A Question on YDNA Naming

Pete from the Whitson/Butler YDNA Group recently had this question:

Can you please help me to further understand the “Y” SNP nomenclature. If I have it correctly, the Alpa prefixing indicates the ‘lab’ in which that SNP was discovered. What does the numeric suffixing delineate? the base pair count placement along the ‘Y’ chromosome?

This is a good question. However, I find it easier to answer these questions in Blog format. Pete is R-S23139. The first R is the major YDNA group that Pete is in. The S is for the lab. According to this website, the S prefix was named by “James F. Wilson, D.Phil. at Edinburgh University”.  The number after the S is just a lab identification number. It has no significance other than the longer number is usually the more recently discovered SNP.

Every YDNA SNP Has a Number

To find out more, Ybrowse.org is a good reference. At that website, they have a browser, similar to the autosomal DNA browser, but this one is for YDNA:

The gray and white bar represents YDNA. Every SNP, such as R-S23139, has a reference number. This gives the location or address of the SNP along millions of locations along the YDNA. The reference number is a more logical designation. These numbers are sequential and lower on the left side of the browser and higher on the right side.

Here, I have put  S23139 into the search box at YBrowse. Conversely, I could have put the reference number in to see if there was a named SNP if I already knew what the number was. In the default browser image above, the red line is at about 14 million.

When I click the search button, I see that the location is here in the 19 million range:

 

In the above image, I cut off the right side of the Y Chromosome Browser.

When I click on the S23139, I get this further information at YBrowse:

Here we see that the mutation at this position went from T to G.

The BigY Test

Here is Pete and two others in his group that have tested for STRs:

Pete is in the middle row in this group of R-U106 people. Pete and the other two did not take the BigY test. However, if Pete did, he would likely get SNPs that are unnamed. They would just be identified with a number. Once someone else in the group BigY tested, they may match on the same numbered SNP. At that point the SNP would be named and they would have a SNP that is just for their Whitson Group. This new SNP could then be considered a family SNP – just for the R-U106 Whitsons. Any additional unnamed SNPs could have developed since the match with the other Whitson-tested person.

Many people upload their Big Y results to a service called YFull where there is further analysis. One important part of the analysis is the estimated date of the SNP and the estimated date of the common ancestor of the people that have tested for the particular SNP. This can be useful when looking for family connections in genealogical research.

Right now, Pete and his closer relatives are sharing R-S23139 with others with German heritage. Perhaps R-S23139 represents the Anglo-Saxons that came to England and those that stayed in what is now Germany.

This shows that R-S23139 represents a point in time before surnames were developed. It probably indicates a time prior to when the Anglo-Saxons came to England.

Here is a table of dates from McDonald.

My understanding of this table is that the tested people within the red above would have a common ancestor around 227 BC. BigY testing would get new SNPs that should be within the genealogical time frame or since the time of surnames.

 

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