sign In screen.

FTDNA Sign In screen

Click the Family Tree DNA logo at the upper left of the screen. On the next page, scroll all the way to the bottom until you see this:

FTDNA Y-DNA Haplotree


You can go directly to the tree by clicking
The tree will open in a new window so that you can explore the tree while reading this.

The Y-DNA Haplotree will take awhile to load. You will then see the tree below. The Countries view is the default, but you can change to the Surnames view or the Variants view. We will leave it in the Countries view.

FTDNA haplotree countries

Using the Countries view

We want to find out if more than two people tested positive for SNP J-Z1295 (the top level of the step chart). Enter the haplogroup name in the "Go to Branch Name" box. You must list the full J-Z1295, not just Z1295, but you don't need to type capital letters. 

Y-DNA Haplotree countries

You will be taken to the precise position on the tree:

Y-DNA Haplotree countries

Haplogroup J-Z1295 is highlighted in blue. Next to J-Z1295 is the number 41. This is the current number of branches within haplogroup J-Z1295. Click the + sign at the left to see the branches.

Y-DNA Haplotree subclades

We now see two branches (subclades) within J-Z1295: J-Z631 has 34 subclades, and J-CTS5789 has five subclades for a total of 41. We can continue to see the further branching of the tree by clicking the + sign next to each branch we want to view.

What else do we see in the above screen? Aside from knowing that J-Z1295 has 41 branches we see four icons on this line. These are flags representing the countries of origin reported by the testees. Each person reports his own country of origin, so if a person believes, for example, that his ancestor came from Scotland you will see the flag of Scotland. You can hover over each flag to see the name of the country it represents. Obviously, since these countries of origin are self-reported, they may not be accurate. The last icon is a question mark which indicates that 21 people did not report a country of origin. So it appears that there are a total of 26 people who currently have haplogroup J-Z1295 as their terminal haplogroup. Since they do not belong to the two branches below J-Z1295 there may be at least one other subclade that has not yet been discovered. As more people take the Big Y-500 test, these people could be moved into a new subclade.

Instead of clicking on each subclade and adding the number of people with flags, we can see a better report by clicking the three dots to the far right of J-Z1295 

Y-DNA Haplotree options

Click Country Report on the menu. 

haplotree country report

We will now see the total number of people who have tested positive for J-Z1295 and its branches.

haplotree country report

We see that 26 people have J-Z1295 as their terminal haplogroup. Their countries of origin are shown. For example, one person in haplogroup J-Z1295 reported Germany as his country of origin, and 17.18% of the people within this haplogroup and subclades reported Germany as their country of origin. We must scroll down to see all reported countries. 379 people are within haplogroup J-Z1295: 26 at J-Z1295, and 353 in its branches. This is far more than the two people we assumed from our Big Y-500 match list! Furthermore, these numbers will continue to grow. 

We can see the total number of men for each branch in our step chart. Here is the Country report for haplogroup J-Z631:

haplotree country report

345 people have been placed in this haplogroup or one of its branches. Now we'll see the number of people in J-Z1043:

haplotree country report

241 people have been placed within this haplogroup by Family Tree DNA. The next subclade, J-Y98609, is where it gets interesting.


There are a total of three testees above. Notice that there is only one man who has haplogroup J-Y98609. His ancestor was from the Czech Republic. The two additional men broke off and formed a new subclade.

Here is the terminal haplogroup J-BY45500:


In this final screen, these are the two people, Carnes and Karns, who are reported as matches in the Big Y-500 Matching list we originally saw. I will repeat the beginning screen:


What we know is that these two people [the "You" (Karns) and the one match (Carnes)] do not share at least 30 SNPs with the man who is still in haplogroup J-Y98609. He is not on the list of matches. We can see a partial list of the SNPs by changing to the Variants view instead of the Countries view in the new Y-DNA Haplotree.

Using the Variants view

Go to the top of the page and select Variants. We still have J-Z1295 in the "Go to Branch" search box.

FTDNA haplotree variants view

The view will change to show SNPs instead of countries.

haplotree variants view

Here we see that the two men at haplogroup J-BY45500 share three SNPs with the man at haplogroup J-Y98609. These shared SNPs are Y98609, BY38005, and Y105578. After that, Carnes and Karns formed their own subclade because they shared 13 named SNPs and had some unnamed variants that the other man did not have. 

