PSHG Haplotype and Genetic Distance

A new page is launched under our Results > Technical Data section – PSHG Haplotype Technical Data.

In the last post we talked about the Y-SNP Haplotree and how we organize clades by branching SNPs.  Today we return to the other method of analyzing Y-DNA, Y-STRs.  Refer to the following blog posts if you need a refresher on the concepts of Y-STRs and Genetic Distance: Mutating DNAPartner Profiles – FTDNA.

The International Society of Genetic Genealogists defines a Y-DNA Haplotype as, “the marker (allele) values obtained from a Y-STR (short tandem repeart) test.  The result for each marker is expressed as a number.”

Let’s look at the first few markers and values of the PSHG Modal Haplotype:

PSHG Haplotype Y7

  • DYS398, DYS390, DYS19, DYS391, DYS385a, DYS385b, and DYS426 across the top row represent the FTDNA names of the Y-STR markers.  Specifically this refers to the named location on the Y Chromosome where a short tandem repeat is identified.
  • The names above, in their order, can be referred to by marker number: 1 – 7 is shown below, but latest Y-STR tests analyze 111 markers.
  • The values of the test result are in the third row.  This number value represents the number of STRs which are found at that marker – your DNA signature.

Example: At Marker #1, named DYS393 by FTDNA, the PSHG Modal Haplotype has a value of 13.

Each person with Y-STR results has their own haplotype.  Patterns emerge when comparing groups of related Y-STR111 test results, even if those group members are related at 8th cousins!  While individual values may differ, if there are enough member test results, a Modal Haplotypes can be established.

Genetic Distance is a way to measure and compare how closely (or far) one haplotype is to another.  Our Haplotype Technical Data page shows a comparison of the PSHG Modal Haplotype compared to those at R1b-FGC13595 and further upstream at R1b-U106.

Visit the PSHG Haplotype Technical Data page to see this detail and to understand how the Genetic Distance compares to other upstream haplotypes.


  1. ISOGG Wiki definition of Haplotype,
  2. FTDNA Learning Center,

PSHG Haplotree and SNP Detail

In a previous blog post, we defined what a SNP is and discussed the haplotree upstream of the PSHG SNPs.  In this post we take another look at the PSHG Haplotree by introducing a new page and taking a dive deep.  We’ll also talk a little bit about SNP naming.

For those new to genetic genealogy or Y-DNA analysis, the concept of SNPs can be intimidating.  One of the reasons may be seemingly abstract SNP names which represent the mutation of an allele at a very specific numeric position on the Y Chromosome.

SNPs are named when a researcher or DNA testing company identifies an unnamed variant in a test kit’s results, validates that it’s viable for genetic genealogy, and is able to develop a primer for it.  You can easily identify each testing company by looking at the SNP prefix.

A – named by YSEQ (see Partner Profile post)

BY – named by FTDNA (see Partner Profile post)

FGC – named by Full Genome Corp (see

S – named by James F. Wilson, D. Phil of Edinburgh University

Therefore, we know the PSHG SNP of FGC13609 was named by Full Genome Corp.  What else can we find out about this SNP?  We turn to the ISOGG YBrowse tool (  Enter FGC13609 into the “Search Landmark or Region” field and click Search.  With the default resolution set to “Show 1 bp” we see below a diagram and location of the SNP on the Y Chromosome and a reference scale.

YBrowse FGC13609

In case the image is too small, click the image to browse to the page.

Click on the yellow & red highlighted FGC13609 in the middle of the page to see SNP details.  Here we can find:

  • Position at 20919447
  • Mutation from T to G
  • Comment including position downstream of DF96
  • Named (ref:) by Full Genomes Corp. (2016)

Sometimes a SNP is named by multiple companies.  Take A16447 which is also known as BY16815.  Search for it in Ybrowse and notice that while it has two names, the chrY position and allele mutation are the same.

Multiple SNPs can also be grouped together.  For example, the group FGC13609, FGC13605, FGC13601, and A1230 are all SNPs shares by 2 PSHG members who have taken the BigY test from FTDNA.  These SNPs will remain grouped together until a test new BigY test taker comes along having one or more, but not all, of those SNPs.  If and when this happens, we learn more about the branches of our Haplotree as it evolves based on the results of additional testing and analysis.

Our website has a new page for keeping an updated haplotree including a table of Y-SNPs from FGC13602 including name, position, and base mutation.  Please visit PSHG Haplotree Technical Data!



FTDNA Holiday Sale – Update!

