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Getting the most from Y-DNA

This post is a great example of how to get the most from your Y-DNA. In this case we will not only prove a Y-DNA relationship, but also pinpoint the exact location in Ireland where a man's ancestors lived. I will explain the different types of Y-DNA tests, how to do your own evaluations of the results, and give a list of further suggestions on how to get the most from your results and what to do next. This will be a long post.


Can we find immigrant origins when there may be no records?

My father is very proud of his Irish heritage, but he wants to know more. From family tradition he knows that his ancestor, William Gibbs, emigrated to Canada from Ireland. That's the only information that he knew about his Irish origins. Can we find out more?


What we know from Canadian records

William Gibbs is first listed in the 1851 census of Sheffield, Addington County, Ontario. His wife was Mary Coulter, and he is listed in the census next to her parents. The census states that William, his wife, and daughter Mary were all born in Ireland.


Gibbs family in 1841 census of Sheffield, Ontario, Canada

William is listed in the 1861 census of Sheffield, but this time the census states that all of his children, including his first daughter, were born in Canada. 


Gibbs family in the 1861 census of Sheffield, Ontario, Canada

Other censuses, and the death record of the daughter Mary, confirm that all children were born in Ontario.

It appears that William may have come to Canada around the time of The Great Famine. There is no passenger list to tell us exactly when he arrived. No record has been found that contains a date of birth or the names of his parents. Luckily, however, his death record [Number 18 in the image below] states that he was born in County Monaghan, Ireland. 

Death of William Gibbs 15 Jun 1882 in Sheffield, Ontario, Canada

So here's all we know from Canadian records about William's origins: William Gibbs was born around 1826 in County Monaghan, Ireland, and was in Canada by 1851.


Searching records in Ireland

First, as you may know, there is a scarcity of Irish records. In many cases we are stuck with just knowing that our ancestor came from Ireland. But that didn't deter me! After seeing that William was born in County Monaghan I immediately began searching through the records that remain. One of the most useful records for the time when William would have been living in Ireland are the Tithe Applotments. These records were taken between 1823-1837 and can be used as a census substitute. In the entire County of Monaghan, there was not a single Gibbs family. I could not find the family in other surviving records, so I eventually gave up.


An unexpected message

I came to stay with my parents in 2019 to help take care of my mother. She died Christmas morning. I was helping my father when the Coronavirus quarantine was announced, so then I stayed. In March of this year he was talking about his family and said, "About 10 years ago, a man named Jebb contacted me from Ireland and said he thought we might be related." I asked, "What made him think that?"  He replied, "DNA."  I asked if he still had the email, and he said he didn't, but he thought that he could find the man's email address. A few minutes later I was sending an email to a man in Ireland using an old email address and hoping that he still used it. The next day Mr. Jebb replied. He lives in Ireland, and his ancestors were from the townland of Billis, County Monaghan, Ireland.


Jebb DNA

Mr. Jebb informed me that many years ago he had done a Y-DNA test with Ancestry.com [Ancestry no longer conducts Y-DNA tests]. Other Jebb men had tested at the same company, and some of them were matches. He said he was also a distant match to Gibbs. He was the only Jebb had also taken a 25-marker Y-DNA test with Family Tree Dna, but he did not have any Jebb or Gibbs matches in the FTDNA database. At the time these men were tested, most companies had only one kind of test available for Y-DNA. This was the STR test.


What is an STR test?

"STR" stands for Short Tandem Repeat. A Short Tandem Repeat means that a short series of bases (nucleotides) is repeated side-by-side several times, something like a hiccup.

Here's an STR example: AGATAGATAGATAGATAGATAGATAGATAGAT. In this example, the sequence "AGAT" is repeated eight times. There are many known locations on the Y-chromosome where these Short Tandem Repeats occur. Each of these locations is identified by a marker. 