The man at J-Y98609 no doubt has a large number of unnamed variants because he is not within 30 SNPs of the other two men. He can recruit another cousin with his surname who will share some of his unnamed variants. They will then form a new subclade of haplogroup J-Y98609. As more distant cousins and closer family members are tested the haplogroups will move closer to the present time, and we can begin to see at which generation each SNP occurred.

Using the Surnames view

We saw in Haplogroup J-Z1295 that there was an option for a Country Report.  The Surname Report has no link, so there are no surnames available for this haplogroup.

haplotree reports

If we go to the top of the Y-DNA haplotree we can search by surname. I removed the branch name from the "Go to Branch Name" search box, so we are now searching for the surname Karns in the entire haplogroup J.

haplotree surnames

There are no results.

Why aren't surnames showing in all haplogroups?

If you choose the surname view you will notice that sometimes you will see surnames, and other times you will not. Here are the reasons you may not be seeing surnames in your haplogroup:

  • At least two men must share the same terminal haplogroup and the same surname.
  • Each man has to have opted into public sharing in his account settings.
  • The surnames currently held by these men must be spelled exactly the same.

In haplogroup J-Y98609 there is only one man in the group, so there can be no matching surname. In haplogroup J-BY45500 you also do not see any surnames. Although the two men in this haplogroup share the same terminal SNP, share a common ancestor named Nicolaus Kern[s], and both have opted into public sharing, the current surnames of these men are not spelled exactly the same. One man spells his surname Carnes, and the other spells his surname Karns, so no surname appears on the haplotree.

Finding a surname

Let's use another example where we have two men with matching surnames. Here we will use my Thompson example from previous blog entries. Thompson is a very common surname, so we should expect to find the name in a surname search of Haplogroup R.

haplotree surname search

The search results say that the surname Thompson is found a total of 27 times and is found 14 times within Haplogroup R.  The screen will then display every Thompson within Haplogroup R.  Here are a few examples:

Thompson haplotree

The haplogroups are highlighted in blue that have at least two Thompsons with that haplogroup as their current terminal haplogroup. In order to appear on the list, they also had to agree to public sharing.

Here are my Thompsons. Their current terminal SNP is FGC65820,  and only the two Thompsons share this SNP. 


Notice that there are options to see both a Country Report and a Surname Report. Here is the Surname Report:


In the surname report for this haplogroup there is only one surname. We can see exactly how many Thompsons have this terminal SNP. The terminal SNP will change as more Thompsons are tested, and they will form subclades of R-FGC65820.

It's pretty exciting seeing my ancestor's surname appearing in this haplogroup.

How can I make sure that my results are on the 
FTDNA public Y-DNA Haplotree?

1. Take a SNP test from Family Tree DNA. You must take a Y-DNA test and be SNP tested. If your test results show the haplogroup in red (such as R-M269), your haplogroup is estimated and has not been confirmed. You must order some kind of SNP test from Family Tree DNA to confirm it. Once you have been SNP tested your haplogroup will be shown in green. I highly recommend ordering the Big Y-700 test if you can afford it because you will likely find new SNPs that have never been discovered, and you may even form a modern haplogroup. The Big Y-700 test can help get your ancestor's name in a haplogroup in the genealogical time frame.

2. Opt into public sharing. Log into your account, and click your name at the upper right of the screen. Then click Account Settings. On the next screen click the Privacy & Sharing tab:

Click the boxes next to "Opt in to sharing," especially the box for Origin Sharing.

3. Enter the country of origin for your most distant known paternal ancestor. Click the genealogy tab:

Under Earliest Known Ancestors choose the Country of Origin for your Direct Paternal ancestor. Family Tree DNA used to ask you not to enter United States unless your ancestor was Native American. This is no longer the case; there is now a choice between United States and United States (Native American). So, for example, if your ancestor lived in the United States and you aren't sure of the country of origin, you should choose United States. You can change the country when you discover more information.

4. Recruit other relatives. In the Carnes/Karns example above I need to recruit more closely-related men.  We would then see two subclades below J-BY45500: one with the surname Carnes and one with the surname Karns.


The new public haplotree is a big step forward. You no longer need to be tested at Family Tree DNA to view the haplotree. The countries of origin, the surnames, and the number of people tested are all new additions to the haplotree. I am grateful to Family Tree DNA for finally making this tree public and for adding these very helpful enhancements. The tree motivated me to do even further Big Y-500 testing to get my ancestral surnames assigned to modern haplogroups on the Y-DNA haplotree.

