Glossary – Terminal SNP

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.

  • One by One

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.

  • SNP Packs

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

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, at $575, 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.

PS – the Big Y is on sale right now, before Christmas 2017, for $475 PLUS it includes a free STR upgrade to 111 markers. Click here to read about this savings.

Even better, this one-time-use code is good for $50 off, in addition to the BIg Y sale prices and free 111 upgrade. R29VZACWPG6X  If that coupon has been redeemed already, click here for additional coupons.

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.

______________________________________________________________________

Standard Disclosure

This standard disclosure appears at the bottom of every article in compliance with the FTC Guidelines.

Hot links are provided to Family Tree DNA, where appropriate. If you wish to purchase one of their products, and you click through one of the links in an article to Family Tree DNA, or on the sidebar of this blog, I receive a small contribution if you make a purchase. Clicking through the link does not affect the price you pay. This affiliate relationship helps to keep this publication, with more than 850 articles about all aspects of genetic genealogy, free for everyone.

I do not accept sponsorship for this blog, nor do I write paid articles, nor do I accept contributions of any type from any vendor in order to review any product, etc. In fact, I pay a premium price to prevent ads from appearing on this blog.

When reviewing products, in most cases, I pay the same price and order in the same way as any other consumer. If not, I state very clearly in the article any special consideration received. In other words, you are reading my opinions as a long-time consumer and consultant in the genetic genealogy field.

I will never link to a product about which I have reservations or qualms, either about the product or about the company offering the product. I only recommend products that I use myself and bring value to the genetic genealogy community. If you wonder why there aren’t more links, that’s why and that’s my commitment to you.

Thank you for your readership, your ongoing support and for purchasing through the affiliate link if you are interested in making a purchase at Family Tree DNA.

Glossary – DNA – Deoxyribonucleic Acid

What is DNA and why do I care?

Good questions. Let’s take a look at the answer in general, then why we use DNA for genealogy.

The Recipe for You

DNA, deoxyribonucleic acid, is the book of life for all organisms. In essence, it’s the recipe for you – and what makes you unique.

DNA is formed of strands that twist to form the familiar double helix pattern.

The two strands are joined together by one of 4 different nucleotides, one extending from each side to connect in the middle. The nucleotides are:

  • Cytosine – C
  • Guanine – G
  • Thymine – T
  • Adenine – A

The nucleotide names don’t really matter for genetic genealogy, but what does matter is that the sequence of these nucleotides when chained together is what encodes information on long structures called chromosomes. Each person carries 22 chromosomes, plus the 23rd chromosome pair which is gender specific.

Using DNA for Genetic Genealogy

There are four different kinds of DNA that genealogists use in different ways for obtaining ancestors’ information relevant to genetic genealogy. Thankfully, we have 4 different kinds of DNA available to us because of unique inheritance patterns for each kind of DNA – meaning we inherited different kinds of DNA from different ancestral paths. If one kind of DNA doesn’t work in a particular situation, chances are good that another type will.

Genetic genealogy makes use of 4 different types of DNA.

  • Y DNA – passed from males to male children, only (your father’s paternal line)
  • Mitochondrial DNA – passed from females to both genders of children, but only females pass it on (your mother’s matrilineal line)

Y and mitochondrial DNA inheritance paths are shown on a pedigree chart in the graphic below, with the blue boxes representing Y DNA and the red circles representing mitochondrial DNA inheritance.

In addition to Y and mitochondrial DNA, genetic genealogists also use two kinds of DNA that reflect inheritance from additional ancestral lines, in addition to the red and blue lines shown above – meaning the ancestral lines with no color.

  • Autosomal DNA – the 22 chromosomes that recombine during reproduction.
  • X Chromosome – always contributed by the mother, but only contributed by the father to female children – this is the 23rd chromosome pair which recombines with a unique inheritance pattern.  You can read more about that in the article, X Marks the Spot.