Each marker is given a name such as DYS393. This abbreviation stands for DNA Y-chromosome Segment 393. At this marker the number of repeats is counted and reported. So, for example, in a 12-marker test the testing company will examine 12 named locations on the Y-chromosome and report the number of repeats at each location.


Old Y-DNA tests

After hearing that Jebb had tested at Ancestry and at Family Tree DNA (FTDNA) I was in quite a quandary. My father had not taken Y-DNA tests with either Ancestry.com or with FTDNA. However, he had taken two Y-DNA tests. In 2006 my father had taken a 12-marker Y-DNA test from National Geographic's Genographic Project. I had transferred the results to Family Tree DNA. He had also taken a 43-marker Y-DNA test from the Sorenson Molecular Genealogy Foundation (SMGF). Although SMGF did not display the results, they did publish their database online. As a person guessed at each marker correctly it would show up in the results. I did exactly that, until all results were showing, and then transferred the SMGF results to Ancestry.com and to YSearch.org. SMGF tested 43 markers, but one of these markers was not tested by Family Tree DNA, so only 42 markers are recorded in the YSearch record.

You would think I'd be safe with the DNA in that many databases. But, unfortunately, all but one of them is now gone. Ancestry.com purchased SMGF in 2010, and removed the SMGF online database. Ancestry then discontinued Y-DNA testing and removed its own Y-DNA database. Family Tree DNA removed the YSearch database. This one was the most devastating because I had tested the Y-DNA of hundreds of men. The Y-DNA test of every man from any company had been entered into YSearch, and all were now gone. Most recently, the Genographic Project has been discontinued, and its database has been taken down.

So what did I have left? I had the 12-marker Genographic Project results that had been transferred to Family Tree DNA, and one more thing--I had taken a screenshot of the Gibbs YSearch results. 


Gibbs 42-marker STR results recorded at YSearch.org


I could compare the Jebb Y-DNA results at Family Tree DNA with the Gibbs 12-marker results that had been transferred there. I immediately looked to see if Jebb was on the Gibbs list of 12-marker Y-DNA matches at Family Tree DNA. He wasn't. Right off the bat, Family Tree DNA is indicating that these two men are not related. If they aren't showing up as matches at only 12 markers, this is not a good sign. But, I still had my YSearch screenshot, and Mr. Jebb allowed me access to his 25-marker Y-DNA results:


Jebb 25-marker STR results

By comparing the two we can see how many differences there are. There is already a difference at the second marker, DYS390, where Gibbs has 24, and Jebb has 23. The second difference is at DYS385b where Gibbs has 16, and Jebb has 15. So these two men have two differences in the first 12 markers. A third difference is at DYS447 where Gibbs has 26 and Jebb has 25. This is definitely not looking promising.

But Mr. Jebb also informed me that he had compiled a database of his Ancestry Y-DNA results comparing them to the results of any possible matches. He sent me the list, and I carefully compared them. In addition to his own results there were three matches named Jebb on his list, and my father's Y-DNA results matched all of the men more closely than his results matched Mr. Jebb's. For example, all three of the Jebb matches had a 24 at DYS390. So there was a chance!

I wrote back to Mr. Jebb and told him that our best shot of solving this was to upgrade both the Jebb and Gibbs Y-DNA tests. I said that it was possible that no matter how many STRs we ordered, these two men might still not show up as matches, but if they were really related a Big Y test would prove it. 

The most recent version of the Big Y test is called Big Y-700. This test will prove the Jebb-Gibbs relationship because not only does it include more than 700 STRs, it includes the very important SNPs. In addition, the Big Y-700 includes a separate test of the first 111 basic STRs.


What is a SNP?

SNP (pronounced "snip") stands for Single Nucleotide Polymorphism. It occurs when a single base (nucleotide) mutates. In the image below the ancestral nucleotide A has mutated to a T in Man 1. [See the fifth letter from the left.]  

SNPs and STRs (Image by Mark Jobling)


The main difference between SNPs and STRs is their stability.