This tree will allow me to leave a lasting record of many of my ancestors, proved by Y-DNA.

What's next?

In an upcoming blog entry we will compare two public haplotrees: FTDNA's new Y-DNA Haplotree and the YTree at YFull. We will see the advantages and disadvantages of each. You may want to consider getting into both. Good news just keeps coming!


Links to Family Tree DNA appear in the sidebar. I receive a small contribution if you make a purchase, but clicking through the link does not affect the price you pay. 

Friday, April 20, 2018

Announcing Family Tree DNA's new Big Y-500 test

Since its inception Family Tree DNA has been conducting Y-chromosome DNA tests. Originally these were STR tests, then Family Tree DNA began SNP testing. For an explanation of the differences between these tests, see Y-DNA STRs, SNPs, and Haplogroups.

Until today, Family Tree DNA's most recent Y-DNA test was called the Big Y which was a SNP discovery test.  But now there is a new, combined Big Y-500 test that is absolutely amazing. Here is how FTDNA describes the new test.

What is Big Y-500?

  • The Big Y and Y-111 will be sold together in a product called Big Y-500
  • It includes all SNP information currently included in Big Y, as well as the 111 STRs of the Y-111 and newly reported STRs 
  • Approximately 45 STRs used in the Y-111 product are also reliably called from Big Y data and will serve as additional cross-checks to control the quality of the Big Y-500 product

Where did the 500 come from?

  • Approximately 450 STRs were chosen from Big Y data because they can be reliably called on a consistent basis 
  • Of the ~450 STRs, at least 389 will be reported and when combined with the Y-111, that gives a total of at least 500 STRs

Note: Everyone with Y500 will have 500 STRs (including the Y-111), but not everyone will have exactly the same 389 additional STRs from the Big Y. There will be a significant overlap, but there will be some STRs that are called for one tester that may not be reliably callable for another tester. Big Y-500 STR values will be displayed on the tester's Y-STR results page. 


If you would like to see how these new STRs look, please see STRs now included in Big Y500 test! 

Family Tree DNA has removed the requirement that a man has to order an STR test before ordering the Big Y.  Anyone can now order the Big Y-500 and will get a 111- marker STR test, the Big Y SNP discovery test, and hundreds of additional STRs. For DNA Day, the new test is on sale for $649 (regularly $799).

If you have previously done some Y-DNA testing with Family Tree DNA the upgrade prices are shown in the following image:

2018 FTDNA DNA Day Sale

It will be fascinating to see what we can discover about our families with the new Y-DNA data!

STRs now included in Big Y500 test!

In my previous post, The amazing power of Y-DNA, I stated the following:

In November 2017, Family Tree DNA announced that in 2018 they would be including about 500 STRs, in addition to the SNPs, in Big Y results. These would not just be for new Big Y testers; anyone who had ever taken a Big Y will see them. There will be no additional charge for these new STRs. While there is no expected date, it is obvious that the "Y500" is now in the pipeline. 

Well, the Big Y500 results have arrived, and it's stunning. 

STRs now included in Big Y500 test!

When you log into your Family Tree DNA account, instead of seeing a section called Big Y you will now see a section called Big Y500:

Big Y 500

The link to Y-STR Results is new. If your Y-STR results are still in process, you will see this at the bottom of your list:

But if they have been completed, you will see a screen that caused me to gasp with shock. Here's the entire screen:

Here is a close up of a portion of it:

On your dashboard, you will still see the section for Y-DNA results. Notice that "Y-STR Results" appears in both the Y-DNA section and the Big Y500 section.

In the Y-DNA section, when you click Y-STR results you will see the same massive list you saw in the Big Y500 section.  However, when you click Matches, your list has not changed. You will see matches for the first 111 markers.

We don't yet know when we will see a list of matches for the Y500 STRs, but it is clear that Family Tree DNA came through on their promise to provide these additional markers. The best part is that previous Big Y testers didn't have to pay any additional fee to get these. These new STRs will appear at no cost in the results of anyone who has already taken the Big Y test, but the cost of new Big Y500 tests has gone up significantly because it is now a combination of the previous Big Y test, a Y-111 STR test, and all the additional new STRs. I can't wait to see what we will be able to do with all this new data.

