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Glossary – Terminal SNP

Roberta Estes

What is a Terminal SNP?

It sounds fatal doesn’t it, but don’t worry, it’s not.

The phrase Terminal SNP is generally used in conjunction with discussing Y DNA testing and haplogroup identification.

SNPs Define Haplogroups

In a nutshell, SNPs, single nucleotide polymorphisms, are the mutations that define different haplogroups. Haplogroups reach far back in time on the direct paternal, generally the surname, line.

SNPs, mutations that define haplogroups are considered to be “once in the lifetime of mankind” events that divide one haplogroup into two subgroups, or branches.

A haplogroup can be thought of as the ancient genetic clan of males – specifically their Y DNA. You might want to read the article, What is a Haplogroup?

If you test your Y DNA with Family Tree DNA, you’ll notice that you receive an estimated haplogroup with the regular Y DNA tests which test STR, or short tandem repeat, markers. STRs are the markers tested in the 37, 67 or 111 marker tests. You can read about the difference between STRs and SNPs in the article, STRs vs SNPs, Multiple DNA Personalities.

STR markers are used for more recent genealogical testing and comparison, while haplogroups reach further back in time.

An estimated haplogroup as provided by Family Tree DNA is based on STR matches to people who have done SNP testing. Estimated haplogroups are quite accurate, as far as they go. However, by necessity, they aren’t deep haplogroups, meaning they aren’t the leaves on the end of the twigs of the branch of your haplotree. Estimated haplogroups are the big branches.

In essence, what a haplogroup provided with STR testing tells you is the name of the town and the main street through town. To get to your house, you may need to turn on a few side streets.

Haplotree

The haplotree, back in the ancient days of 2002 used to hold less than 100 haplogroups, each main branch called by a different letter of the alphabet. The main branches or what is referred to as the core backbone is shown in this graphic from Wikipedia.

Today, the haplotree shown for each Y DNA tester on their personal page at Family Tree DNA, has tens of thousands of branches. No, that’s not a misprint.

The haplotree is the phylogenetic tree that defines all of the branches of mankind and groups them into increasingly refined “clans” or groups, the further down the tree you go.

In other words, Y Adam is at the root, then his “sons” who, due to specific mutations, formed different base haplogroups. As more mutations occurred in the son’s descendants’ lines, more haplogroups were born. Multiply that over tens of thousands of years, and you have lots of branches and twigs and even leaves on the branches of this tree of humanity.

Let’s look at the terminal SNP of my cousin, John, on his Haplotree and SNP page at Family Tree DNA.

John’s terminal SNP is R-BY490. R indicates the main branch and BY490 is the name of the SNP that is the further down the tree – his leaf, for lack of a better definition.

In John’s case, we know this is the smallest leaf on his branch, because he took the Big Y test which reads all of his SNPs on the Y chromosome.

Haplogroup R is quite large with thousands of branches and leaves – each one with its own distinct history that is an important part of your genealogy. Tracking where and when these mutations happened tells you the migration history of your paternal ancestor.

How else would you ever know?

How Do I Discover My Terminal SNP?

Sometimes “terminal SNP” is used to mean the SNP for which a man has most recently tested. It may NOT mean that he has tested for all of the available SNPs. What this really means is that when someone gives you a terminal SNP name, or you see one listed someplace, you’ll need to ask about the depth of the testing undergone by the man in question.

Let’s look at an example.

I’ve condensed John’s tree into only the SNPs for which he tested positive. The entire tree includes SNPs that John tested negative for, and their branches which are not relevant to John – although we certainly didn’t know that they weren’t relevant before he tested. However, he may want to reference the large and accurate scientific tree, so all information is provided to John. It’s like seeing a map that includes all roads, not just the one you’re traveling.

I’ve created a descendant chart style tree below. Y line Adam is the first male. Some several thousands of years later, his descendant had a mutation that created haplogroup R defined by the SNP M207, in yellow.