STRs can mutate back and forth. For example, in the image above we don't know which of the repeat values came first. Man 1 has CTA repeated 5 times, but CTA is repeated 6 times in Man 2's results and 7 times in Man 3's results. Which is the ancestral value--was it first a 5 that changed to a 6 in Man 2 and then a 7 in Man 3? Or was it first a 6 that mutated down to a 5 in Man 1 and up to a 7 in Man 3? Or was it first a 7 that mutated down in Men 1 and 2? There is no way to tell. Furthermore, these not the only three options--STRs can mutate up in one generation and back down in another generation making two men look more closely related than they really are.

SNPs, on the other hand, are generally one-time events. When a SNP occurs it is passed down to all future generations. Some SNPs are proven to have occurred thousands of years ago. Others occurred in recent times. When a new SNP is found through Y-DNA testing it is given a name and placed on the human Y-DNA tree (called the haplotree). The name of this SNP can become the name of a new haplogroup. A haplogroup is simply a group of men who share a SNP. SNP testing is progressing so rapidly that SNPs occurring in the genealogical time period are being now placed onto the Y-DNA haplotree.


The Big Y test is ordered

The day after I suggested upgrading to Mr. Jebb, I received a reply stating that he had ordered the Big Y on March 7.  

I normally wait until the Big Y is on sale to upgrade, but I thought that if I ordered the test right at that time, the 111 STRs might be completed by Father's Day. That would be the best Father's Day present ever if I could show my dad that he was very likely related to Mr. Jebb. So I immediately ordered the Big Y test.


Back to the records

I spent the next few months working almost non-stop reading any records relating to the Jebb family. In case the Y-DNA results showed that these men were really related, I wanted to find the possible Gibbs ancestor (which seemed impossible). I read every Jebb deed, went through surviving church records, etc. For example, although there were no Gibbs families in the Tithe Applotments for County Monaghan there were Jebb families there. The Tithe Applotments can be searched at The National Archives of Ireland where we see that there were fourteen Jebb families listed:


Index to Tithe Applotments at The National Archives of Ireland

I wanted to trace all of the Jebb emigrants to see which ones ended up in Canada. I also wanted to find descendants of multiple Jebb lines for possible future Y-DNA tests. This was much more work than I had ever imagined because multiple Jebb descendants had left County Monaghan and emigrated to Scotland, England, India, Australia, Canada, and the United States. Many of them had migrated through multiple countries. I was going through the records in all of these countries compiling lists of Jebb families.

I eliminated many Jebb men as the possible ancestors of William Gibbs, and narrowed it down to just a few. One of them is the best candidate, but since there is no baptismal or other record for William Gibbs the proof can only be provided with Y-DNA.


Y-STR Results

The 111 STR results came in on June 10. Father's Day was June 21, so I had a few days to prepare the presentation of records and to show my father the most exciting news--the DNA results. At 111 markers Mr. Jebb was my father's only match:


STR match list

In the Genetic Distance Column you see the number 5. This means that there were five differences between the two men in the 111 markers. We know that two of them occurred within the first 12 markers, and that would normally indicate that these two men are not related.

The 111 STRs indicate that these men probably are related, and if so, the SNPs will prove it.

Big Y results

Mr. Jebb's Big Y results came in first. I checked every day to see my father's results, but they did not show. I called Family Tree DNA, and they said that his test had failed and had to be redone. Mr. Jebb had no matches yet. 

The Big Y testing is done in two stages, the first part is automated, and the second stage involves a manual review of the results to more accurately identify the SNPs, name them, and place them on the haplotree. At the end of the automated process, you will see results that may be later modified by the manual review. Family Tree DNA will place each person on a tree called the Block Tree which is a tree showing where that man belongs in the tree of mankind from the earliest ancestors down to the most recent ones. 

After logging into the Family Tree DNA account, there is a Big Y section for those who have taken the test.  Click "Block Tree" to see your placement on the tree.

