A little explanation of Y-DNA results.

A father passes down a near-exact copy of his chromosome Y (chrY) to his son. Imperfections during replication result in slight differences (e.g. single nucleotide polymorphisms; SNPs) that may be unique to the son. Genealogists use these patterns of similarities and differences to reconstruct paternal ancestry (the Y-tree). The FamilyTreeDNA team (FTDNA) released Big Y in 2013 to provide these patterns directly to customers. At that time, there were thousands of SNPs on the Y-tree connecting hundreds of men. Since then, tens of thousands of men have been studied, and hundreds of thousands of SNPs have been identified. In 2018, armed with this information, updates to the genomic reference sequence, and expansion of the Y-tree, FTDNA decided to replace Big Y with a product that would account for updated knowledge of genealogically important regions and increase the overall coverage of chrY.
 
Chromosome Y has roughly 57,200,000 nucleotides, or base pairs (bp).

STR’s; These are locations of the Y-DNA where there are repeats in patterns of proteins. If you flatten out the double helix of the DNA you get something that looks like a ladder. The “rungs” of the ladder, base pairs,  are proteins whose names are represented by the first letter of the protein, C, T A and G. At certain locations of the DNA there are lengths that have patterns, eg CTTG. The number of times the pattern is repeated is given as a STR value. So at DYS455 the name of the region of the DNA a pattern is repeated 10 times. STR results can be used to show how close people are related or can be used to indicate what is the possible branch on the SNP tree a tester may be. When testers join the project, we are able to look at each others STR results. One of the key benefits of this is finding certain results which are unique and can be used to differentiate between other lines. DYS455=10 and DYS392=15 are 2 on the R-S47 branch of the R-Z56 tree for R-Z44.

 

An SNP, eg R-Z56, is a mutation of a protein on a specific point, or rung on the ladder, of the DNA that is unique to men of that group. As an example, at location 8241647 instead of the normal A, men in the R-S47 branch of R-Z56 have a T, which has been given the name R-BY3949. All these unique SNP’s are passed on and there are many which end up creating a kind of SNP family tree. Have a look at a tree for R-Z56 at https://www.ytree.net/DisplayTree.php?blockID=2153. SNP’s are only put on the tree when another tester tests positive for the same unnamed variant, becoming a named SNP.

 

You will notice there are blocks of SNP’s on the trees. As more people test these blocks get smaller as we don’t always share all SNP’s in a block. As other men do the BigY test the blocks get smaller and you can get a new SNP and branch.

Glossary
Haplotype: A haplotype is the set of values for a set of DNA. For example, the results of the Y-DNA 12 test for one person is their haplotype. Two individuals that match exactly on all markers have the same haplotype.

Haplogroup: A haplogroup is a major branch on either the maternal or paternal tree of humankind. Haplogroups are associated with early human migrations. Today these can be associated with a geographic region or regions.

SNP: A single nucleotide polymorphism (SNP) is a change in your DNA code at a specific point.

STR: A short DNA motif (pattern) repeated in tandem. ATGC repeated eleven times would give the marker a value or allele of 11. 

        DYS - D=DNA, Y=Y-chromosome, S= (unique) segment.

Phylogenetic Tree: A phylogenetic tree is the reconstruction through genetics of a lineage.

Subclade: A subclade is a subgrouping in the haplogroups of the human genetic trees. This may be either the Y-chromosome tree or the mitochondrial tree. Subclades are more specific to a location or population group than the major branches (haplogroups).

Base: A base is a unit or building block of DNA. Adenine (A), cytosine (C), guanine, (G), and thymine (T) are the four primary bases in DNA. The order of bases is the sequence of DNA. 

Double Helix: A double helix is the twisted shape DNA forms when its two strands bond together. It looks like a twisting or rotating ladder. The rungs being the bases which come in pairs. Thymine always pairs with Adenine, Cytosine always pairs with Guanine.

SNP PREFIX NAMING
An abbreviated list

A= Thomas Krahn YSEQ.net. Berlin, Germany
B= Estonian Genome Centre
BY= BigY testing, FTDNA
CTS= Chris Tyler-Smith. The Welcome Trust Sanger Institute, Hinxton, England
F= Li Jin Phd. Fudan University, Shanghai China
FGC= Full Genomes Corp.
M= Peter Underhill Ph D. Of Stanford University
P= Michael Hammer, Ph D. University of Arizona
PF= Paolo Franalacci, Ph D. Universita di Sassari, Sassari Italy
PH= Pille Hillast Ph D, University of Leicester, England
U= Lynn M Sims, University of Central Florida; Dennis Garvey Ph D, Gonzaga University; and Jack Ballantyne, Ph D, University of Central Florida
Z= Gregory Magoon, Ph D, Richard Rocca, etal, independent researchers of publicly available whole genome sequence and datasets, and Thomas Krahn, MSc.

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