The 2017 Holiday Sale has begun at Family Tree DNA.  The Y-111 DNA Test (required for PSHG Membership) is on sale for $299 – a savings of $60 off of the regular price.  Visit for sale details.

The sale will continue until December 31, 2017.  As we draw closer to the holidays, Admins expect to receive coupon codes to further reduce costs.

UPDATE – 15 NOV 2017

FTDNA Users and Group Administrators are now receiving weekly coupons.  As Group Administrators we have access to a collection of coupon codes, so contact an Admin if you’re interested in a specific test.

Coupons are ranging from:

  • $10 – $20 off for yDNA 37/67/111
  • $10 – $30 off for mtDNA
  • $5 off for Family Finder (atDNA)
  • $25 off for BigY

The holidays are a great time to test if you’ve been on the fence!

FTDNA Friends & Family Sale

FamilyTreeDNA notified Group Administrators that the “Friends & Family Sale” will start tomorrow, August 1st at 10 am CDT.

The graphic below (courtesy of FTNDA) was included in the notification and seems to indicate that the Sales are primarily targeted to Add-on & Upgrade Tests.


This is a great opportunity for PSHG Members who have already tested with Y-111 and may be interested in ordering the BigY test; however, it’s not yet clear if the Y-111 new test will also be discounted – which is potentially disappointing for pending members.

Check back for updates!

Update – 2 Aug 2017: Y-111 single test is not included on the summer sale.

FTDNA New Sign In Page & Backbone SNP Pack made a couple of announcements this past week.

First, a new sign in page.  You shouldn’t notice any difference in behavior.  For Project Administrators it clarifies that either a Kit Number or GAP Username can be used to login.  If you have a bookmark or favorite saved, you might need to update it to:


There were also some changes to their Password settings:

  • The Password Reset will send a link to the kit’s primary email address.  If you have any issues with this, contact an administrator.
  • While the password qualification still between 5 – 25 characters, passwords are now case sensitive.

The second announcement came in a new product offer – “R1b-M343 & M269v2 Backbone SNP Pack”.  Since PSHG members belong to the upstream haplogroup R1b-M343 (which includes R-M269) you may have received an email about about the new product.  Since PSHG members first test for the downstream SNPs FGC13609/FGC13605, this new SNP pack will probably not provide you any benefit.

For members interested in their SNPs downstream from FGC13609/FGC13605, the BigY test is recommended.

Celebrate DNA Day with Discounts!

April 25 is National DNA Day!  What better way to celebrate than to buy DNA Tests – ON SALE!

FamilyTreeDNA is offering sales on all of their products:

2017 DNA Day Sales

PSHG Members will have already ordered the Y111 test – so Y37, Y67, SNP Backbone, and SNP Packs may not be of much interest.  However, if you’re interested in your SNPs downstream of FGC13609 and FGC13609, now is a great time to order the BigY!  I heard it reported from others that the BigY test has never been this cheap without a coupon code.

Stock up on Family Finder for Autosomal DNA testing or mtFull Sequence for mitochondrial DNA testing.  Rumor has it that AncestryDNA (autosomal) tests will also be on sale, but I have not seen this yet (US market).

Don’t miss this one.  We’ll have to wait and see if there will be sales around Mother’s Day, Father’s Day, late Summer, and Christmas.

Happy testing.

Ancient Origins – The Work of R1b-U106

The PSHG Y-DNA Haplogroup lineage downstream of Y-SNP U106 [1] is:

R1b-U106 > Z381 > Z156 > Z306 > Z304 > DF96 > FGC13326 > S22047 > FGC46344 > FGC13602 > FGC13595 > FGC13604 > FGC13609/FGC13605

FGC13609 and FGC13605 are SNPs which are (so far) shared only by the descendants of Peter Staple located in the United States.

According to ISOGG, “A single-nucleotide polymorphism (SNP, pronounced snip) is a DNA sequence variation occurring when a single nucleotide adenine (A), thymine (T), cytosine (C), or guanine (G) in the genome (or other shared sequence) differs between members of a species or paired chromosomes in an individual.”[2]  Looking at a specific SNPs, for example the PSHG SNPs, some SNPs are upstream (“older”, meaning the mutation occurred before the PSHG SNP) and others are downstream (“younger”, meaning the mutation occurred after the SNP in question).  Analyzing both upstream and downstream SNPs can reveal a wealth of information about ourselves and from where we came.

SNPs that occur downstream of the PSHG SNPs can be found by taking FamilyTreeDNA’s Big-Y test.  The test may reveal “singletons” or locations on the Y-DNA which do not match any other haplotype.  These locations can be sent to YSEQ via their “Wish A SNP” product for analysis.  The result may be a Direct Paternal Lineage SNP which belongs to your line!  Fascinating for better understanding your personal DNA.