Big Y menu: Click Block Tree

When you first click on the Block tree, you will see this welcome message with an explanation of the tree:

Block Tree Welcome message

Click "Show me around" to see how to navigate the tree, then see the tree itself. 

For people who have not taken the Big Y test, the public Block Tree can be accessed by going to the Family Tree DNA website. Then go to the bottom of the page and click "Y-DNA Haplotree." You can then search for any position on the tree. 

Family Tree DNA Y-DNA Haplotree


Jebb's position on the Block Tree

Mr. Jebb appeared on the Big Y Block Tree in a branch called R-BY50723:

Branch R-BY50723 in Block Tree

At the top of the above screenshot is a white block [your own branch of the Block Tree is always shown in white] containing 26 SNPs with names like BY50723, BY137843, etc. They are grouped together because the order in which these occurred is not yet known. When a new Big Y tester has some of these SNPs, but not others, the ones that are shared by the new tester will then be known to have occurred in earlier generations than the SNPs that are not shared. As more people test, it is possible for many of these SNPs to be placed in generational order on the tree. The SNPs beginning with the letters BY were discovered with earlier Big Y tests, and the ones beginning with the letters FT were discovered with the more recent Big Y-700 test (which is the test Jebb and Gibbs took).

I looked at Mr. Jebb's results, and he did not have some of the SNPs in the R-BY50723 branch, but his results alone were not enough to determine exactly where he belonged in the branch. R-BY50723 is considered for now to be his "terminal" haplogroup, however this "terminal" haplogroup can change multiple times as more closely-related men take the Big Y test and provide a more precise placement on the tree. 

In the branches below R-BY50723 there is only one SNP whose exact position in the haplotree is now known; it is SNP BY152878, and it has formed a new haplogroup called R-BY152878. 

Here is the bottom of the above screen showing that Mr. Jebb is sharing branch R-BY50723 with one person from England.

Y-DNA matches in Big Y Block Tree

You will notice in Mr. Jebb's branch that it says there is an average of 16 Private Variants between the two men in that branch. Even though these two men are on the same branch of the haplotree, they are not considered to be a match because matches at FTDNA only include people who have no more than 30 total SNP differences which include private variants and named SNPs.


What are private variants?

In the Family Tree DNA Learning Center, FTDNA provides an explanation:

On the Big Y Block Tree, you will see blocks labeled Private Variants. Private Variants are one of the following;

    • mutations that are not named nor are shared between any branch members.
    • mutations that have not yet been validated and placed on the Haplotree.

It is important to note that Private Variants are filtered to only include SNP calls from regions of the Y chromosome that can be reliably mapped with NGS technology. For this reason, the block tree number might be lower than what you see in your personal Big Y Private Variants list.


Family Tree DNA used to list "Private Variants" as "Unnamed Variants" [See the "Examining variants with the Chromosome Browser" section of The Big Y could be the best DNA test ever!], but now most of them are named even though the official names do not appear on the list of private variants. Instead, private variants are listed by their position number on the Y chromosome. 

As previously stated, the Block Tree indicates that there is an average of 16 private variants between the two men in haplogroup R-BY50723. We want to see the actual list of private variants for Mr. Jebb.

List of Private Variants

The private variants can be seen by clicking either the Matches link or the Results link in the Big Y section of the home page.

Big Y options

You will then see a tab for Private Variants.

Private Variants tab

I checked Mr. Jebb's Big Y results, and he had 22 private variants. The private variants are ones that were not seen in other men. They are listed below in three screens:

Jebb Private Variants 1-10

Jebb Private Variants 11-20

Jebb Private Variants 21-22

With 22 private variants, Mr Jebb is remotely related to the other men on the Block Tree and is definitely not related to any of them within the genealogical time period.