Receiving What Kind of DNA from Whom

While the Y and mitochondrial DNA have unique and very prescribed inheritance patterns as shown by the red arrows pointing to the blue Y chromosome below at far left, and the red mitochondrial circles at far right, the 22 autosomal chromosomes are contributed equally by each parent. In other words, for each chromosome, a child inherits half of each parent’s DNA. How the selection of which DNA is contributed to each child is unknown.

A child’s gender is determined by the parent’s contributions to the 23rd chromosome, not shown above. The following chart explains gender determination by the X and Y combinations of the 23rd chromosome.

Received from Mother Received from Father
Male child X Y
Female child X X

The Y chromosome is what makes males male.

No Y chromosome?  You’re a female.

However, this X chromosome inheritance pattern provides us with the ability to look at X matches for males and know immediately that they had to have come from his mother’s lineage – because males don’t inherit an X chromosome from their father.

Autosomal DNA and Genetic Genealogy

The 22 non-gender chromosomes recombine in each generation, with half of each chromosome being contributed by each parent, as shown in the illustrations above.

You can see that in the first generation, the child received one blue and one yellow, or one pink and one green, chromosome. In giving each child exactly half of their DNA, each parent contributes some amount of ancestral DNA from generations upstream, as you can see in the mother/father and son/daughter generations.

For example, each child receives, on average, 25% of each of their grandparent’s DNA – although they can receive somewhat more or less than 25%, depending on the random nature of recombination.

Therefore, genetic genealogy testing companies compare tester’s autosomal DNA with other testers and look for common segments contributed by common ancestors, resulting in autosomal matching.

When relatively large segments match between three or more relatives who are not immediate family, we can attribute that DNA to a common ancestor. Of course, the challenge, and the thrill, is to determine which common ancestor contributed that common DNA to our triangulated match group. It’s a great way to verify our research and to break down brick walls.

Let’s face it, you received ALL of your DNA from SOME combination of ancestors, and if you carry large enough pieces from any specific ancestor, we can, hopefully, identify the source of that DNA segment by looking at the genealogy of those we match on that segment.

It’s a great puzzle to unravel, and best of all, it’s the puzzle of you.

More Info

The great news is that you can utilize your Y DNA, mitochondrial DNA and autosomal DNA differently, to provide you with different kinds of information about different ancestors and genealogy lines.

If you’d like to read more about how the 4 Kinds of DNA can be used, please read the short article, 4 Kinds of DNA for Genetic Genealogy.

You can also enter any word or phrase into the search box in the upper right hand corner of this blog to find additional useful information about any topic.

If You Want to Test

If you’d like to learn more about the various kinds of DNA tests available, and which one or ones would be the best for you, please read the article, Which DNA Test is Best?

Right now, the Y DNA, mitochondrial and autosomal (Family Finder) tests are on sale at Family Tree DNA, through the end of August, 2017.

______________________________________________________________________

Standard Disclosure

This standard disclosure will now appear at the bottom of every article in compliance with the FTC Guidelines.

Hot links are provided to Family Tree DNA, where appropriate. If you wish to purchase one of their products, and you click through one of the links in an article to Family Tree DNA, or on the sidebar of this blog, I receive a small contribution if you make a purchase. Clicking through the link does not affect the price you pay. This affiliate relationship helps to keep this publication, with more than 850 articles about all aspects of genetic genealogy, free for everyone.

I do not accept sponsorship for this blog, nor do I write paid articles, nor do I accept contributions of any type from any vendor in order to review any product, etc. In fact, I pay a premium price to prevent ads from appearing on this blog.

When reviewing products, in most cases, I pay the same price and order in the same way as any other consumer. If not, I state very clearly in the article any special consideration received. In other words, you are reading my opinions as a long-time consumer and consultant in the genetic genealogy field.

I will never link to a product about which I have reservations or qualms, either about the product or about the company offering the product. I only recommend products that I use myself and bring value to the genetic genealogy community. If you wonder why there aren’t more links, that’s why and that’s my commitment to you.

Thank you for your readership, your ongoing support and for purchasing through the affiliate link if you are interested in making a purchase at Family Tree DNA.