The main topic of this blog post is upstream of the PSHG SNPs – all the way up the R Haplotree to U106.  The R1b-U106 Project exists at and is administered by Charles Moore and co-administered by: Dan Draghici, Iain McDonald, Michael Maddi, Raymond Wing, and Wayne Kauffman.

Testing positive for FGC13609 and/or FGC13605 means that PSHG members also belong to the the R1b-U106 clade.  According to the Project’s Overview page, “This project is dedicated to clade formation, and age analysis of the clades, as well as helping move you into your subclade in order to see who your clademate families are, and where they lived, in order to help you better determine your further ancestry.“[3]  The group also has a very lively Yahoo Groups forum which discusses news, recent studies, and serves as a venue for questions & answers.  PSHG members who are interested in the objectives of the R1b-U106 project can request additional information through the PSHG Administrator or Co-Administrator, who are members of the R1b-U106 project.

Understanding that SNPs represent mutations across time & patrilineal generations means that experts can estimate the age of these haplogroups.  Dr. Iain McDonald’s analysis estimates U106 to have occurred in about 3100 BC [4].

Other clades of interest:

  • Z156 about 3000 BC
  • DF96 about 1947 BC
  • FGC13326 about 1627 BC
  • S22047 about 1423 BC
  • FGC13595 about 310 AD

The PSHG may be unique (and very fortunate!) in that if you start out searching for Staples ancestry in Maine, you’ll quickly come across Art B. Staples, Jr.’s site.  Thanks to Art’s (and the original study members’) work we already have PSHG SNPs.  What’s even more remarkable is that PSHG members range in relationship to each other from father/son and first and third cousin up to 7th – 9th cousins (and Genetic Distances at Y-111 from 3 to 11)!  This isn’t the case for all DNA testers.  Sometimes the furthest progress one can make is to drill down through the clades in Raymond Wing’s U106 Tree [1] and seek out those in your subclade for more information.

The R1b-U106 group contains many brilliant individuals who donate their own time and resources to further the understanding of our Ancient Origins.  Their work benefits not only the members, but the genetic genealogy community in general.

[1] U106 project haplotree by Raymond Wing –

Partner Profiles – FTDNA

This is the second of our dual blog posts regarding current DNA testing partners.  Please also check out our Partner Profile on YSEQ.

Family Tree DNA (FTDNA) is a modern powerhouse for DNA testing – Autosomal (atDNA), mtDNA, and yDNA.  Its own website front page boasts, “We have the most comprehensive Y chromosome, autosomal, and mitochondrial ancestry DNA database for genetic genealogists!”[1]  FTDNA circa 2006 received major contributions from familiar folks when Thomas & Astrid Krahn (see Partner Profile on YSEQ) sold the assets of their company DNA-Fingerprint and opened the Genomics Research Center in Houston, TX.[2]  FamilyTreeDNA was founded by Bennett Greenspan (who today serves as President & CEO), Max Blankfeld and Jim Warren.[2]

The PSHG relies on FTDNA’s Y-111 STR test to place members into family groups and to confirm claims made by traditional genealogy.  By analyzing the Y-111 STR results, group administrators can help to verify from which of Peter’s three sons (Peter Jr., John, or James) a member descends.  The test also reveals mutations which can occur naturally through the family group generations.  Click to follow to the PSHG at FTNDA group results.

FTNDA offers lesser marker Y-STR tests (12, 37, 67), but these do not provide enough marker information to be useful to the PSHG.  The Y-STR test will unlock Certified Y-STR Results, Matches, Ancestral & Haplogroup Origins, Haplotree & SNPs data, and Maps related to Matches, Migration, and SNPs.[1].  A similar set of tools can be unlocked by purchasing a Mitochondrial (mtDNA) test to trace one’s maternal lineage.  Family Finder is the Autosomal (atDNA) product comparable to AncestryDNA.  Tools available with this product are: Matches, Chromosome Browser, Linked Relationship, myOrigins, and ancientOrigins.  Returning to Y-DNA products, the Big Y test can provide a detailed SNP analysis and Matches.  When analyzed by a project group such as R1b-U106, one can identify Singleton SNPs which can be further tested and named.

Family Tree DNA’s tests may appear to be expensive to the novice; however, genetic genealogists and DNA hobby enthusiasts appreciate the testing options and relative (compared to historical capabilities and prices) low cost.  Keep an eye out for sales (Summer & Winter) and take advantage.