To see the new test announcement see Announcing Family Tree DNA's new Big Y-500 test.

The title of one of my blog posts was, "The Big Y could be the best DNA test ever!" I feel even more strongly about that now.

Tuesday, April 17, 2018

The amazing power of Y-DNA

The amazing power of Y-DNA can help you break through brick walls in many of your ancestral lines. For example, when there are several men with similar surnames who lived in the same location, it is can be very frustrating to attempt to determine their true relationship. But Y-DNA can point us in the right direction and can even prove our theories.

You don't have to depend on your own Y-DNA or the Y-DNA of close relatives. I try to track down direct male descendants of all of my ancestral lines to see what Y-DNA can do. Since the Y-chromosome is passed from father to son, I need to find a man who is my ancestor's son's son's son . . . . If the surname remained unchanged the descendant will be carrying the surname. This time I want to find more about my maternal grandmother's ancestors.

My problem was particularly troublesome because I am descended from two men named Michael Kerns (spelled Carn, Carnes, Karns, Karnes, Kern, etc. in the various records) who both lived in Bedford County, Virginia. One died 1807 in Bedford County, and the other left Virginia and died 1814 in Knox County, Tennessee. The daughter of Michael of Bedford married the son of Michael of Knox, so that's why I descend from both of them. Genealogists have confused the two men for decades and have placed them in multiple lineages.

Researching in Colonial Virginia is difficult, and deeds are your most important resource for this time period. So years ago I went through all of the deeds of the two Michael Karnes, and I now know where each man lived and have determined the children of both men. But I want to find their fathers. Y-DNA testing can be a great way to do this.

If you are relatively new to Y-DNA testing, you may wish to review this post: Y-DNA STRs, SNPs, and Haplogroups. The page will open in a new window, so you won't lose your place here.


I found men who were willing to take DNA tests and ordered Y-DNA tests from Family Tree DNA (FTDNA) for two descendants of Michael Karnes of Knox County, and one for Michael of Bedford. This test is an STR test, and I originally ordered 37-marker tests for these men. The descendant of Michael Kern from Bedford does not have any Y-DNA matches and does not appear to be related to the Michael of Knox, but I need at least one more tester to be sure. The Michael Karnes of Knox has several DNA matches, so we can find out more about him. 

The Y-DNA results include a list of people who closely match your STRs. Below is the list of matches for one of the descendants Michael Karnes of Knox County. This man's surname is now spelled Karns. Mr. Karns is not listed here; these are the people who match his Y-DNA. Notice the spelling of the various surnames: Carnes, Kern, Karnes. There's even one Moreno, but he doesn't have a family tree. From DNA we know that all of these men are probably related. 

Y-DNA matches
Y-DNA STR Matches

The genetic distance in the first column gives us a clue to how closely related these men are. The first man on the list is the other descendant of Michael Karnes. After ordering the initial test, I ordered a SNP test for him and upgraded his STR test to 67 markers. 

Family Tree DNA shows what tests were taken by each man. For example, the fourth man on the list has tested 111 markers, has taken the Family Finder (FF) test, and the Big Y test. If Mr. Karns took the Family Finder test, these men may not be on his list of matches because they may not share any autosomal DNA segments with him. This is one reason that Y-DNA is so powerful--Y-DNA is passed relatively unchanged with each generation and does not get broken up like autosomal DNA segments do. 

As I was looking through the above DNA matches, I noticed that one Kern was descended from Adam Kern of Frederick County, Virginia.  

Genealogical research from DNA clues

The earliest record I could find of Michael Karnes was a 1766 deed in Frederick County, Virginia. In 1773 Michael left Frederick County and had deeded some of his land to a man named Adam Kern. Adam's name is showing up as a Y-DNA match, so now I decided to get all of Adam’s deeds to see what I could find. As it turns out, Adam split that land into several parts, and in one significant 1796 deed to his first son Nicholas [Frederick County,Virginia, Deed Book 24B, page 565] Adam stated that he received this land from his brother Michael. 

relationships in Virginia deed
Deed from Adam Karn to his son Nicholas

I started crying.  It had long been believed that Adam might have a brother named Henry, a brother named Michael, and a brother named Nicholas, but nobody had ever determined the exact relationships. I traced the children of all four men and noticed that Michael, Adam, and Henry had each named their first son Nicholas. So I decided that all family trees were likely incorrect, and that these men were probably sons of a man named Nicholas. I checked the list of DNA matches again. Although all the men had family trees there was no common ancestor, so I traced the lineage of the men on the list. In addition to the two men whom I know are descended from Michael, two men on the DNA match list are descended from Adam, and one is descended from Henry. The lineage of one man is still uncertain.