Gibbs Big Y

The Gibbs Big Y results were not finished until September, but they were worth the wait. As suspected, he had one match:

Big Y match list

In the above screen you can see the name of the match [I have erased his given name], an envelope for sending an email to the person, an icon for comments, the list of non-matching variants, the number of shared variants, and the date the match was discovered. We will examine some of these later. 

In addition to accessing the Block Tree from your home page, you can click on the Blue link at the top of the above screen to "View Big Y Block Tree" and see your placement on the tree. 

The Block Tree now looks quite different from the way it appeared before the Gibbs Big Y results were completed:

Big Y Block Tree with new match

The Jebb-Gibbs branch of the tree is the white block on the right. The original R-BY50723 block of 26 SNPs (which was previously shown in white because it was considered to be Mr. Jebb's block) has been now been broken into two blocks called R-BY50725 (9 SNPs) and R-BY50723 (17 SNPs). This is because Jebb and Gibbs both had the SNPs BY50725, BY50788, BY50811, BY50831, BY50848, BY73197, FT123034, FT123036, and FT94586, but they did not have the rest of the SNPs in block R-BY50723 which all of the other men have. 

The SNPs in each block are listed in alphanumeric order because the order in which they occured is not yet known. What is now known, however, is that all of the SNPs in block R-BY50725 occurred before the ones in block R-BY50723. Jebbs and Gibbs are now on their own new branch of the tree which is called R-FT368124.


Jebb and Gibbs common ancestors

Jebb and Gibbs share 20 SNPs in the block R-FT368124 that have not been seen before. All of these SNPs represent an ancestor, but since a SNP did not occur at the birth of every male ancestor, these SNPs represent at least 20 generations of common ancestors. In the left column of the Block Tree, you can see that Family Tree DNA estimates that their branch of the tree was formed about 33 SNP generations ago. If we use an average of 80-100 years per SNP generation, this branch is about 2640-3300 years old. 

Estimated SNP Generations

At the bottom of the branch is where we see the most recent common ancestor (MRCA) of Jebb and Gibbs. The most recent common ancestor is when the two branches of Jebb and Gibbs separated. These two men have an average of 3 private variants since that time:

Private Variants on Block Tree

You will notice that in the Family Tree DNA Block Tree the placement of more recent generations is far less reliable. FTDNA seems to be placing the most recent common Jebb-Gibbs ancestor at about 13 SNP generations ago, but as you can see there is a wide variation of private and shared SNPs at the bottom of the tree. Unless we have genealogical evidence of the most recent common ancestor, we can only broadly estimate the time to this ancestor by examining the private SNPs. This is because in some families Y-DNA mutates more than others, there may be uncertainty about the validity of some of the private variants, etc. The date estimation becomes more accurate as more men take the Big Y test.

To find our more about the most recent common ancestor, we will need to examine the private variants that are not shared between the two men. This is the only part of the Big Y that may require work. Before we look at the private variants, I will provide an explanation on how variants are identified.


How are variants identified?

Now we get to the difficult part. How do we know if a private variant or SNP is valid?  How do we know whether we have more or fewer variants than FTDNA identified?  

We must first understand how variants are determined. During the testing process, your DNA is not read in one continuous stretch. Instead, your DNA is broken into random fragments. The test reads these fragments from each end. These are called the forward read and the reverse read. Some positions are read many more times than others. Some locations on the Y-chromosome can be read in one person's test and not in other. After being read, the fragments are aligned to the reference sequence, and differences from the reference sequence are identified. The difference from the reference value is your "derived" value. 

Unfortunately, not all of the reads may give the same result. One read may show the reference allele (for example a C) and another read may show a derived value (for example a G). 

To be considered a high quality SNP by Family Tree DNA the position must usually be read at least ten times. The number of differing calls is then taken into account. A position that was read a few times with different results will be considered to be a much less reliable variant than one that was read many times with a consistent result.

We will see how this works when we examine the Chromosome Browser in the next section.




This post first appeared on The Ultimate Family Historians, please read the originial post: here

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