John, based on his STR matches, was predicted to be R-M269. On his results page, that’s the estimated haplogroup that was showing when his results were first returned.

If you had asked John about his terminal SNP, he would have probably told you R-M269. At that time, to the best of his knowledge, that WAS his terminal SNP – but it wasn’t really.

John could choose three ways to test for additional SNPs to discover his actual terminal SNP.

John could selectively test one SNP at a time to see if he was positive, meaning that he has that mutation. SNPs cost $39 each to test, as of the time this article was written. Of course, John could also be negative for that SNP, meaning he doesn’t have the SNP, and therefore does not descend from that line. That’s good information too, but then John would have to select another branch to test by purchasing the SNP associated with that new branch.

If John had selected any of the SNPs on the list above to test, he would have tested positive. So, let’s say John decided to test L21, a major branch. If he tested positive, that means that all of the branches directly above L21, between L21 and M207, are also positive, by inference.

At that point, John would tell you that his terminal SNP is L21, but it isn’t actually.

Now, John wants to purchase a more cost-effective SNP pack, because he can test 100 or more SNP locations by purchasing one SNP pack for $99. That’s a great value, so John purchases the SNP pack offered on his personal page. A SNP pack tests selective SNPs all over the relevant portion of the tree in an attempt to place a man on a relatively low branch. These SNPs are selected to find an appropriate branch, not the appropriate leaf. They confirm (or disprove) SNPs that have already been discovered.

Let’s say, in John’s case, the SNP pack moves him down to R-ZP21. If you asked him now about his terminal SNP, he would probably tell you R-ZP21, but it still isn’t actually.

SNP packs are great and do move people down the tree, but the only way to move to the end of the twigs is the Big Y test.

The Big Y test tests for all known SNPs as well as what were called Novel Variants and are now called Unnamed Variants which are new SNPs discovered that are as yet unnamed. You may have a new SNP in your line waiting to be discovered. The Estes family has one dating from sometime before 1495 that, to date, has only been found in Estes descendant males from that common ancestor who was born in 1495.

The Big Y test scans virtually the entire Y chromosome in order to place testers on the lowest leaf of the tree. You can’t get there any other way with certainty and you’ll never know if you have any as yet undiscovered SNPs or leaves unless you take the Big Y.

In John’s case, that leaf was 4 more branches below R-ZP21, at R-BY490.

Why Does a Terminal SNP Matter?

Haplogroup R-M269 is the most common haplogroup of European men.

Looking at the SNP map, you can see that there are so many map locations as to color the map of the UK entirely red.

Genealogically, this isn’t helpful at all.

However, looking now at DF49, below, we see many fewer locations, suggesting perhaps that men with this terminal SNP are clustered in particular areas.

SNPS further down John’s personal haplotree tell an increasingly focused and granular story, each step moving closer in time.

Summary

Men generally want to discover their terminal SNP with the hope that they can learn something interesting about the migration of their ancestors before the genesis of surnames.

Perhaps they will discover that they match all men with McSurnames, suggesting perhaps a Scottish origin. Or maybe their terminal SNP is only found in a mountainous region of Germany, or perhaps their Big Y matches all have patronymic surnames from Scandinavia.

Big Y testing is also a community sourced citizen science effort to expand the Y haplotree – and quite successfully. The vast majority of SNPs on the publicly available ISOGG Y tree today are from individual testers, not from academic studies.

Haplogroups, and therefore terminal SNPs are the only way we have to peek back behind the veil of time.

If you’re interested in discovering your terminal SNP, you’ll be money ahead to simply purchase the Big Y up front and skip individual SNP testing along with SNP packs. In addition to discovering your terminal SNP, you are also matched to other men who have taken the Big Y test.

You can order the Big Y, individual SNPs or SNP packs by clicking on this link, signing on to your account, and then clicking on the blue “Upgrade” button, either in the Y DNA section, shown below, or in the upper right hand corner of your personal page.

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