Adam Kern had married in York County, Pennsylvania shortly after coming to Frederick County, Virginia, so I went looking for a man named Nicholas in York County. I found him, and knowing the names of some of his children, I was actually able to trace the entire family to their hometown in Germany.

Johann Nicolaus Kern married Maria Apollonia Spicker 13 Feb 1738 in Flonheim, Germany.  The marriage record stated that the father of Nicolaus was Nicolaus Kern, deceased, from Erbes-Bűdesheim, and the father of Maria Apollonia was Hermann [sometimes spelled Hermanes] Spicker of Flonheim.

Johann Nicolaus and Maria Apollonia Kern had the following children baptized in Flonheim. I will show images for the first three men, because our DNA testers are descended from them:

Johann Henrich Kern, 7 Aug 1740

Johann Henrich Kern Flonheim
Baptism of Johann Henrich Kern

Johann Adam Kern 26 Mar 1742

Johann Adam Kern Flonheim
Baptism of Johann Adam Kern

Johann Michael Kern 7 Jul 1744

Johann Michael Kern Flonheim
Baptism of Johann Michael Kern

Johann Nicholas Kern 5 Jun 1746
Johann Georg Kern 12 May 1748
Johann Paul Kern 2 Oct 1749

The family left Germany and went to America to join Maria Apollonia’s family. Her parents Hermann Spicker and Maria Ursula Brűcker went to Pennsylvania and arrived 15 Sep 1749 on the ship Edinburgh. Nicholas and Maria Apollonia Kern took the same ship two years later and arrived in Philadelphia 16 Sep 1751. It must have been a miserable trip for Maria because she gave birth in York County the next month. They had the following children baptized in York County, Pennsylvania:

Maria Magdalena Kern 11 Oct 1751
Carl Kern 1 Apr 1753 
John Kern 21 Sep 1754
John Kern  2 Sep 1756
Anna Maria Kern 2 Sep 1756

Henry Spicker [brother of Maria Apollonia] and Maria Ursula Spicker [mother of Maria Apollonia] were witnesses to the baptism of Carl Kern in 1753. The Kerns and Spickers were on multiple documents together in York County, Pennsylvania.

The Kern family moved to Frederick County, Virginia, about 1765. Nicholas Kern [spelled Carn on the administration bond] died that year, and his wife Mary was appointed administrator. Her son Henry Carn [the signature is spelled Henrich Kern] and brother Julius Spicker signed the administration bond.

Virginia administration bond
Administration bond for Nicholas Carn

These Kerns do not yet appear to be related to any other Kern family in Colonial America. I notified all of the men on the Y-DNA matches list about my new findings, and here is a portion of how they currently appear in the Kern surname project:

Kern surname project
Kern surname project at Family Tree DNA

The lineage of one man is still uncertain, but he has ordered a Big Y test, so we should be able to find out more by examining Big Y results. This past December the Big Y test went on sale and included a free upgrade to 111 markers. I ordered this test for Mr. Karns. By comparing the Big Y results of the two men who have tested, we can begin to learn more about the Kern lineage.

Haplogroups and SNPs

Before we examine the Big Y results, notice in the above screenshot for the Kern surname project that STR results indicate that the men are related, but these STRs are not enough to distinguish between the various lineages. Now look at the third column. The third column is for haplogroup. A haplogroup is a group of people who are related genetically and share a common ancestor. These haplogroups seem to be very different and can make it look like these men are not related. But they are! The haplogroups in red are predicted haplogroups. This means that Family Tree DNA looked at the STR patterns of these men and predicted that they belong to haplogroup J-M172. J-M172 is an ancient haplogroup that has been estimated to be between 19,000 - 24,000 years old. We are not going to be able to determine the name of our common ancestor that far back! We can get closer in time by ordering something called a SNP test. I did this for one of the men, and he was confirmed to be in haplogroup J-Z1296. His haplogroup is colored green which indicates that it is not merely predicted; it has actually been confirmed with a SNP test. J-Z1296 is a branch of J-M172. estimates J-Z1296 to be about 4500 years old. That's much closer in time, but still not useful for genealogy. So we need to discover new SNPs that can bring us into the genealogical time frame. That is the purpose of the Big Y test. Now look at the two green haplogroups J-BY45500. This haplogroup is brand new. Haplogroup J-BY45500 was discovered with the Big Y tests of these men.



