Learning – Peter Staple Heritage Group (PSHG)

Announcing ‘Side Study’ Blog Category

Posted on December 20, 2018 by bmstaples

While this website is primarily focused on the Goals of the Peter Staple Heritage Group, sometimes we get distracted. A necessary component of Genetic Genealogy is of course Genealogy, where it’s easy to spend time diving down the other (non-paternal) branches of the family tree. In fact, many people may get their first interest in genealogy by that Ancestry.com commercial or the hand written scroll given to you by your uncle.

Side Study blog posts will serve as general information related to genealogy – not specifically to the study of Y-DNA. They may be personal lessons learned along the way, methods to push us to acting more like professional genealogists, or interesting discoveries.

In the end, genetic genealogy teaches us that it’s all related. There are things to learn in the practice of genealogy that will be helpful when studying genetic genealogy.

Have you come across something interesting that could help others? Want to contribute your own Side Study? Comment below!

PSHG Haplotype and Genetic Distance

Posted on March 3, 2018 by bmstaples

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 DNA; Partner 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:

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.

References:

ISOGG Wiki definition of Haplotype, https://isogg.org/wiki/Haplotype
FTDNA Learning Center, https://www.familytreedna.com/learn/user-guide/y-dna-myftdna/y-str-results-page/

PSHG Haplotree and SNP Detail

Posted on February 17, 2018February 21, 2018 by bmstaples

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 https://www.fullgenomes.com/)

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 (http://ybrowse.org/gb2/gbrowse/chrY/?). 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.

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!

References:

Ancient Origins – The Work of R1b-U106

Posted on April 7, 2017 by bmstaples

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 FamilyTreeDNA.com 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.

References:
[1] U106 project haplotree by Raymond Wing – https://app.box.com/s/afqsrrnvv2d51msqcz2o
[2] https://isogg.org/wiki/Single-nucleotide_polymorphism
[3] https://www.familytreedna.com/groups/u106/about/background
[4] http://www.jb.man.ac.uk/~mcdonald/genetics/table.html

Mutating DNA

Posted on February 4, 2017January 27, 2019 by bmstaples

DNA Mutates.

The fact that it does mutate, slowly over time (generations) allows genetic genealogists to determine Genetic Distance between samples and also estimate change over the ages.

The International Society of Genetic Genealogists defines Genetic Distance as, “the term used to describe the number of differences or mutations between two sets of Y-chromosome DNA or mitochondrial DNA test results. A genetic distance of zero means that there are no differences in the two results and there is an exact match.”

Measuring a member’s Y-STR111 results against the PSHG Modal Haplotype provides clues for how DNA has mutated among the different member branches. This basic analysis depends on the property mentioned above, slowly occurring mutations. But what happens when DNA is changed by external forces like scientific advancements in gene replacement, or from prolonged time in outer space? What’s the effect on the results of autosomal or Y-DNA tests that we are familiar with today?

These articles don’t address the questions from a genetic genealogy perspective; but, I couldn’t help wonder – and think about the future.

Time’s The CRISPR Pioneers – http://time.com/time-person-of-the-year-2016-crispr-runner-up/

And, as reported from many news sources, long term space travel changes DNA – https://www.google.com/#q=dna+changes+in+space&safe=off&tbm=nws