LESSON 4: Exploring the Y Part 2: SNPS & Haplogroups

Screen grab from The Tree of Mankind Video by Mike Sager

Thanks to Angie Bush for her contributions to this lesson.

Y-SNPs are different than Y-STRs and they serve a very different purpose for genetic genealogists. Y again stands for the Y- Chromosome and SNP stands for Single-Nucleotide Polymorphism (pronounced “snip”). Y-SNPs are used to designate the Y-Haplogroup. Haplogroups are the big branches of the ancient human family tree. They have letter names from A thru R. Unfortunately the naming does not always reflect the age. The most recent branch of the Y- tree is “R” and the earliest “A.”

Each Y-SNP mutation or change in the Y’s DNA sequence at a specific location happened just once in the history of mankind (with very few exceptions) for each Y-SNP, all men bearing that SNP (mutation) are related. If we started with the proverbial “ADAM” the first mutation in Y-SNPs happened maybe 60,000 years ago and separated Haplogroup A into A and B. Each time a mutation happens it separates the tree into finer and finer branches and the relationship moves closer to the present. By following the tree we can trace any man from “ADAM” to the most recent or “terminal SNP.” A terminal SNP is just the furthest down the tree branch we get a positive result. Even if two men have the same values on 67/67 markers (also written 67 of 67) they cannot be related in the past 1,000 years if they belong to different haplogroups. Here’s an easy way to think of it — the oldest branch of the human tree went along until there was a mutation in a Y-SNP and then every single male that descended from that man carries that mutation. Then every 100 years or so another mutation creeps in so you can sort all the men in the world into groups that identify their ancient origins. As we get further and further down the tree (there are more and more mutations) you can follow the branch you are on so this helps to break men into finer and finer groups.  Here is where a picture is worth a thousand words please view Journey of Man Interactive Map.

YDNA map

A Migration Map from FTDNA for Haplogroup R

In the map above we move from the oldest Y Haplogroup “A” to the newest in this case Showing “R”


Beyond the broad letter Haplogroups we have SNPs that denote further branches of the tree. Unfortunately for all of us there are older and newer naming protocols that the various companies and organizations have used to designate ever finer subdivisions of the Y-DNA hapolgroup and it can be confusing. So a name at 23andMe for a Y Haplogroup may look different but be the same as a different name at FTDNA. A few years ago the genetic genealogy community, in an effort to simplify the labels, have moved to a protocol where the Haplogroup followed by the terminal SNP is the recommended way to report a haplogroup.

R1b1a2a1a1b3c at FTDNA

R1b1b2a1a2d3* at 23andMe


Even with the ISOGG recommendation you may see both. The former tracks the whole progression whereas the latter is an easier to deal with shorthand.

Wheaton Project Screen shot

Returning to our screenshot from the Wheaton project again let’s look at the 4th column for haplogroup. Group “A” and group “B” are both haplogroup R-M269 (also referred to as R1b) however it is there they part ways.  Back 4,000-10,000 years ago they shared a common ancestor and are all descendants of the man in which the SNP R-M269 first occurred. The haplogroups printed in red are predicted and those in green have been tested. You will note that the  Group A  is labeled likely L21. L21 is a major SNP under M269. Group B I have shown the progression of major SNPS R1B> U152> L2> FGC22501> FGC2250> FGC22538>A7496> FGC22503. However FTDNA has selected the SNP FGC22526 as the terminal SNP Shown in green.   Often there are a group of SNPS that occurred over a few hundred year period that seem to “travel together” which means all then men of a surviving surname may have all the same SNPS. In a later lesson we will discuss the ways you can arrive at your terminal SNP. And to be clear the terminal SNP may be a moving target. More on that later. Also it is important to note that even though two men may show different Haplogroup Terminal SNPS they may be closely related, just some have done more testing than others. Yes all very confusing!

Men of Different letter Haplogroups like “I” and “R” cannot be related via their YDNA. There common ancestor would be back 25,000-50,000 years ago. As we have seen in the example above even men with the same R Haplogroup are not always related in a genealogical time frame. Genealogical time frame is generally used to denote the extent of written records and often those post surname adoption.

Each SNP refers to a mutation in which one group breaks off from the other into those that carry the mutation and those that do not. In the old way of naming each mutation was denoted by a series of numbers and letters. With the longhand name such as “R1b1a21a1b” you could trace the actual path from the earliest SNP to the terminal one. Since the advent of Next Generation sequencing with tests like the Big Y and Y Elite we have had an explosion of new SNPS discovered and the tree has grown so that I cannot even begin to show you a small part of it. Please check on the ISOGG Y Haplogroup Tree and you can explore what I am talking about. Below is a small piece of the R ISOGG tree that shows R1b1a1b1a1a2b1d aka FGC22501. You can see there are many SNPs below FGC22501.


Here is a graphical tree with much more detail that illustrates SNPS below FGC22501 by Jan Suhr.  This tree represents many different surnames in many different regions that are all descended from the man who had the mutation called SNP FGC22501 which likely occurred 4,000-5,000 years ago.


At FTDNA there are 3 main types of projects: Surname, Haplogroup and Location. You may belong to multiple projects at FTDNA. So you could belong to the “Wheaton Surname Project,”  the “R1b1 and  Subclades Project,” and the “Rehoboth Massachusetts Project.” I  highly suggest working with your surname project administrator and/or that of one of the major haplogroup projects  for advice on SNP testing.

In case you are wondering subclades are just sub-groups of haplogroups– “Subclades” is just easier to say than a sub-group of a haplogroup. It helps to remember that if a man is “R” this is their clade or haplogroup and L2 would be their subclade. Another way to think of it is clan and subclan since these represent groups of men tied together by a common ancestor (man) as in “x” number of great-grandfathers back in time. So your subclade may represent a mutation that occurred with your 20th great-grandfather but your clade or major Haplogroup might be the mutation of your 300th great-grandfather.  Many Y-SNPs are included in 23andMe’s test and some broad sub-divison YSNPs are included in the Living DNA test.

Note: all project administrators are volunteers and are not employed by FTDNA and do not receive any compensation.



YSEQ has a free utility called Clade FinderDownload your Ancestry DNA, 23andMe, or MyHeritage DNA raw data file, leave it zipped. It will pull out an YSNPS in your atDNA test

Terminal SNPs versus haplogroup subclade names by CeCe Moore

What is a Haplogroup by Roberta Estes

Why Y-SNP Testing is Very Important by Robert Casey

Y DNA Haplogroup Predictor Tool by Whit Athey

Predicitng Y-DNA Haplogroups in One Step  by Steve P. Morse

Eupedia Distribution of Y Haplogroups Some of the very best flow charts, maps and graphics. Just scroll through the side bar and click.

ISOGG List of Testing Companies

Copyright 2020 Kelly Wheaton. All Rights reserved

1 Comments on “LESSON 4: Exploring the Y Part 2: SNPS & Haplogroups”

  1. Pingback: New Ancient DNA Results = New Sheldon Matches - Sheldon Genealogy

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