The Big Y test can find SNPs that have never been discovered. It can take your haplogroup from an ancient time period to a more modern one, and even find SNPs that only you have. When we get our Big Y results we should first look at the Matching tab. We will see our new haplogroup displayed along with a list of matches. The haplogroup of Mr. Karns is reported as J-Y98609, and he has only one match--a Mr. Carnes.

Big Y Matching
Big Y Matching

This is where I could get depressed and say, "I only have one match, and my haplogroup didn't change much. What a waste." But this is just the beginning of the process.  

Next to the name of the match, there is a list of Non-Matching Variants. The Non-matching Variants are the SNPs that are not shared between the two men. You will want to compare this list to the list of Unnamed Variants

Unnamed Variants

Many people have misinterpreted the Unnamed Variants and have assumed that these are private SNPs not found in anyone else. According to FTDNA, however, "The Unnamed Variants tab displays your SNP markers that are not on the list of ~70,000 known SNPs. These markers may or may not be unique to you as an individual. Men in related lineages may share some Unnamed Variants." This means that in the Big Y process all previously-unnamed SNPs that are found in your results are automatically put into the Unnamed Variants section even if these SNPs are shared with another tester. The naming of new SNPs is not automated, and the initial results will require a manual review by Family Tree DNA.

When you click on the Unnamed Variants tab you may see a long list of unnamed variants. Compare this list to the list of Non-Matching Variants in your Matching tab. The Unnamed Variants that are not in the Non-Matching Variants list may be shared with your match. In the screenshot in the section above, there are eight Non-matching Variants [BY28657, etc], but there are many Unnamed Variants:

Big Y unnamed variants
Big Y Unnamed Variants

Submitting the Big Y results for review

There are often many Unnamed Variants that do not appear on the Non-Matching Variants list, and some of these could be shared with one or more people on the list of matches. After you receive your initial Big Y results it may take awhile for the manual review process, but take a screenshot of the Unnamed Variants list and a screenshot of the Non-Matching Variants results because these will probably change during the FTDNA review. Family Tree DNA will name any matching SNPs, create a new haplogroup, and maybe even remove a couple of variants from the list.

After the Big Y review

After the Big Y results of the two kits have been compared and reviewed by Family Tree DNA, we actually have results we can work with. Here is the new haplogroup:

Big Y haplogroup step chart
New haplogroup from Big Y results

The haplogroup is now reported as J-BY45500. We still have one match at each of the five haplogroup levels. We need to review what we are really seeing here and understand that these results are fantastic! Here are the important points:

  • First, we need to know why there is only one match. If I click on the person icon next to Haplogroup J-Z1297, I will see that person's results. In this case, I see the same name (Carnes) at all levels.  Does this mean that only one other person has tested positive for SNPs J-Z1297, J-Z1295, J-Z631, J-Y98609, and J-BY45500? Absolutely not. Family Tree DNA will only display matches who have no more than a 30-SNP difference with you. If someone is not related within 30 SNPs, they are probably not related within at least a thousand years. So here's the first good news--I'm not going to waste my time trying to find the names of common ancestors when it will not be possible. I can look at the haplogroup projects if I want to see distantly-related people.
  • Second, there has to be at least one more person at haplogroup Y98609, otherwise these two Karns/Carnes men would not have formed a new haplogroup under it. The other men who share haplogroup Y98609 cannot be within 30 SNPs of Mr. Karns, or they would be on his match list.
  • Third, since there is only one match at five haplogroup levels, Mr. Karns must share several SNPs with this person because they both share all of those five SNPs, and possibly more. 
  • Fourth, the "terminal" haplogroup, J-BY45500 is not actually final. It is the last SNP, or group of SNPs, that is shared between these two people. Mr. Karns had several unnamed variants that Family Tree DNA has now named and placed on the human haplotree. In a final group of SNPs, there is no way to determine the order in which they occurred. Family Tree DNA chooses one of these SNPs as the haplogroup designation and groups the rest of the SNPs with it. When other testers in the future have some of these SNPs, but not others, Family Tree DNA can then decide the order of the SNPs, and new haplogroups will be formed. In addition, when a future tester shares one or more of your unnamed variants, your haplogroup will be further refined.
  • Fifth, if there is nobody else within 30 SNPs, we have just uncovered new SNPs and made a great contribution to science and to family history.

Doing our own evaluation of Big Y results

Let's find out how many SNPs are shared between Mr. Karns and Mr. Carnes. Click the myFTDNA tab, Y-DNA, then click Haplotree and SNPs.

Haplotree and SNPs
Haplotree and SNPs

You will be taken to your exact position on the human haplotree. Your haplogroup will be highlighted in green. Click "More" next to BY45500 to see a list of other SNPs. In this case we see 12 SNPs in addition to BY45500. Since Mr. Karns has only one DNA match in his newly-created haplogroup BY45500, the two men share these 13 SNPs.

Y-chromosome haplotree
Confirmed haplogroup with SNPs

We can see the details of each of these SNPs by using the Big Y chromosome browser. From your Big Y Results screen click the Named Variants tab, and enter the name of the SNP in the SNP Name Search box.

SNP search FTDNA chromosome browser
SNP Name Search

When the SNP name appears under the search box, click the link to see this SNP in the Y-Chromosome Browsing Tool.

FTDNA SNP search
SNP Name Search for BY45501

From the Y- Chromosome Browsing Tool we can find details about SNP BY45501. It is Position 8005382. The Reference Sequence has a T in this position, and Mr. Karns has a G. 

Big Y chromosome browser
Chromosome Browser

Because it is now named, position 8005382 should no longer appear on the list of Unnamed Variants. We can look up each named SNP in the chromosome browser and see its details. There are 13 total named SNPs, but Mr. Karns originally had 21 unnamed variants.

Since 13 SNPs have been named we might now expect to see eight Unnamed Variants. However, in his new list of Unnamed Variants Mr. Karns now has only four. FTDNA names SNPs when they are shared with someone else. Since these mutations are not shared with Mr. Carnes, these all probably occurred in the line of Michael Karnes and his descendants. We can know exactly in which generation each mutation occurred by testing more descendants of Michael.

There are now 13 shared SNPs and four "private" SNPs (the unnamed variants that remain for Mr. Karns). But originally there were 21 unnamed variants. What happened to the other four SNPs? We can use the Y-chromosome browser at to look up the four positions and see that these SNPs had already been named and should not have appeared on the list of "unnamed variants."  Here is one of them:

Details for position 15274092

This position had already been named A5563, but was not on FTDNA's list of named SNPs. The SNP name was found during the manual review. 

By examining each position from our screenshot of the previous list of Unnamed Variants, we can know what happened to all 21 unnamed variants during the Family Tree DNA review and know the full set of shared and unshared mutations. I contacted the person who manages Mr. Carnes account and asked what his unknown variants are. He has five of them. If at least one of these mutations did not occur in any of the descendants of Nicholas Kern (1715-1765), Mr. Carnes could be a more distant relation.  

The amazing power of Y-DNA

  • I used Y-DNA to solve a decades-long mystery about my mother's mother's mother's father's mother's father's father's father--eight generations back, weaving between maternal and paternal lines. All we have to do is find a direct paternal descendant of any of our ancestral lines and do a Y-DNA test.

  • Because of the clues from Y-DNA STRs, we now know the exact lineage of all of the matching Kerns except for one. Each of these lines has been extended multiple generations back to its German origins. The STRs were not enough to help pinpoint the ancestral line of Mr. Carnes, but he does know that he is related to this group of German Kern men and is not related to men from Ireland, for example, who may have spelled their name Cairns. 
  • STR results were enough to help me trace the origins of my ancestor Michael Karnes back to Europe, but the SNPs in the Big Y test did even more. Even though we may never be able to know names such as Johann Kern for generations further back, I can use the Haplotree and SNPs screen to see that I have ancestors who have been given the names BY45500, Y98609, Z631, and so on, all the way back to "Y-Chromosomal Adam." Genealogy doesn't get better than that. 

  • Mr. Karns and Mr. Carnes share 13 SNPs that have not been seen in anyone else. The two men are definitely related. These 13 SNPs have now become part of the human haplotree and will be available for family historians and scientists. Because we know the geographic origins of this family, we will eventually be able to assign at least one of these SNPs to a precise location.

  • Mr. Karns has four, and Mr. Carnes has five unnamed variants. These mutations occurred in their own family line and not in the line of the other man. These unnamed variants can be named and tied to specific ancestors by testing more Kerns descendants. When any of these unnamed variants is found in another man, a new haplogroup will be formed.

What can we do next?

1. YBrowse: We have seen that can be very valuable to our research. Submit the 13 newly-named SNPs to YBrowse.

2. YSeq: Submit the named SNPs and the unnamed variants to the Wish-a-SNP program at YSeq so that anyone can test one or more of these SNPs.

3. YFull: In many haplogroups, including the J2 haplogroups, further evaluation by YFull is highly encouraged. One good reason for this is to further preserve your results. Are there any other good reasons? Will YFull tell us anything further? We're about to find out in an upcoming blog post.

4. STR upgrades: Encourage current Kerns Y-DNA testers to upgrade their STRs to 111 markers. There are three differences in the 68-111 marker panel between Mr. Karns and Mr. Carnes. Seeing these in the tests of the other men will help to verify the lineages. 

5. Big Y Upgrades: Encourage current Kerns Y-DNA testers to consider taking the Big Y test. Encouraging more Big Y testing is especially important for Mr. Carnes because he does not know where he fits into this lineage, and he has five unnamed variants. If some of these show up in the Big Y tests results of other men whose lineage is known, his own lineage will be obvious. If they do not show up, it could indicate that Mr. Carnes is a descendant of another son of Nicholas or even one of the brothers or other relatives of Nicholas Kern who could have immigrated to America. Each man taking the Big Y test will verify his lineage and discover the private SNPs that occurred in his own Kern line. He will be able to determine the exact ancestor in whom each SNP occurred by testing more relatives.

6. New testers: Encourage new Kerns men to take a Y-DNA test. The more data we have, the better. For example, Nicholas (the brother of Henry, Adam, and Michael) has known descendants, and their DNA has not yet been tested. This step will be critical to Mr. Carnes if the Big Y test results of current Kerns testers don't match his. By testing more men with the Kern surname, maybe I'll even be able to find the father of my other ancestor Michael Karnes!

7. SNP packs: Work with a haplogroup administrator to get some of these newly-discovered SNPs into one of the Family Tree DNA SNP Packs so that they are easily available for testing.

8. New STRs: I was going to write that we've gone as far as we can go with Family Tree DNA until someone else decides to do further Y-DNA testing, but then I noticed that there were pending DNA  test results. 

FTDNA pending results

 I clicked on the above link and I saw this:

Big Y 500 STRs

In November 2017, Family Tree DNA announced that in 2018 they would be including about 500 STRs, in addition to the SNPs, in Big Y results. These would not just be for new Big Y testers; anyone who had ever taken a Big Y will see them. There will be no additional charge for these new STRs. While there is no expected date, it is obvious that the "Y500" is now in the pipeline. Ahhhh, the gifts just keep on coming.

See the incredible update here: STRs now included in Big Y500 test!


Y-DNA can focus on a specific lineage and do what no other DNA test can do. If you have not yet started Y-DNA testing in your family, please consider it. Each DNA test helps not only you but others as well. I would not have been able to achieve this incredible breakthough if other men had not taken a Y-DNA test. The Y-chromosome is carried only by men, so only men can take this test. Remember, though, that you can use Y-DNA of cousins and other more distantly-related men for any of your ancestral lines. 

Every year there is a DNA Day Sale in the month of April. In 2018 DNA Day in April 25. Family Tree DNA's new Big Y-500 test is currently on sale until April 28, 2018, and you may want to jump on it. See Announcing Family Tree DNA's new Big Y-500 test.

With the new Big Y-500 you will get not only recent, newly-discovered SNPs, but you will know your decent all the way back to "Y-Chromosomal Adam." In addition, you'll be getting a complete 111-STR test and new STRs giving you at least 500 total. You can use the amazing power of Y-DNA to help your own family history research as well as preserve a story about your family for future generations.

Update: Were the these men related: Michael Karnes of Bedford and Michael Karnes of Knox. We now have the answer! See Y-DNA testing for Genealogy: Are these men related?
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